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Rhodes ME, Pace AD, Benjamin MM, Ghent H, Dawson KS. Establishment of a Halophilic Bloom in a Sterile and Isolated Hypersaline Mesocosm. Microorganisms 2023; 11:2886. [PMID: 38138031 PMCID: PMC10745797 DOI: 10.3390/microorganisms11122886] [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: 10/20/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Extreme environments, including hypersaline pools, often serve as biogeographical islands. Putative colonizers would need to survive transport across potentially vast distances of inhospitable terrain. Hyperhalophiles, in particular, are often highly sensitive to osmotic pressure. Here, we assessed whether hyperhalophiles are capable of rapidly colonizing an isolated and sterile hypersaline pool and the order of succession of the ensuing colonizers. A sterile and isolated 1 m3 hypersaline mesocosm pool was constructed on a rooftop in Charleston, SC. Within months, numerous halophilic lineages successfully navigated the 20 m elevation and the greater than 1 km distance from the ocean shore, and a vibrant halophilic community was established. All told, in a nine-month period, greater than a dozen halophilic genera colonized the pool. The first to arrive were members of the Haloarchaeal genus Haloarcula. Like a weed, the Haloarcula rapidly colonized and dominated the mesocosm community but were later supplanted by other hyperhalophilic genera. As a possible source of long-distance inoculum, both aerosol and water column samples were obtained from the Great Salt Lake and its immediate vicinity. Members of the same genus, Haloarcula, were preferentially enriched in the aerosol sample relative to the water column samples. Therefore, it appears that a diverse array of hyperhalophiles are capable of surviving aeolian long-distance transport and that some lineages, in particular, have possibly adapted to that strategy.
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Affiliation(s)
- Matthew E. Rhodes
- Department of Biology, College of Charleston, Charleston, SC 29424, USA; (A.D.P.); (H.G.)
| | - Allyson D. Pace
- Department of Biology, College of Charleston, Charleston, SC 29424, USA; (A.D.P.); (H.G.)
| | - Menny M. Benjamin
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Heather Ghent
- Department of Biology, College of Charleston, Charleston, SC 29424, USA; (A.D.P.); (H.G.)
| | - Katherine S. Dawson
- Institute of Earth, Ocean, and Atmospheric Science, Rutgers University, Piscataway, NJ 08854, USA;
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Wheelock CE, Looney DP, Potter AW, Pryor RR, Pryor JL, Florian J, Hostler D. Diver Underwater Cycling Endurance After Short-Term Warm and Hot Water Acclimation. Mil Med 2023; 188:3071-3078. [PMID: 35822881 DOI: 10.1093/milmed/usac204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/11/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION It is unclear whether immersion heat acclimation benefits exercise in warm water conditions. This study examined the effects of heat acclimation strategies on heart rate (HR), core temperature, and time to exhaustion (TTE) during cycling exercise in varying warm water conditions. METHODS Twenty male divers completed this study at the Navy Experimental Diving Unit. Subjects were randomly assigned to one of two 9-day heat acclimation groups. The first group (WARM; n = 10) cycled for 2 hours at 50 W in 34.4 °C water, while the second group (HOT; n = 10) cycled for 1 hour against minimal resistance in 36.7 °C water. Following acclimation, TTE was tested by underwater cycling (30 W) in 35.8 °C, 37.2 °C, and 38.6 °C water. RESULTS Throughout acclimation, the rate of core temperature rise in the first 30 minutes of exercise increased (P = .02), but the maximum core temperature reached was not different for either group. Time to exhaustion (TTE) was reduced, and the rate of core temperature rise during performance testing increased (both P < .001) with increasing water temperature but was not different between groups. Core temperature and HR increased throughout performance testing in each water condition and were lower in the HOT compared to the WARM acclimation group (all P < .05) with the exception of core temperature in the 37.2 °C condition. CONCLUSIONS Underwater exercise performance did not differ between the two acclimation strategies. This study suggests that passive acclimation to a higher water temperature may improve thermoregulatory and cardiovascular responses to exercise in warm water. Hot water immersion adaptations are dependent on exercise intensity and water temperature.
