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Han D, Richter-Heitmann T, Kim JH, Friedrich MW, Yin X, Elvert M, Ryu JS, Jang K, Nam SI. Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments. Front Microbiol 2023; 14:1231839. [PMID: 37700860 PMCID: PMC10493304 DOI: 10.3389/fmicb.2023.1231839] [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: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.
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Affiliation(s)
- Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung-si, Gangwon-do, Republic of Korea
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ji-Hoon Kim
- Marine Geology & Energy Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, Republic of Korea
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Organic Geochemistry Group, Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jong-Sik Ryu
- Department of Earth and Environmental Sciences, Pukyong National University, Busan, Republic of Korea
| | - Kwangchul Jang
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Seung-Il Nam
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
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2
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Salazar A, Warshan D, Vasquez‐Mejia C, Andrésson ÓS. Environmental change alters nitrogen fixation rates and microbial parameters in a subarctic biological soil crust. OIKOS 2022. [DOI: 10.1111/oik.09239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alejandro Salazar
- Faculty of Environmental and Forest Sciences, Agricultural Univ. of Iceland Reykjavik Iceland
| | - Denis Warshan
- Faculty of Life and Environmental Sciences, Univ. of Iceland Reykjavik Iceland
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, Univ. of Iceland Reykjavik Iceland
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3
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Microbial Diversity in Subarctic Biocrusts from West Iceland following an Elevation Gradient. Microorganisms 2021; 9:microorganisms9112195. [PMID: 34835321 PMCID: PMC8624075 DOI: 10.3390/microorganisms9112195] [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: 08/30/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/16/2022] Open
Abstract
Biological soil crusts (biocrusts) are essential communities of organisms in the Icelandic soil ecosystem, as they prevent erosion and cryoturbation and provide nutrients to vascular plants. However, biocrust microbial composition in Iceland remains understudied. To address this gap in knowledge, we applied high-throughput sequencing to study microbial community composition in biocrusts collected along an elevation gradient (11–157 m a.s.l.) stretching away perpendicular to the marine coast. Four groups of organisms were targeted: bacteria and cyanobacteria (16S rRNA gene), fungi (transcribed spacer region), and other eukaryotes (18S rRNA gene). The amplicon sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Within the cyanobacteria, filamentous forms from the orders Synechococcales and Oscillatoriales prevailed. Furthermore, fungi in the biocrusts were dominated by Ascomycota, while the majority of reads obtained from sequencing of the 18S rRNA gene belonged to Archaeplastida. In addition, microbial photoautotrophs isolated from the biocrusts were assigned to the cyanobacterial genera Phormidesmis, Microcoleus, Wilmottia, and Oscillatoria and to two microalgal phyla Chlorophyta and Charophyta. In general, the taxonomic diversity of microorganisms in the biocrusts increased following the elevation gradient and community composition differed among the sites, suggesting that microclimatic and soil parameters might shape biocrust microbiota.
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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5
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Finore I, Vigneron A, Vincent WF, Leone L, Di Donato P, Schiano Moriello A, Nicolaus B, Poli A. Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments. Microorganisms 2020; 8:microorganisms8091282. [PMID: 32842646 PMCID: PMC7563700 DOI: 10.3390/microorganisms8091282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.
