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Jankoski PR, Correa APF, Brandelli A, Motta ASDA. Biological activity of bacteria isolated from wetland sediments collected from a conservation unit in the southern region of Brazil. AN ACAD BRAS CIENC 2021; 93:e20191269. [PMID: 34287454 DOI: 10.1590/0001-3765202120191269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/23/2020] [Indexed: 11/22/2022] Open
Abstract
Wetlands are ecosystems rich in biodiversity and their ecological importance is recognized worldwide. Sediment samples were subjected to physical-chemical analysis and organic carbon content varied from 3.0% to 4.8%, the clay between 32 and 40%, silt with 41% and 43%, sand coarse varied between 6 and 11% and fine sand between 7 and 16%. The nitrogen values varied from 0.25% to 0.48%, the pH from 5.4 to 7.5 and the humidity varied from 44 to 56%. The selected isolates were evaluated for enzymatic properties and 64% showed positive results for amylase, 16% for gelatinase, 37% for lipase, 91% for protease and 2.7% for inulinase. Six bacterial isolates were selected for the overlapping assay and Bacillus sp. sed 2.2 showed inhibitory activity against Corynebacterium fimi NCTC 7547, and the antimicrobial substance was partially purified. The characterization of the substance was carried and the substance was stable at 100° C for up to 10 minutes and sensitive to the enzymes papain and trypsin. This substance was active against some species of Listeria, including Listeria monocytogenes ATCC 7644. The microorganims obtained from sediment samples were important sources of bioactive compounds, including enzymes and peptides, being a source of bioactive compounds to be studied.
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Affiliation(s)
- Priscila R Jankoski
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Microbiologia, Imunologia e Parasitologia, Rua Sarmento Leite, 500, sala 216, Cidade Baixa, 90050-170 Porto Alegre, RS, Brazil
| | - Ana Paula F Correa
- Universidade Federal do Rio Grande do Sul, Instituto de Ciência e Tecnologia de Alimentos, Departamento de Ciência dos Alimentos, Av. Bento Gonçalves, 9500, Campus do Vale, Prédio 43212, Santo Antônio, 91501-970 Porto Alegre, RS, Brazil
| | - Adriano Brandelli
- Universidade Federal do Rio Grande do Sul, Instituto de Ciência e Tecnologia de Alimentos, Departamento de Ciência dos Alimentos, Av. Bento Gonçalves, 9500, Campus do Vale, Prédio 43212, Santo Antônio, 91501-970 Porto Alegre, RS, Brazil
| | - Amanda S DA Motta
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Microbiologia, Imunologia e Parasitologia, Rua Sarmento Leite, 500, sala 216, Cidade Baixa, 90050-170 Porto Alegre, RS, Brazil
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2
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Ramoneda J, Hawes I, Pascual-García A, J Mackey T, Y Sumner D, D Jungblut A. Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system. FEMS Microbiol Ecol 2021; 97:6174672. [PMID: 33729491 DOI: 10.1093/femsec/fiab044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/14/2021] [Indexed: 11/14/2022] Open
Abstract
Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA gene sequencing, we evaluated microbial mat and planktonic communities within a connected freshwater system in the McMurdo Wright Valley, Antarctica, to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined communities from glacial Lake Brownworth, the perennially ice-covered Lake Vanda and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar. Despite the higher physical connectivity and dispersal opportunities between bacterial communities in the shallow parts of the system, environmental abiotic conditions dominated over dispersal in driving community structure. Functional metabolic pathway predictions suggested differences in the functional gene potential between the microbial mat communities located in shallower and deeper water depths. The findings suggest that increasing temperatures and meltwater due to future climate change will affect bacterial diversity and functioning in Antarctic freshwater ecosystems.
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Affiliation(s)
- Josep Ramoneda
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Tauranga 3110, New Zealand
| | - Alberto Pascual-García
- Theoretical Biology, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich 8006, Switzerland
| | - Tyler J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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3
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Hawes I, Howard-Williams C, Gilbert N, Joy K. Towards an Environmental Classification of Lentic Aquatic Ecosystems in the McMurdo Dry Valleys, Antarctica. ENVIRONMENTAL MANAGEMENT 2021; 67:600-622. [PMID: 33559688 DOI: 10.1007/s00267-021-01438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The McMurdo Dry Valleys are the largest single ice-free area in Antarctica, and of considerable scientific and conservation value as an extreme polar desert. This is recognised through the McMurdo Dry Valleys Antarctic Specially Managed Area (ASMA), where management's goals focus on protection of its unique features, while facilitating science access. Using a mix of remote sensing and existing cartography, we have identified over 6000 lakes and ponds in the ASMA. This study develops a classification of those aquatic ecosystems to provide a framework for management. It uses a limited top-down, hierarchical classification to define 13 class separations based on physical attributes that could largely be ascribed from existing databases or remotely sensed information. The first hierarchical level was based on landscape position, separating coastal kettle holes (reflecting recent glacial history), from other "topographic" water bodies. The second level was based on endorheic vs exorheic drainage, the third on mid-summer ice condition (no-ice cap; ice capped; frozen to base) and the fourth on source of inflow (glacial or non-glacial). Kettles were sub-classed by mid-summer ice only. Classes were tested against a set of field observations and an expert workshop validation process considered management implications for the ASMA. This study shows how the classification assists our understanding of Dry Valley landscapes and addresses management issues faced by researchers, environmental managers and policy makers. The approach to classification, rather than the detailed classes that may be specific to the Dry Valleys, has potential for wider use in other polar landscapes.