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Affiliation(s)
- Courtney E Wheelock
- Center for Research and Education in Special Environments (CRESE), Department of Exercise and Nutrition Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - David P Looney
- Military Performance Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, MA 01760, USA
| | - Adam W Potter
- Thermal and Mountain Medicine Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, MA 01760, USA
| | - Riana R Pryor
- Center for Research and Education in Special Environments (CRESE), Department of Exercise and Nutrition Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - J Luke Pryor
- Center for Research and Education in Special Environments (CRESE), Department of Exercise and Nutrition Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - John Florian
- Navy Experimental Diving Unit (NEDU), Panama City, FL 32407, USA
| | - David Hostler
- Center for Research and Education in Special Environments (CRESE), Department of Exercise and Nutrition Sciences, University at Buffalo, Buffalo, NY 14214, USA
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Cohen D, Portugal-Cohen M, Oron M, Frusic-Zlotkin M, Soroka Y, Ma'or Z, Amar D, Kohen R. Cutaneous Nrf2-Keap1 pathway modulation by environmental factors: The Dead Sea area as a test case. Biofactors 2022; 49:428-437. [PMID: 36522798 DOI: 10.1002/biof.1926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
The skin is constantly exposed to exogenous environmental stressors and has to cope with excessive oxidative stress and tissue damage. However, exposure to moderate environmental stressors may be beneficial for the cutaneous tissue and assist in protecting against oxidative damage via the enhanced activation of the nuclear factor erythroid 2-related factor 2-Kelch-like ECH-associated protein 1 (Nrf2-Keap1) pathway. Such moderate stressors can be found in various locations around the globe. In this manuscript, we chose to focus on the Dead Sea (DS) area as a test case to study the effect of moderate stressors on the cutaneous tissue because of the unique combinations of moderate stressors in this area. The exceptional location of the DS at an altitude of -438 meters below sea level (the lowest place on earth) is responsible for its rare accumulation of moderate stressors such as high-water salinity, high atmospheric pressure, and unique solar radiation. In this manuscript, we hypothesized that the unique solar radiation in the DS area generates moderate oxidative stress in the skin leading to the induction of intracellular electrophiles, which in turn can activate the protecting Nrf2-Keap1 pathway. We showed that exposure of human skin organ culture from the same donor to solar radiation at the DS resulted in significant activation of the Nrf2-Keap1 pathway, induction of phase II enzymes, and lower apoptotic activity compared to a nearby location at a higher altitude (Jerusalem +700 m). This remarkable effect of activating the Nrf2 protecting pathway and the importance and characteristics of the solar irradiation at the DS is discussed.
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Affiliation(s)
- Dror Cohen
- The Myers Skin Research Laboratory, Faculty of Medicine, Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Skin Research Institute, The Dead Sea & Arava Science Center, Masada, Israel
| | | | - Miriam Oron
- Miriam Oron Mingelgrin Consulting, Jerusalem, Israel
| | - Marina Frusic-Zlotkin
- The Myers Skin Research Laboratory, Faculty of Medicine, Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yoram Soroka
- The Myers Skin Research Laboratory, Faculty of Medicine, Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ze'evi Ma'or
- The Dead Sea Hub department, Fosun Jinmei (Shanghai) Cosmetics Co., Ltd, Shanghai, China
| | - Dalit Amar
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Kohen
- The Myers Skin Research Laboratory, Faculty of Medicine, Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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Beddal A, Boutaiba S, Laassami A, Hamaidi F, Enache M. Characterization by polyphasic approach of some indigenous halophilic archaea of Djelfa's rock salt "Hadjr el Meelh", Algeria. IRANIAN JOURNAL OF MICROBIOLOGY 2022; 14:535-544. [PMID: 36721520 PMCID: PMC9867634 DOI: 10.18502/ijm.v14i4.10240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background and Objectives Hadjr El Melh of Djelfa is an example of hypersaline ecosystems, which can harbor a wide variety of microorganisms under hostile physicochemical conditions. Given the importance of the study of halophilic microorganisms present there in terms of fundamental and applied microbiology, the purpose of this study was to characterize some halophilic archaea isolated from the brines of this environment. Materials and Methods Eight water samples were chosen randomly and collected for physicochemical and microbiological analyses. Isolation of halophilic archaea was carried out by membrane filter technique. Ten strains were identified by polyphasic approach and tested for enzymes production. Results Water samples of Djelfa's rock salt were slightly acidic to neutral in pH (6.55-7.36) with salinity ranging from 258.68 g/l to 493.91 g/l. Phenotypic, biochemical, taxonomic and phylogenetic characteristics indicated that all strains were classified within the family of Halobacteiaceae. Based on the comparison of DNA sequences encoded 16S rRNA, it was determined that seven strains were affiliated to the genus Haloarcula, two strains were related to the genus Halobacterium and one strain within the genus Haloferax. Production of different enzymes such as protease, amylase, esterase, lipase, lecithinase, gelatinase and cellulase on solid medium indicated that one strain (S2-2) produced amylase, esterase, lecithinase and protease. However, no strains showed cellulolytic or lipolytic activity. Gelatinase was found in all tested strains. Conclusion This report constitutes the first preliminary study of culturable halophilic archaea recovered from the brines of Djelfa's rock salt with a promising enzymatic potential in various fields of biotechnology.