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Affiliation(s)
- Ilaria Finore
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Adrien Vigneron
- Centre d’études nordiques (CEN) & Département de Biologie, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
| | - Warwick F. Vincent
- Centre d’études nordiques (CEN) & Département de Biologie, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
| | - Luigi Leone
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Paola Di Donato
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
- Department of Science and Technology, University of Naples Parthenope, Centro Direzionale, Isola C4, 80143 Naples, Italy
| | - Aniello Schiano Moriello
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Barbara Nicolaus
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Annarita Poli
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
- Correspondence: ; Tel.: +39-0818675311
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6
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Trout-Haney JV, Heindel RC, Virginia RA. Picocyanobacterial cells in near-surface air above terrestrial and freshwater substrates in Greenland and Antarctica. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:296-305. [PMID: 32134187 DOI: 10.1111/1758-2229.12832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Bioaerosols are an important component of the total atmospheric aerosol load, with implications for human health, climate feedbacks and the distribution and dispersal of microbial taxa. Bioaerosols are sourced from marine, freshwater and terrestrial surfaces, with different mechanisms potentially responsible for releasing biological particles from these substrates. Little is known about the production of freshwater and terrestrial bioaerosols in polar regions. We used portable collection devices to test for the presence of picocyanobacterial aerosols above freshwater and soil substrates in the southwestern Greenland tundra and the McMurdo Dry Valleys of Antarctica. We show that picocyanobacterial cells are present in the near-surface air at concentrations ranging from 2,431 to 28,355 cells m-3 of air, with no significant differences among substrates or between polar regions. Our concentrations are lower than those measured using the same methods in temperate ecosystems. We suggest that aerosolization is an important process linking terrestrial and aquatic ecosystems in these polar environments, and that future work is needed to explore aerosolization mechanisms and taxon-specific aerosolization rates. Our study is a first step toward understanding the production of bioaerosols in extreme environments dominated by microbial life.
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Affiliation(s)
- Jessica V Trout-Haney
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, Hanover, NH, 03755
| | - Ruth C Heindel
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO
| | - Ross A Virginia
- Environmental Studies Program and Institute of Arctic Studies, Dartmouth College, Hanover, NH, 03755
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7
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Leung PM, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C. Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems. mSystems 2020; 5:e00495-19. [PMID: 32291352 PMCID: PMC7159902 DOI: 10.1128/msystems.00495-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.
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Affiliation(s)
- Pok Man Leung
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Sean K Bay
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Dimitri V Meier
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Eleonora Chiri
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, Victoria, Australia
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8
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Chen Q, Meyer WA, Zhang Q, White JF. 16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates. PeerJ 2020; 8:e8417. [PMID: 31942261 PMCID: PMC6956778 DOI: 10.7717/peerj.8417] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.
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Affiliation(s)
- Qiang Chen
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - William A Meyer
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Qiuwei Zhang
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - James F White
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
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Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
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10
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Rego A, Raio F, Martins TP, Ribeiro H, Sousa AGG, Séneca J, Baptista MS, Lee CK, Cary SC, Ramos V, Carvalho MF, Leão PN, Magalhães C. Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods. Front Microbiol 2019; 10:1018. [PMID: 31214128 PMCID: PMC6555387 DOI: 10.3389/fmicb.2019.01018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Francisco Raio
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Teresa P Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Hugo Ribeiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - António G G Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Joana Séneca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,School of Science, University of Waikato, Hamilton, New Zealand
| | - S Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand.,School of Science, University of Waikato, Hamilton, New Zealand
| | - Vitor Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Porto, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal
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11
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Metagenomic survey of the bacterial communities in the rhizosphere of three Andean tuber crops. Symbiosis 2019. [DOI: 10.1007/s13199-019-00631-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Rippin M, Lange S, Sausen N, Becker B. Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding. FEMS Microbiol Ecol 2019. [PMID: 29514253 DOI: 10.1093/femsec/fiy036] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here, we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage. In terms of algal and cyanobacterial biodiversity, the genera Chloromonas, Coccomyxa, Elliptochloris and Nostoc were identified in all samples regardless of origin confirming their ubiquitous distribution. For the first time, we found the chrysophyte Spumella to be common in polar BSCs as it was present in all analyzed samples. Co-occurrence analysis revealed the presence of sulfur metabolizing microbes indicating that BSCs also play an important role for the sulfur cycle. In general, phototrophs were most abundant within the BSCs but there was also a diverse community of heterotrophs and saprotrophs. Our results show that BSCs are unique microecosystems in polar environments with an unexpectedly high biodiversity.