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Affiliation(s)
- Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Sulphur Point, Tauranga, 3110, New Zealand.
| | - Clive Howard-Williams
- National Institute of Water and Atmospheric Research, Lt Box 8602, Christchurch, New Zealand
| | - Neil Gilbert
- Constantia Consulting Ltd, 310 Papanui Road, Christchurch, 8052, New Zealand
| | - Kurt Joy
- Department of Biological Science, University of Waikato, Hamilton, New Zealand
- Orbica Ltd, 128 Litchfield St., Christchurch, 8011, New Zealand
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4
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16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.
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Porcino N, Cosenza A, Azzaro M. A review on the geochemistry of lakes in Victoria Land (Antarctica). CHEMOSPHERE 2020; 251:126229. [PMID: 32171943 DOI: 10.1016/j.chemosphere.2020.126229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
This paper reports briefly the concentrations of major elements of 3116 samples of lakes in the Victoria Land region. The data obtained by different works were processed through multivariate chemometric techniques to gain insight into the biogeochemical processes taking place in the lacustrine systems. Antarctic ice-free areas contain lakes and ponds that have interesting chemical features and are of wide global significance as early warning indicators of climatic and environmental change.
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Affiliation(s)
- Nunziatina Porcino
- Institute for Marine Biological Resources and Biotechnology (IRBIM), National Research Council (CNR), Section of Messina, Spianata San Raineri, 86, 98122, Messina (ME), Italy.
| | - Alessandro Cosenza
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri 86, 98122, Messina (ME), Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (ISP-CNR), Spianata San Raineri 86, 98122, Messina (ME), Italy
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6
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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.
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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
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7
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Jungblut AD, Hawes I. Using Captain Scott's Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? Proc Biol Sci 2018. [PMID: 28637848 DOI: 10.1098/rspb.2017.0833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evidence of climate-driven environmental change is increasing in Antarctica, and with it comes concern that this will propagate to impacts on biological communities. Recognition and prediction of change needs to incorporate the extent and timescales over which communities vary under extant conditions. However, few observations of Antarctic microbial communities, which dominate inland habitats, allow this. We therefore carried out the first molecular comparison of Cyanobacteria in historic herbarium microbial mats from freshwater ecosystems on Ross Island and the McMurdo Ice Shelf, collected by Captain R.F. Scott's 'Discovery' Expedition (1902-1903), with modern samples from those areas. Using 16S rRNA gene surveys, we found that modern and historic cyanobacteria assemblages showed some variation in community structure but were dominated by the same genotypes. Modern communities had a higher richness, including genotypes not found in historic samples, but they had the highest similarity to other cyanobacteria sequences from Antarctica. The results imply slow cyanobacterial 16S rRNA gene genotype turnover and considerable community stability within Antarctic microbial mats. We suggest that this relates to Antarctic freshwater 'organisms requiring a capacity to withstand diverse stresses, and that this could also provide a degree of resistance and resilience to future climatic-driven environmental change in Antarctica.
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Affiliation(s)
- Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ian Hawes
- University of Waikato, 58 Cross Road, Tauranga 3110, New Zealand
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8
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Obbels D, Verleyen E, Mano MJ, Namsaraev Z, Sweetlove M, Tytgat B, Fernandez-Carazo R, De Wever A, D'hondt S, Ertz D, Elster J, Sabbe K, Willems A, Wilmotte A, Vyverman W. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw041. [PMID: 26936447 DOI: 10.1093/femsec/fiw041] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 11/12/2022] Open
Abstract
The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations.