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Affiliation(s)
- Amira Beddal
- Department of Natural and Life Science, Faculty of Science and Technology, University of Tissemsilt, Bougara, Algeria,Department of Biology, Faculty of Natural and Life Science, University of Blida 1, Ouled Yaïch, Algeria,Department of Biology, Faculty of Natural and Life Science, University of Djelfa, Djelfa, Algeria,Corresponding author: Amira Beddal, Ph.D, Department of Natural and Life Science, Faculty of Science and Technology, University of Tissemsilt, Bougara, Algeria; Department of Biology, Faculty of Natural and Life Science, University of Blida 1, Ouled Yaïch, Algeria; Department of Biology, Faculty of Natural and Life Science, University of Djelfa, Djelfa, Algeria. Tel: +213553712526 Fax: +21346574511
| | - Saad Boutaiba
- Department of Biology, Faculty of Natural and Life Science, University of Djelfa, Djelfa, Algeria
| | - Affaf Laassami
- Department of Natural and Life Science, Ecole Normale Supérieure, Kouba, Algiers
| | - Fella Hamaidi
- Department of Biology, Faculty of Natural and Life Science, University of Blida 1, Ouled Yaïch, Algeria
| | - Madalin Enache
- Department of Microbiology, Institute of Biology-Bucharest, Romanian Academy, Bucharest, Romania
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Abbas S, Mahmoud H. Identification of Sponge-Associated Bacteria From the Coast of Kuwait and Their Potential Biotechnological Applications. Front Microbiol 2022; 13:896718. [PMID: 35859748 PMCID: PMC9289682 DOI: 10.3389/fmicb.2022.896718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
Sponges are among the most ancient animals harboring complex microbial communities with potential applications in biotechnology. The Arabian Gulf is a thermally stressed enclosed body of water located in an arid region where sponges and their halobionts are understudied. This study combined 16S rRNA next-generation gene amplicon sequencing and cultivation techniques to explore the abundance and diversity of sponge-associated bacteria. Culture-independent techniques showed the associations of more than 25 bacterial phyla with Amphimedon sp., Chondrilla australiensis, Haliclona sp., and Niphates spp. Regarding cultivable bacteria, 315 bacterial isolates associated with the sponge Haliclona sp. were cultivated; these isolates were affiliated with the phyla Proteobacteria and Firmicutes and were distributed among six bacterial genera. Selected strains of Bacillus, Ferrimonas, Pseudovibrio, Shewanella, Spongiobacter, and Vibrio were tested for antimicrobial activity against indicator microorganisms and protease enzyme production. Seven Bacillus strains exhibited weak to moderate growth inhibition against Bacillus subtilis, Staphylococcus aureus, and Candida albicans. Furthermore, 29 different strains of Bacillus, Ferrimonas, Shewanella, and Vibrio exhibited different degrees of positive protease activity. In addition, cultivated strains of Bacillus, Shewanella, Pseudovibrio, and Vibrio were tested for their biomineralization abilities. Herein we report for the first time the isolation of biomineralizing bacteria from sponge tissue where eleven bacterial isolates produced different shapes of calcium carbonate crystals on agar. Our observations shed light on the diversity and biotechnological potentials of sponges-associated bacteria inhabiting one of the world’s hottest seas.