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Affiliation(s)
- Martin Rippin
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Sebastian Lange
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Nicole Sausen
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Burkhard Becker
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
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13
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Malard LA, Pearce DA. Microbial diversity and biogeography in Arctic soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:611-625. [PMID: 30028082 DOI: 10.1111/1758-2229.12680] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO2 , CH4 and N2 O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
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14
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Delgado-Baquerizo M, Maestre FT, Eldridge DJ, Bowker MA, Jeffries TC, Singh BK. Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents. THE NEW PHYTOLOGIST 2018; 220:824-835. [PMID: 29607501 DOI: 10.1111/nph.15120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/16/2018] [Indexed: 05/23/2023]
Abstract
Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 S. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
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15
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Microbial connectivity and sorting in a High Arctic watershed. ISME JOURNAL 2018; 12:2988-3000. [PMID: 30087410 DOI: 10.1038/s41396-018-0236-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 06/09/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
Abstract
Aquatic ecosystems in the High Arctic are facing unprecedented changes as a result of global warming effects on the cryosphere. Snow pack is a central feature of northern landscapes, but the snow microbiome and its microbial connectivity to adjacent and downstream habitats have been little explored. To evaluate these aspects, we sampled along a hydrologic continuum at Ward Hunt Lake (latitude 83°N) in the Canadian High Arctic, from snow banks, water tracks in the permafrost catchment, the upper and lower strata of the lake, and the lake outlet and its coastal marine mixing zone. The microbial communities were analyzed by high-throughput sequencing of 16 and 18S rRNA to determine the composition of potentially active Bacteria, Archaea and microbial Eukarya. Each habitat had distinct microbial assemblages, with highest species richness in the subsurface water tracks that connected the melting snow to the lake. However, up to 30% of phylotypes were shared along the hydrologic continuum, showing that many taxa originating from the snow can remain in the active fraction of downstream microbiomes. The results imply that changes in snowfall associated with climate warming will affect microbial community structure throughout all spatially connected habitats within snow-fed polar ecosystems.
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16
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Large Blooms of Bacillales ( Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity. mBio 2018; 9:mBio.01366-16. [PMID: 29511079 PMCID: PMC5844995 DOI: 10.1128/mbio.01366-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) account for a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a suite of ecosystem services, such as carbon sequestration, water retention and nutrient cycling, and climate regulation. Biocrust assemblages are extremely well adapted to survive desiccation and to rapidly take advantage of the periodic precipitation events typical of arid ecosystems. Here we focus on the wetting response of incipient cyanobacterial crusts as they mature from "light" to "dark." We sampled a cyanobacterial biocrust chronosequence before (dry) and temporally following a controlled wetting event and used high-throughput 16S rRNA and rRNA gene sequencing to monitor the dynamics of microbial response. Overall, shorter-term changes in phylogenetic beta diversity attributable to periodic wetting were as large as those attributable to biocrust successional stage. Notably, more mature crusts showed significantly higher resistance to precipitation disturbance. A large bloom of a few taxa within the Firmicutes, primarily in the order Bacillales, emerged 18 h after wetting, while filamentous crust-forming cyanobacteria showed variable responses to wet-up across the successional gradient, with populations collapsing in less-developed light crusts but increasing in later-successional-stage dark crusts. Overall, the consistent Bacillales bloom accompanied by the variable collapse of pioneer cyanobacteria of the Oscillatoriales order across the successional gradient suggests that the strong response of few organisms to a hydration pulse with the mortality of the autotroph might have important implications for carbon (C) balance in semiarid ecosystems.IMPORTANCE Desert biological soil crusts are terrestrial topsoil microbial communities common to arid regions that comprise 40% of Earth's terrestrial surface. They successionally develop over years to decades to deliver a suite of ecosystem services of local and global significance. Ecosystem succession toward maturity has been associated with both resistance and resilience to disturbance. Recent work has shown that the impacts of both climate change and physical disturbance on biocrusts increase the potential for successional resetting. A larger proportion of biocrusts are expected to be at an early developmental stage, hence increasing susceptibility to changes in precipitation frequencies. Therefore, it is essential to characterize how biocrusts respond to wetting across early developmental stages. In this study, we document the wetting response of microbial communities from a biocrust chronosequence. Overall, our results suggest that the cumulative effects of altered precipitation frequencies on the stability of biocrusts will depend on biocrust maturity.