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Affiliation(s)
- Dagmar Obbels
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Marie-José Mano
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Zorigto Namsaraev
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium Winogradsky Institute of Microbiology RAS, Pr-t 60-letya Oktyabrya, 7/2, Moscow 117312, Russia NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 12 31 82, Russia
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Rafael Fernandez-Carazo
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Aaike De Wever
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Damien Ertz
- Botanic Garden Meise, Department Bryophytes-Thallophytes, Nieuwelaan 38, B-1860 Meise, Belgium Federation Wallonia-Brussels, General Administration of the Non-Compulsory Education and Scientific Research, Rue A. Lavallée 1, 1080 Brussels, Belgium
| | - Josef Elster
- Centre for Polar Ecology, Faculty of Sciences, University of South Bohemia, Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 379 82, Třeboň, Czech republic
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
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9
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Lylloff JE, Hansen LBS, Jepsen M, Sanggaard KW, Vester JK, Enghild JJ, Sørensen SJ, Stougaard P, Glaring MA. Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases. Microb Biotechnol 2016; 9:245-56. [PMID: 26834075 PMCID: PMC4767292 DOI: 10.1111/1751-7915.12343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography–tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin‐like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20°C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity.
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Affiliation(s)
- Jeanette E Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Lea B S Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Jepsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Kristian W Sanggaard
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan K Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jan J Enghild
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Mikkel A Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
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10
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. Multiple adaptations to polar and alpine environments within cyanobacteria: a phylogenomic and Bayesian approach. Front Microbiol 2015; 6:1070. [PMID: 26528250 PMCID: PMC4602134 DOI: 10.3389/fmicb.2015.01070] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major primary producers in the polar and alpine regions contributing significantly to nitrogen and carbon cycles in the cryosphere. Recent advancements in environmental sequencing techniques have revealed great molecular diversity of microorganisms in cold environments. However, there are no comprehensive phylogenetic analyses including the entire known diversity of cyanobacteria from these extreme environments. We present here a global phylogenetic analysis of cyanobacteria including an extensive dataset comprised of available small subunit (SSU) rRNA gene sequences of cyanobacteria from polar and high altitude environments. Furthermore, we used a large-scale multi-gene (135 proteins and 2 ribosomal RNAs) genome constraint including 57 cyanobacterial genomes. Our analyses produced the first phylogeny of cold cyanobacteria exhibiting robust deep branching relationships implementing a phylogenomic approach. We recovered several clades common to Arctic, Antarctic and alpine sites suggesting that the traits necessary for survival in the cold have been acquired by a range of different mechanisms in all major cyanobacteria lineages. Bayesian ancestral state reconstruction revealed that 20 clades each have common ancestors with high probabilities of being capable of surviving in cold environments.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
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11
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Glaring MA, Vester JK, Lylloff JE, Abu Al-Soud W, Sørensen SJ, Stougaard P. Microbial diversity in a permanently cold and alkaline environment in Greenland. PLoS One 2015; 10:e0124863. [PMID: 25915866 PMCID: PMC4411134 DOI: 10.1371/journal.pone.0124863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/09/2015] [Indexed: 02/01/2023] Open
Abstract
The submarine ikaite columns located in the Ikka Fjord in Southern Greenland represent a unique, permanently cold (less than 6°C) and alkaline (above pH 10) environment and are home to a microbial community adapted to these extreme conditions. The bacterial and archaeal community inhabiting the ikaite columns and surrounding fjord was characterised by high-throughput pyrosequencing of 16S rRNA genes. Analysis of the ikaite community structure revealed the presence of a diverse bacterial community, both in the column interior and at the surface, and very few archaea. A clear difference in overall taxonomic composition was observed between column interior and surface. Whereas the surface, and in particular newly formed ikaite material, was primarily dominated by Cyanobacteria and phototrophic Proteobacteria, the column interior was dominated by Proteobacteria and putative anaerobic representatives of the Firmicutes and Bacteroidetes. The results suggest a stratification of the ikaite columns similar to that of classical soda lakes, with a light-exposed surface inhabited by primary producers and an anoxic subsurface. This was further supported by identification of major taxonomic groups with close relatives in soda lake environments, including members of the genera Rhodobaca, Dethiobacter, Thioalkalivibrio and Tindallia, as well as very abundant groups related to uncharacterised environmental sequences originally isolated from Mono Lake in California.