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Levy EJ, Thomas C, Antler G, Gavrieli I, Turchyn A, Grossi V, Ariztegui D, Sivan O. Intensified microbial sulfate reduction in the deep Dead Sea during the early Holocene Mediterranean sapropel 1 deposition. GEOBIOLOGY 2022; 20:518-532. [PMID: 35384246 PMCID: PMC9325388 DOI: 10.1111/gbi.12493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 01/25/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The hypersaline Dead Sea and its sediments are natural laboratories for studying extremophile microorganism habitat response to environmental change. In modern times, increased freshwater runoff to the lake surface waters resulted in stratification and dilution of the upper water column followed by microbial blooms. However, whether these events facilitated a microbial response in the deep lake and sediments is obscure. Here we investigate archived evidence of microbial processes and changing regional hydroclimate conditions by reconstructing deep Dead Sea chemical compositions from pore fluid major ion concentration and stable S, O, and C isotopes, together with lipid biomarkers preserved in the hypersaline deep Dead Sea ICDP-drilled core sediments dating to the early Holocene (ca. 10,000 years BP). Following a significant negative lake water balance resulting in salt layer deposits at the start of the Holocene, there was a general period of positive net water balance at 9500-8300 years BP. The pore fluid isotopic composition of sulfate exhibit evidence of intensified microbial sulfate reduction, where both δ34S and δ18O of sulfate show a sharp increase from estimated base values of 15.0‰ and 13.9‰ to 40.2‰ and 20.4‰, respectively, and a δ34S vs. δ18O slope of 0.26. The presence of the n-C17 alkane biomarker in the sediments suggests an increase of cyanobacteria or phytoplankton contribution to the bulk organic matter that reached the deepest parts of the Dead Sea. Although hydrologically disconnected, both the Mediterranean Sea and the Dead Sea microbial ecosystems responded to increased freshwater runoff during the early Holocene, with the former depositing the organic-rich sapropel 1 layer due to anoxic water column conditions. In the Dead Sea prolonged positive net water balance facilitated primary production and algal blooms in the upper waters and intensified microbial sulfate reduction in the hypolimnion and/or at the sediment-brine interface.
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Affiliation(s)
- Elan J. Levy
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
- Geological Survey of IsraelJerusalemIsrael
- Department of Climate GeochemistryMax Planck Institute for ChemistryMainzGermany
| | - Camille Thomas
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
| | - Gilad Antler
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
- The Interuniversity Institute for Marine Sciences in EilatEilatIsrael
| | | | | | - Vincent Grossi
- Laboratoire de Géologie de LyonUniv. Lyon 1CNRSENSLVilleurbanneFrance
| | - Daniel Ariztegui
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
| | - Orit Sivan
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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Glaeser SP, Silva LMR, Prieto R, Silva MA, Franco A, Kämpfer P, Hermosilla C, Taubert A, Eisenberg T. A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales. MICROBIAL ECOLOGY 2022; 83:18-33. [PMID: 33745062 PMCID: PMC8881428 DOI: 10.1007/s00248-021-01729-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/03/2021] [Indexed: 05/08/2023]
Abstract
Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.
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Affiliation(s)
- Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Liliana M R Silva
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Rui Prieto
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
- MARE-Marine and Environmental Sciences Centre, Lisbon, Portugal
| | - Mónica A Silva
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
| | - Angel Franco
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Anja Taubert
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Giessen, Germany
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Vijayan J, Ammini P, Nathan VK. Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3967-3982. [PMID: 34398377 DOI: 10.1007/s11356-021-15772-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.
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Affiliation(s)
- Jasna Vijayan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
| | - Parvathi Ammini
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India.
- Department of Biotechnology, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
| | - Vinod Kumar Nathan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
- School of Chemical and Biotechnology, Sastra Deemed University Tirumalaisamudram, Thanjavur, Tamilnadu, 613401, India
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Ersoy Omeroglu E, Sudagidan M, Yurt MNZ, Tasbasi BB, Acar EE, Ozalp VC. Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples. Sci Rep 2021; 11:18364. [PMID: 34526632 PMCID: PMC8443733 DOI: 10.1038/s41598-021-97980-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/25/2021] [Indexed: 01/21/2023] Open
Abstract
Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.