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17
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Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol 2017; 8:1974. [PMID: 29109701 PMCID: PMC5660283 DOI: 10.3389/fmicb.2017.01974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Parag Vaishampayan
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Blue Marble Space Institute of Science, Seattle, WA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Mina Bashir
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Chris P McKay
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States
| | - Keith Schubert
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, Baylor University, Waco, TX, United States
| | - Rosalba Bornaccorsi
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,SETI Institute, Mountain View, CA, United States
| | - Ernesto Gomez
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, California State University, San Bernardino, San Bernardino, CA, United States
| | - Sneha Tharayil
- College of Education, University of Texas at Austin, Austin, TX, United States.,Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoffrey Payton
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Orchard Academies 2B: Arts and Media, Bell, CA, United States
| | - Juliana Capra
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Foothills Middle School, Arcadia, CA, United States
| | - Jessica Andaya
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Leonard Bacon
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Maple Hill High School, Castleton-on-Hudson, NY, United States
| | - Emily Bargoma
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - David Black
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,American Academy of Innovation, Jordan, UT, United States
| | - Katie Boos
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michaela Brant
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michael Chabot
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Danny Chau
- Orchard Academies 2B: Arts and Media, Bell, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica Cisneros
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoff Chu
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jane Curnutt
- Department of Computer Science, Baylor University, Waco, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica DiMizio
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Christian Engelbrecht
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Caroline Gott
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Raechel Harnoto
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Ruben Hovanesian
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Shane Johnson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Britne Lavergne
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Gabriel Martinez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Paul Mans
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Ernesto Morales
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Gary Peplow
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Smiley Elementary School, Redlands, CA, United States
| | - Ryan Piaget
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Nicole Ponce
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Eduardo Renteria
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Monica Santander
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Khamille Sarmiento
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Allison Scheppelmann
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Gavin Schroter
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Devan Sexton
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jenin Stephenson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Kristin Symer
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Tatiane Russo-Tait
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Bill Weigel
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Mary B Wilhelm
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
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18
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Singh P, Singh SM, Singh RN, Naik S, Roy U, Srivastava A, Bölter M. Bacterial communities in ancient permafrost profiles of Svalbard, Arctic. J Basic Microbiol 2017; 57:1018-1036. [DOI: 10.1002/jobm.201700061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/13/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Purnima Singh
- Birla Institute of Technology and Science (BITS); Pilani-K.K. Birla Goa Campus; Zuarinagar Goa India
| | - Shiv M. Singh
- National Centre for Antarctic and Ocean Research; Ministry of Earth Sciences; Vasco-Da-Gama Goa India
| | - Ram N. Singh
- National Bureau of Agriculturally Important Microorganisms (NBAIM); Uttar Pradesh India
| | - Simantini Naik
- National Centre for Antarctic and Ocean Research; Ministry of Earth Sciences; Vasco-Da-Gama Goa India
| | - Utpal Roy
- Birla Institute of Technology and Science (BITS); Pilani-K.K. Birla Goa Campus; Zuarinagar Goa India
| | - Alok Srivastava
- National Bureau of Agriculturally Important Microorganisms (NBAIM); Uttar Pradesh India
| | - Manfred Bölter
- Institute of Ecosystem Research; Christian-Albrechts-Universität zu Kiel; Kiel Germany
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19
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Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS, Burns BP, Ferrari BC. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods. Front Microbiol 2017; 8:591. [PMID: 28439263 PMCID: PMC5383709 DOI: 10.3389/fmicb.2017.00591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/22/2017] [Indexed: 01/07/2023] Open
Abstract
Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.