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Affiliation(s)
- Mikkel A. Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jan K. Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jeanette E. Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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12
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Zhang L, Jungblut AD, Hawes I, Andersen DT, Sumner DY, Mackey TJ. Cyanobacterial diversity in benthic mats of the McMurdo Dry Valley lakes, Antarctica. Polar Biol 2015. [DOI: 10.1007/s00300-015-1669-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Echenique-Subiabre I, Villeneuve A, Golubic S, Turquet J, Humbert JF, Gugger M. Influence of local and global environmental parameters on the composition of cyanobacterial mats in a tropical lagoon. MICROBIAL ECOLOGY 2015; 69:234-244. [PMID: 25260923 DOI: 10.1007/s00248-014-0496-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/08/2014] [Indexed: 06/03/2023]
Abstract
Cyanobacteria-dominated microbial mat communities thrive widely and year round in coral reefs and tropical lagoons, with periodic massive development of benthic blooms. We studied the diversity and spatiotemporal variation of the cyanobacterial dominance in mats of the shallow lagoon of La Réunion Island in the Indian Ocean by means of denaturing gradient gel electrophoresis and cloning-sequencing approaches targeting the 16S rRNA gene, combined with macromorphological and micromorphological characterization of corresponding phenotypes. The mat-forming cyanobacteria were highly diversified with at least 67 distinct operational taxonomic units identified in the lagoon, encompassing the entire morphological spectrum of the phylum Cyanobacteria, but with striking dominance of Oscillatoriales and Nostocales. It appeared also that selective pressures acting at different geographical scales have an influence on the structure and composition of these mats dominated by cyanobacteria. First, large changes were observed in their diversity and composition in relation to local changes occurring in their environment. Second, from the data obtained on the richness and composition of the mats and from the comparison with similar studies in the world, tropical mats seem to display wider cyanobacterial richness than in temperate and cold areas. Moreover, these tropical mats share more species with mats in other tropical regions than with those in temperate and cold climatic regions, suggesting that marine cyanobacteria in biofilms and mats display a biogeographic structure.
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Affiliation(s)
- Isidora Echenique-Subiabre
- The Institut Pasteur, Collection des Cyanobactéries, Department of Microbiology, 28 rue du Docteur Roux, 75724, Paris CEDEX 15, France
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Lv X, Yu J, Fu Y, Ma B, Qu F, Ning K, Wu H. A meta-analysis of the bacterial and archaeal diversity observed in wetland soils. ScientificWorldJournal 2014; 2014:437684. [PMID: 24982954 PMCID: PMC4058131 DOI: 10.1155/2014/437684] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 04/10/2014] [Accepted: 04/24/2014] [Indexed: 12/31/2022] Open
Abstract
This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03), representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs), Bacteroidetes (868 OTUs), Acidobacteria (731 OTUs), Firmicutes (540 OTUs), and Actinobacteria (418 OTUs). The genus Flavobacterium (11.6% of bacterial sequences) was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.
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Affiliation(s)
- Xiaofei Lv
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbao Yu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
| | - Yuqin Fu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Ma
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
| | - Fanzhu Qu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
| | - Kai Ning
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, China
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Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microb Cell Fact 2014; 13:72. [PMID: 24886068 PMCID: PMC4035831 DOI: 10.1186/1475-2859-13-72] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/13/2014] [Indexed: 02/01/2023] Open
Abstract
Background The use of cold-active enzymes has many advantages, including reduced energy consumption and easy inactivation. The ikaite columns of SW Greenland are permanently cold (4-6°C) and alkaline (above pH 10), and the microorganisms living there and their enzymes are adapted to these conditions. Since only a small fraction of the total microbial diversity can be cultured in the laboratory, a combined approach involving functional screening of a strain collection and a metagenomic library was undertaken for discovery of novel enzymes from the ikaite columns. Results A strain collection with 322 cultured isolates was screened for enzymatic activities identifying a large number of enzyme producers, with a high re-discovery rate to previously characterized strains. A functional expression library established in Escherichia coli identified a number of novel cold-active enzymes. Both α-amylases and β-galactosidases were characterized in more detail with respect to temperature and pH profiles and one of the β-galactosidases, BGalI17E2, was able to hydrolyze lactose at 5°C. A metagenome sequence of the expression library indicated that the majority of enzymatic activities were not detected by functional expression. Phylogenetic analysis showed that different bacterial communities were targeted with the culture dependent and independent approaches and revealed the bias of multiple displacement amplification (MDA) of DNA isolated from complex microbial communities. Conclusions Many cold- and/or alkaline-active enzymes of industrial relevance were identified in the culture based approach and the majority of the enzyme-producing isolates were closely related to previously characterized strains. The function-based metagenomic approach, on the other hand, identified several enzymes (β-galactosidases, α-amylases and a phosphatase) with low homology to known sequences that were easily expressed in the production host E. coli. The β-galactosidase BGalI17E2 was able to hydrolyze lactose at low temperature, suggesting a possibly use in the dairy industry for this enzyme. The two different approaches complemented each other by targeting different microbial communities, highlighting the usefulness of combining methods for bioprospecting. Finally, we document here that ikaite columns constitute an important source of cold- and/or alkaline-active enzymes with industrial application potential.
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Timescales of growth response of microbial mats to environmental change in an ice-covered antarctic lake. BIOLOGY 2013; 2:151-76. [PMID: 24832656 PMCID: PMC4009872 DOI: 10.3390/biology2010151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022]
Abstract
Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm−2 y−1. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure.
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