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Affiliation(s)
- Esra Ersoy Omeroglu
- Biology Department, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, 35040, Bornova, Izmir, Turkey.
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Mediha Nur Zafer Yurt
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Behiye Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Elif Esma Acar
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, 42080, Meram, Konya, Turkey
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Medical School, Atilim University, 06830, Ankara, Turkey
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12
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Apostolopoulos N, Glaeser SP, Bagwe R, Janssen S, Mayer U, Ewers C, Kämpfer P, Neiger R, Thom N. Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing. PLoS One 2021; 16:e0250695. [PMID: 33939741 PMCID: PMC8092680 DOI: 10.1371/journal.pone.0250695] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
Atopic dermatitis is one of the most common skin diseases in dogs. Pathogenesis is complex and incompletely understood. Skin colonizing bacteria likely play an important role in the severity of this disease. Studying the canine skin microbiota using traditional microbiological methods has many limitations which can be overcome by molecular procedures. The aim of this study was to describe the bacterial microbiota of the skin and ear canals of healthy non-allergic and allergic German shepherd dogs (GSDs) without acute flare or concurrent skin infection and to compare both. Bacterial 16S rRNA gene amplicon sequence data revealed no differences of bacterial community patterns between the different body sites (axilla, front dorsal interdigital skin, groin, and ear canals) in non-allergic dogs. The microbiota at the different body sites of non-allergic GSDs showed no significant differences. Only for the samples obtained from the axilla the bacterial microbiota of allergic dogs was characterized by a lower species richness compared to that of non-allergic dogs and the bacterial community composition of the skin and ear canals of allergic dogs showed body site specific differences compared to non-allergic dogs. Actinobacteria was the most abundant phylum identified from the non-allergic dogs and Proteobacteria from allergic dogs. Macrococcus spp. were more abundant on non-allergic skin while Sphingomonas spp. were more abundant on the allergic skin. Forward step redundancy analysis of metadata indicated that the household the dogs came from had the strongest impact on the composition of the skin microbiome followed by sex, host health status and body site.
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Affiliation(s)
- Neoklis Apostolopoulos
- Department of Dermatology, Small Animal Clinic—Internal Medicine, Justus Liebig University, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Ruchi Bagwe
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Janssen
- Algorithmic Bioinformatics, Justus Liebig University Giessen, Giessen, Germany
| | - Ursula Mayer
- Department of Dermatology, Small Animal Clinic AniCura Kleintierspezialisten Augsburg GmbH, Augsburg, Germany
| | - Christa Ewers
- Institute for Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Nina Thom
- Department of Dermatology, Small Animal Clinic—Internal Medicine, Justus Liebig University, Giessen, Germany
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13
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Satjarak A, Graham LE, Piotrowski MJ, Trest MT, Wilcox LW, Cook ME, Knack JJ, Arancibia-Avila P. Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria). JOURNAL OF PHYCOLOGY 2021; 57:39-50. [PMID: 33070358 DOI: 10.1111/jpy.13084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/01/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free-living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.
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Affiliation(s)
- Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 103330, Thailand
| | - Linda E Graham
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | | | - Marie T Trest
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Lee W Wilcox
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Martha E Cook
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Jennifer J Knack
- Department of Biology, University of Minnesota, Duluth, Minnesota, 55812, USA
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14
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Glaeser SP, Gabur I, Haghighi H, Bartz JO, Kämpfer P, Snowdon R, Obermeier C. Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum. FEMS Microbiol Ecol 2020; 96:5643882. [PMID: 31769797 DOI: 10.1093/femsec/fiz188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 01/23/2023] Open
Abstract
Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.
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Affiliation(s)
- Stefanie P Glaeser
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Hossein Haghighi
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.,Department of Life Sciences, University of Modena and Reggio Emilia, Via Kenedy 17/I, 42124 Reggio Emilia, Italy
| | - Jens-Ole Bartz
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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15
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Palmer R, Fleming GTA, Glaeser S, Semmler T, Flamm A, Ewers C, Kämpfer P, Budich O, Berrow S, O'Brien J, Siebert U, Collins E, Ruttledge M, Eisenberg T. Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon. DISEASES OF AQUATIC ORGANISMS 2020; 139:161-174. [PMID: 32406871 DOI: 10.3354/dao03478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.