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Affiliation(s)
- Sarita Pudasaini
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - John Wilson
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Anne S Palmer
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
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20
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Özçelik Ü, Çevik H, Bircan HY, Yarbuğ Karakayalı F, Işıklar İ, Haberal M. Evaluation of Transplanted Kidneys and Comparison with Healthy Volunteers and Kidney Donors with Diffusion-Weighted Magnetic Resonance Imaging: Initial Experience. EXP CLIN TRANSPLANT 2017. [PMID: 28332960 DOI: 10.6002/ect.2016.0341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate the feasibility of diffusion-weighted magnetic resonance, by comparing imaging in renal allograft recipients for functional assessment of kidney transplants versus imaging of these features in healthy volunteers and kidney donors with native kidneys. MATERIALS AND METHODS Seventy renal transplant recipients (group A) with stable graft function at postoperative month 1, 40 healthy volunteers (group B), and 40 kidney donors (group C) underwent diffusion-weighted magnetic resonance imaging. An echo-planar diffusion-weighted imaging sequence was performed in coronal orientation by using 6 b values (0, 200, 400, 600, 800, 1000 s/mm²). The apparent diffusion coefficients were determined for the upper and lower poles of the kidney cortex and medulla. Relations between apparent diffusion coefficients and allograft function, determined by the estimated glomerular filtration rate (comparing rates > 60 mL/min/1.73 m² [group A1] versus < 60 mL/min/1.73 m² [group A2]), were investigated in renal transplant recipients, and apparent diffusion coefficients in groups A, B, and C were compared. RESULTS Apparent diffusion coefficients were statistically higher in group A1 than in group A2 (P < .05) and statistically higher in group A than in groups B and C (P < .001). There were no significant differences between groups B and C (P > .05). CONCLUSIONS We observed that apparent diffusion coefficients of transplanted kidneys at postoperative month 1 were higher than values in native kidneys of healthy volunteers and kidney donors. In addition, apparent diffusion coefficients of transplanted kidneys with estimated glomerular filtration rates > 60 mL/min/1.73 m² were higher than transplanted kidneys with rates < 60 mL/min/1.73 m².
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Affiliation(s)
- Ümit Özçelik
- Department of General Surgery, Baskent University School of Medicine, Ankara, Turkey
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Ivanova AA, Kulichevskaya IS, Merkel AY, Toshchakov SV, Dedysh SN. High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia. Front Microbiol 2016; 7:2065. [PMID: 28066382 PMCID: PMC5177623 DOI: 10.3389/fmicb.2016.02065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
A wide variety of terrestrial ecosystems in tundra have a ground vegetation cover composed of reindeer lichens (genera Cladonia and Cetraria). The microbial communities of two lichen-dominated ecosystems typical of the sub-arctic zone of northwestern Siberia, that is a forested tundra soil and a shallow acidic peatland, were examined in our study. As revealed by molecular analyses, soil and peat layers just beneath the lichen cover were abundantly colonized by bacteria from the phylum Planctomycetes. Highest abundance of planctomycetes detected by fluorescence in situ hybridization was in the range 2.2-2.7 × 107 cells per gram of wet weight. 16S rRNA gene fragments from the Planctomycetes comprised 8-13% of total 16S rRNA gene reads retrieved using Illumina pair-end sequencing from the soil and peat samples. Lichen-associated assemblages of planctomycetes displayed unexpectedly high diversity, with a total of 89,662 reads representing 1723 operational taxonomic units determined at 97% sequence identity. The soil of forested tundra was dominated by uncultivated members of the family Planctomycetaceae (53-71% of total Planctomycetes-like reads), while sequences affiliated with the Phycisphaera-related group WD2101 (recently assigned to the order Tepidisphaerales) were most abundant in peat (28-51% of total reads). Representatives of the Isosphaera-Singulisphaera group (14-28% of total reads) and the lineages defined by the genera Gemmata (1-4%) and Planctopirus-Rubinisphaera (1-3%) were present in both habitats. Two strains of Singulisphaera-like bacteria were isolated from studied soil and peat samples. These planctomycetes displayed good tolerance of low temperatures (4-15°C) and were capable of growth on a number of polysaccharides, including lichenan, a characteristic component of lichen-derived phytomass.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | - Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
| | | | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia
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Delgado‐Baquerizo M, Maestre FT, Reich PB, Trivedi P, Osanai Y, Liu Y, Hamonts K, Jeffries TC, Singh BK. Carbon content and climate variability drive global soil bacterial diversity patterns. ECOL MONOGR 2016. [DOI: 10.1002/ecm.1216] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Manuel Delgado‐Baquerizo
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Fernando T. Maestre
- Área de Biodiversidad y Conservación Departamento de Biología y Geología, Física y Química Inorgánica Escuela Superior de Ciencias Experimentales y Tecnología Universidad Rey Juan Carlos Calle Tulipán Sin Número 28933 Móstoles Spain
| | - Peter B. Reich
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- Department of Forest Resources University of Minnesota St. Paul Minnesota 55108 USA
| | - Pankaj Trivedi
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Yui Osanai
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Yu‐Rong Liu
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing 100085 China
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Thomas C. Jeffries
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith 2751 New South Wales Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith 2751 New South Wales Australia
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Wang NF, Zhang T, Yang X, Wang S, Yu Y, Dong LL, Guo YD, Ma YX, Zang JY. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area. Front Microbiol 2016; 7:1170. [PMID: 27516761 PMCID: PMC4963411 DOI: 10.3389/fmicb.2016.01170] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 07/14/2016] [Indexed: 11/13/2022] Open
Abstract
This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p < 0.001), water content (p < 0.01), ammonium nitrogen (NH4+-N, p < 0.01), silicate silicon (SiO42--Si, p < 0.01), nitrite nitrogen (NO2--N, p < 0.05), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the bacterial community composition. The results suggest soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.