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Affiliation(s)
- Roy Palmer
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91TK33, Ireland
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16
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Compte-Port S, Fillol M, Gich F, Borrego CM. Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. PLoS One 2020; 15:e0231238. [PMID: 32267873 PMCID: PMC7141681 DOI: 10.1371/journal.pone.0231238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.
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Affiliation(s)
- Sergi Compte-Port
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M. Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
- * E-mail:
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17
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Multi- and inter-disciplinary approaches towards understanding the sinkholes’ phenomenon in the Dead Sea Basin. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2146-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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18
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Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon. Sci Rep 2020; 10:3298. [PMID: 32094390 PMCID: PMC7040004 DOI: 10.1038/s41598-020-59681-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/04/2019] [Indexed: 11/18/2022] Open
Abstract
Halophilic proteins subjected to below about 15% salt in vitro denature through misfolding, aggregation and/or precipitation. Halobacteria, however, have been detected in environments of fluctuating salinity such as coastal salterns and even around fresh water springs in the depths of the Dead Sea. In order to identify the underlying mechanisms of low salt survival, we explored the reactivation capacity of Halobacterium (Hbt) salinarum sub-populations after incubation in low salt media and recovery in physiological salt. Respiratory oxygen consumption was assessed in stressed cells and cell viability was estimated by Live/Dead staining and flow cytometry. In vivo neutron scattering experiments showed that the recovery of Hbt salinarum sub-populations exposed to severe low salt conditions is related to a rapid retrieval of functional molecular dynamics in the proteome. In the hypothesis that the observations on Hbt salinarum have wider relevance, they could be of key ecological significance for the dispersion of extremophiles when environmental fluctuations become severe.
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19
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Bižić M, Klintzsch T, Ionescu D, Hindiyeh MY, Günthel M, Muro-Pastor AM, Eckert W, Urich T, Keppler F, Grossart HP. Aquatic and terrestrial cyanobacteria produce methane. SCIENCE ADVANCES 2020; 6:eaax5343. [PMID: 31998836 PMCID: PMC6962044 DOI: 10.1126/sciadv.aax5343] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.
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Affiliation(s)
- M. Bižić
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Corresponding author. (M.B.); (H.-P.G.)
| | - T. Klintzsch
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
| | - D. Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - M. Y. Hindiyeh
- Department of Water and Environmental Engineering, German Jordanian University, Amman, Jordan
| | - M. Günthel
- Department of Biosciences, Swansea University, SA2 8PP Swansea, UK
- Medical University of Gdańsk, Department of International Research Agenda 3P–Medicine, Marii Skłodowskiej-Curie 3a, 80-210 Gdańsk, Poland
| | - A. M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - W. Eckert
- Israel Oceanographic and Limnological Research, Yigal Allon Kinneret Limnological Laboratory, Migdal 14650, Israel
| | - T. Urich
- Institute of Microbiology, Center for Functional Genomics, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - F. Keppler
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, 69120 Heidelberg, Germany
| | - H.-P. Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
- Corresponding author. (M.B.); (H.-P.G.)
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20
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The Impact of a Fish Cannery Wastewater Discharge on the Bacterial Community Structure and Sanitary Conditions of Marine Coastal Sediments. WATER 2019. [DOI: 10.3390/w11122566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The effects of fish cannery discharge (FCD) on bacteria in marine coastal sediments were investigated. Redox potentials were measured, and granulometry was determined by wet ASTM sieving, and with the Sedigraph method. Prokaryotic abundance (PA) was determined by epifluorescence microscopy (DAPI staining), and faecal indicator bacteria (FIB) enumerated with the multiple test tube and most probable number method. Total lipids were determined gravimetrically, and sterols analysed by GC/MSD. Bacterial community composition was determined after total DNA isolation, Illumina MiSeq amplification, and SILVAngs processing pipeline. The FCD was rich in lipids, heterotrophic prokaryotes and FIB. The bacterial community of the FCD was dominated by Firmicutes and Gammaproteobacteria and many potentially pathogenic bacteria. Highly porosusgravelly sands clogged with fish remains transitioned to less permeable sandy muds away from the FCD. All sediments were anoxic with extremely negative potentials around the outfall. High surface PA and FIB spread 300 m from the outfall. Gammaproteobacteria and Deltaproteobacteria appeared in all sediments. Sulfurovum and Anaerolineaceae characterized the most polluted locations where gammaproteobacterial Woeseiaceae/JTB255 marine benthic group declined. Gammaproteobacteria and Bacteroidetes characterized surface sediments, while Chloroflexi and Deltaproteobacteria prevailed in deeper layers. The FCD enriched sediments in lipids and allochthonous bacteria degrading sanitary quality, lowering the permeability, redox potential, and bacterial diversity.