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Affiliation(s)
- Neng Fei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences Beijing, China
| | - Xiao Yang
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Shuang Wang
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Yong Yu
- Polar Research Institute of China Shanghai, China
| | - Long Long Dong
- Department of Bioengineering and Biotechnology, Qingdao University of Science and Technology Qingdao, China
| | - Yu Dong Guo
- Department of Bioengineering and Biotechnology, Qingdao University of Science and Technology Qingdao, China
| | - Yong Xing Ma
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Jia Ye Zang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration Qingdao, China
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24
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Pushkareva E, Johansen JR, Elster J. A review of the ecology, ecophysiology and biodiversity of microalgae in Arctic soil crusts. Polar Biol 2016. [DOI: 10.1007/s00300-016-1902-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Cyanobacteria and Algae of Biological Soil Crusts. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_4] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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26
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Arctic soil microbial diversity in a changing world. Res Microbiol 2015; 166:796-813. [DOI: 10.1016/j.resmic.2015.07.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/23/2023]
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27
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Pushkareva E, Pessi IS, Wilmotte A, Elster J. Cyanobacterial community composition in Arctic soil crusts at different stages of development. FEMS Microbiol Ecol 2015; 91:fiv143. [PMID: 26564957 PMCID: PMC4668365 DOI: 10.1093/femsec/fiv143] [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] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
Cyanobacterial diversity in soil crusts has been extensively studied in arid lands of temperate regions, particularly semi-arid steppes and warm deserts. Nevertheless, Arctic soil crusts have received far less attention than their temperate counterparts. Here, we describe the cyanobacterial communities from various types of soil crusts from Svalbard, High Arctic. Four soil crusts at different development stages (ranging from poorly-developed to well-developed soil crusts) were analysed using 454 pyrosequencing of the V3-V4 variable region of the cyanobacterial 16S rRNA gene. Analyses of 95 660 cyanobacterial sequences revealed a dominance of OTUs belonging to the orders Synechococcales, Oscillatoriales and Nostocales. The most dominant OTUs in the four studied sites were related to the filamentous cyanobacteria Leptolyngbya sp. Phylotype richness estimates increased from poorly- to mid-developed soil crusts and decreased in the well-developed lichenized soil crust. Moreover, pH, ammonium and organic carbon concentrations appeared significantly correlated with the cyanobacterial community structure.