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21
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Warden JG, Coshell L, Rosen MR, Breecker DO, Ruthrof KX, Omelon CR. The importance of groundwater flow to the formation of modern thrombolitic microbialites. GEOBIOLOGY 2019; 17:536-550. [PMID: 31119865 DOI: 10.1111/gbi.12344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 02/11/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
Modern microbialites are often located within groundwater discharge zones, yet the role of groundwater in microbialite accretion has yet to be resolved. To understand relationships between groundwater, microbialites, and associated microbial communities, we quantified and characterized groundwater flow and chemistry in active thrombolitic microbialites in Lake Clifton, Western Australia, and compared these observations to inactive thrombolites and lakebed sediments. Groundwater flows upward through an interconnected network of pores within the microstructure of active thrombolites, discharging directly from thrombolite heads into the lake. This upwelling groundwater is fresher than lake water and is hypothesized to support microbial mat growth by reducing salinity and providing limiting nutrients in an osmotically stressful and oligotrophic habitat. This is in contrast to inactive thrombolites that show no evidence of microbial mat colonization and are infiltrated by hypersaline lake water. Groundwater discharge through active thrombolites contrasts with the surrounding lakebed, where hypersaline lake water flows downward through sandy sediments at very low rates. Based on an appreciation for the role of microorganisms in thrombolite accretion, our findings suggest conditions favorable to thrombolite formation still exist in certain locations of Lake Clifton despite increasing lake water salinity. This study is the first to characterize groundwater flow rates, paths, and chemistry within a microbialite-forming environment and provides new insight into how groundwater can support microbial mats believed to contribute to microbialite formation in modern and ancient environments.
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Affiliation(s)
- John G Warden
- Jackson School of Geosciences, University of Texas at Austin, Austin, Texas
| | - Lee Coshell
- Coshell and Associates, South Perth, Western Australia, Australia
| | | | - Daniel O Breecker
- Jackson School of Geosciences, University of Texas at Austin, Austin, Texas
| | - Katinka X Ruthrof
- Murdoch University, Murdoch, Western Australia, Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Christopher R Omelon
- Department of Mining and Materials Engineering, McGill University, Montréal, Québec, Canada
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22
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D'Angeli IM, Ghezzi D, Leuko S, Firrincieli A, Parise M, Fiorucci A, Vigna B, Addesso R, Baldantoni D, Carbone C, Miller AZ, Jurado V, Saiz-Jimenez C, De Waele J, Cappelletti M. Geomicrobiology of a seawater-influenced active sulfuric acid cave. PLoS One 2019; 14:e0220706. [PMID: 31393920 PMCID: PMC6687129 DOI: 10.1371/journal.pone.0220706] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.