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Affiliation(s)
- Ekaterina Pushkareva
- Centre for Polar Ecology, University of South Bohemia, 37005 ČeskéBudějovice, Czech Republic
| | - Igor S Pessi
- Centre for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, 37005 ČeskéBudějovice, Czech Republic Institute of Botany, Academy of Science of the Czech Republic, 37982 Třeboň, Czech Republic
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28
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Ferrari BC, Bissett A, Snape I, van Dorst J, Palmer AS, Ji M, Siciliano SD, Stark JS, Winsley T, Brown MV. Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems. Environ Microbiol 2015; 18:1834-49. [DOI: 10.1111/1462-2920.13034] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Andrew Bissett
- CSIRO Agriculture Flagship; PO Box 1600 Canberra ACT 2601 Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Anne S. Palmer
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Steven D. Siciliano
- Department of Soil Science; University of Saskatchewan; Saskatoon Saskatchewan S7N 5A8 Canada
| | - Jonathon S. Stark
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Tristrom Winsley
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
- Department of Soil Science; University of Saskatchewan; Saskatoon Saskatchewan S7N 5A8 Canada
| | - Mark V. Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
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29
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Raanan H, Oren N, Treves H, Berkowicz SM, Hagemann M, Pade N, Keren N, Kaplan A. Simulated soil crust conditions in a chamber system provide new insights on cyanobacterial acclimation to desiccation. Environ Microbiol 2015; 18:414-26. [PMID: 26234786 DOI: 10.1111/1462-2920.12998] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmental research often faces two major hurdles: (i) fluctuating spatial and temporal conditions and consequently large variability in the organisms' abundance and performance, and (ii) complex, costly logistics involved in field experiments. Measurements of physiological parameters or molecular analyses often represent single shot experiments. To study desiccation acclimation of filamentous cyanobacteria, the founders and main primary producers in desert biological soil crusts (BSC), we constructed an environmental chamber that can reproducibly and accurately simulate ambient conditions and measure microorganism performance. We show that recovery from desiccation of BSC cyanobacteria and Leptolyngbya ohadii isolated thereof are strongly affected by dehydration rate following morning dew. This effect is most pronounced in cells exposed to high light and temperature in the dry phase. Simultaneous measurements of water content, gas exchange and fluorescence were performed during dehydration. Photosynthetic performance measured by fluorescence begins declining when light intensity reaches values above 100 μmol photons m(-2) s(-1), even in fully hydrated cells. In contrast, photosynthetic rates measured using O2 evolution and CO2 uptake increased during rising irradiance to the point where the water content declined below ∼ 50%. Thus, fluorescence cannot serve as a reliable measure of photosynthesis in desert cyanobacteria. The effects of drying on gas exchange are discussed.
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Affiliation(s)
- Hagai Raanan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Nadav Oren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Simon M Berkowicz
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.,Arid Ecosystems Research Center, Edmond J. Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Martin Hagemann
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Nadin Pade
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.,Arid Ecosystems Research Center, Edmond J. Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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30
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Climate change and physical disturbance manipulations result in distinct biological soil crust communities. Appl Environ Microbiol 2015; 81:7448-59. [PMID: 26276111 DOI: 10.1128/aem.01443-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/09/2015] [Indexed: 11/20/2022] Open
Abstract
Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.
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31
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Raanan H, Felde VJMNL, Peth S, Drahorad S, Ionescu D, Eshkol G, Treves H, Felix-Henningsen P, Berkowicz SM, Keren N, Horn R, Hagemann M, Kaplan A. Three-dimensional structure and cyanobacterial activity within a desert biological soil crust. Environ Microbiol 2015; 18:372-83. [DOI: 10.1111/1462-2920.12859] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/26/2015] [Accepted: 03/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Hagai Raanan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Vincent J. M. N. L. Felde
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Stephan Peth
- Deparment of Soil Science; Faculty of Ecological Agriculture; University of Kassel; 37213 Witzenhausen Germany
| | - Sylvie Drahorad
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Danny Ionescu
- The Max Planck Institute for Marine Microbiology; Celsius Str. 1 28359 Bremen Germany
| | - Gil Eshkol
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Peter Felix-Henningsen
- Institute of Soil Science and Soil Conservation; Justus Liebig University Giessen; 35392 Giessen Germany
| | - Simon M. Berkowicz
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
- Arid Ecosystems Research Center; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
| | - Rainer Horn
- Institute of Plant Nutrition and Soil Science; Christian Albrechts University of Kiel; 24118 Kiel Germany
| | - Martin Hagemann
- Institut für Biowissenschaften; Universität Rostock; D-18059 Rostock Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
- Arid Ecosystems Research Center; Edmond J. Safra Campus, Givat Ram; The Hebrew University of Jerusalem; Jerusalem 9190401 Israel
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Crevecoeur S, Vincent WF, Comte J, Lovejoy C. Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems. Front Microbiol 2015; 6:192. [PMID: 25926816 PMCID: PMC4396522 DOI: 10.3389/fmicb.2015.00192] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 11/15/2022] Open
Abstract
Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO2 and CH4 to the atmosphere. In the Nunavik subarctic region (northern Québec, Canada), these numerous, shallow ponds become well-stratified during summer. This creates a physico-chemical gradient of temperature and oxygen, with an upper oxic layer and a bottom low oxygen or anoxic layer. Our objective was to determine the influence of stratification and related limnological and landscape properties on the community structure of potentially active bacteria in these waters. Samples for RNA analysis were taken from ponds in three contrasting valleys across a gradient of permafrost degradation. A total of 1296 operational taxonomic units were identified by high throughput amplicon sequencing, targeting bacterial 16S rRNA that was reverse transcribed to cDNA. β-proteobacteria were the dominant group in all ponds, with highest representation by the genera Variovorax and Polynucleobacter. Methanotrophs were also among the most abundant sequences at most sites. They accounted for up to 27% of the total sequences (median of 4.9% for all samples), indicating the importance of methane as a bacterial energy source in these waters. Both oxygenic (cyanobacteria) and anoxygenic (Chlorobi) phototrophs were also well-represented, the latter in the low oxygen bottom waters. Ordination analyses showed that the communities clustered according to valley and depth, with significant effects attributed to dissolved oxygen, pH, dissolved organic carbon, and total suspended solids. These results indicate that the bacterial assemblages of permafrost thaw ponds are filtered by environmental gradients, and are complex consortia of functionally diverse taxa that likely affect the composition as well as magnitude of greenhouse gas emissions from these abundant waters.
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Affiliation(s)
- Sophie Crevecoeur
- Département de Biologie and Takuvik Joint International Laboratory, Université Laval Québec, QC, Canada ; Centre d'Études Nordiques, Université Laval Québec, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
| | - Warwick F Vincent
- Département de Biologie and Takuvik Joint International Laboratory, Université Laval Québec, QC, Canada ; Centre d'Études Nordiques, Université Laval Québec, QC, Canada
| | - Jérôme Comte
- Département de Biologie and Takuvik Joint International Laboratory, Université Laval Québec, QC, Canada ; Centre d'Études Nordiques, Université Laval Québec, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie and Takuvik Joint International Laboratory, Université Laval Québec, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada ; Québec Océan, Université Laval Québec, QC, Canada
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Li K, Bai Z, Zhang H. Community succession of bacteria and eukaryotes in dune ecosystems of Gurbantünggüt Desert, Northwest China. Extremophiles 2014; 19:171-81. [PMID: 25253412 DOI: 10.1007/s00792-014-0696-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
Abstract
Pyrosequencing and quantitative polymerase chain reaction of small subunit rRNA genes were used to provide a comprehensive examination of bacterial, cyanobacterial, and eukaryotic communities in the biological soil crusts (BSCs) of Gurbantünggüt Desert sand dunes (China). Three succession stages were recognized based on the analyses of eukaryotic communities: a late succession stage of BSCs in a swale with eukaryotes mainly related to the Bryophyta clade, an initial succession stage in a slope with barely any eukaryotic phototrophic microorganisms detected, and an intermediate succession type detected from both the swale and slope BSCs dominated by the phylum Chlorophyta. Moreover, the cyanobacterial community dominated all of the BSCs (48.2-69.5% of the total bacteria) and differed among the three succession stages: sequences related to Microcoleus steenstrupii and the genus Scytonema were abundant in the later succession stage, whereas both the initial and intermediate stages were dominated by Microcoleus vaginatus. Compared with swales, BSCs from slopes are exposed to a harsher environment, e.g., higher irradiance and lower water availability, and thus may be restricted from developing to a higher succession stage. Other disturbances such as wind and grazing may explain the different succession stages observed in swales or slopes. However, no clear differences were detected from non-phototrophic bacterial communities of the three succession stages, and sequences related to Alphaproteobacteria and Actinobacteria were most abundant in all the BSCs. The closest matches for the most frequent non-phototrophic bacterial genera were mainly derived from harsh environments, indicating the robustness of these genera.
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Affiliation(s)
- Ke Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
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34
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Cheema S, Lavania M, Lal B. Impact of petroleum hydrocarbon contamination on the indigenous soil microbial community. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0868-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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