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Affiliation(s)
- Ilenia M D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefan Leuko
- DLR Institute of Aerospace Medicine, Radiation Biology, Köln, Germany
| | - Andrea Firrincieli
- School of Environmental and Forest Science, University of Washington, Seattle, WA, United States of America
| | - Mario Parise
- Department of Geological and Environmental Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Fiorucci
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Bartolomeo Vigna
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Daniela Baldantoni
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Cristina Carbone
- DISTAV, Department of Geological, Environmental and Biological Sciences, University of Genoa, Genoa, Italy
| | | | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Sevilla, Spain
| | | | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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23
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Kirstein IV, Wichels A, Gullans E, Krohne G, Gerdts G. The Plastisphere - Uncovering tightly attached plastic "specific" microorganisms. PLoS One 2019; 14:e0215859. [PMID: 31013334 PMCID: PMC6478340 DOI: 10.1371/journal.pone.0215859] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/09/2019] [Indexed: 12/02/2022] Open
Abstract
In order to understand the degradation potential of plastics in the marine environment, microorganisms that preferentially colonize and interact with plastic surfaces, as opposed to generalists potentially colonising everything, need to be identified. Accordingly, it was hypothesized that i.) plastic "specific" microorganisms are closely attached to the polymeric surface and ii.) that specificity of plastics biofilms are rather related to members of the rare biosphere. To answer these hypotheses, a three phased experiment to stepwise uncover closely attached microbes was conducted. In Phase 1, nine chemically distinct plastic films and glass were incubated in situ for 21 months in a seawater flow through system. In Phase 2, a high-pressure water jet treatment technique was used to remove the upper biofilm layers to further, in Phase 3, enrich a plastic "specific" community. To proof whether microbes colonizing different plastics are distinct from each other and from other inert hard substrates, the bacterial communities of these different substrates were analysed using 16S rRNA gene tag sequencing. Our findings indicate that tightly attached microorganisms account to the rare biosphere and suggest the presence of plastic "specific" microorganisms/assemblages which could benefit from the given plastic properties or at least grow under limited carbon resources.
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Affiliation(s)
- Inga Vanessa Kirstein
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Antje Wichels
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Elisabeth Gullans
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Georg Krohne
- University of Würzburg, Biocenter, Imaging Core Facility, Würzburg, Germany
| | - Gunnar Gerdts
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
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24
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Looney DP, Long ET, Potter AW, Xu X, Friedl KE, Hoyt RW, Chalmers CR, Buller MJ, Florian JP. Divers risk accelerated fatigue and core temperature rise during fully-immersed exercise in warmer water temperature extremes. Temperature (Austin) 2019; 6:150-157. [PMID: 31312674 PMCID: PMC6620004 DOI: 10.1080/23328940.2019.1599182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/14/2019] [Accepted: 03/20/2019] [Indexed: 02/03/2023] Open
Abstract
Physiological responses to work in cold water have been well studied but little is known about the effects of exercise in warm water; an overlooked but critical issue for certain military, scientific, recreational, and professional diving operations. This investigation examined core temperature responses to fatiguing, fully-immersed exercise in extremely warm waters. Twenty-one male U.S. Navy divers (body mass, 87.3 ± 12.3 kg) were monitored during rest and fatiguing exercise while fully-immersed in four different water temperatures (Tw): 34.4, 35.8, 37.2, and 38.6°C (Tw34.4, Tw35.8, Tw37.2, and Tw38.6 respectively). Participants exercised on an underwater cycle ergometer until volitional fatigue or core temperature limits were reached. Core body temperature and heart rate were monitored continuously. Trial performance time decreased significantly as water temperature increased (Tw34.4, 174 ± 12 min; Tw35.8, 115 ± 13 min; Tw37.2, 50 ± 13 min; Tw38.6, 34 ± 14 min). Peak core body temperature during work was significantly lower in Tw34.4 water (38.31 ± 0.49°C) than in warmer temperatures (Tw35.8, 38.60 ± 0.55°C; Tw37.2, 38.82 ± 0.76°C; Tw38.6, 38.97 ± 0.65°C). Core body temperature rate of change increased significantly with warmer water temperature (Tw34.4, 0.39 ± 0.28°C·h−1; Tw35.8, 0.80 ± 0.19°C·h−1; Tw37.2, 2.02 ± 0.31°C·h−1; Tw38.6, 3.54 ± 0.41°C·h−1). Physically active divers risk severe hyperthermia in warmer waters. Increases in water temperature drastically increase the rate of core body temperature rise during work in warm water. New predictive models for core temperature based on workload and duration of warm water exposure are needed to ensure warm water diving safety.
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Affiliation(s)
- David P Looney
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Edwin T Long
- Navy Experimental Diving Unit (NEDU), Panama City, Florida, USA
| | - Adam W Potter
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA.,Rutgers University, School of Biomedical and Health Sciences, Newark, New Jersey, USA
| | - Xiaojiang Xu
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Karl E Friedl
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Reed W Hoyt
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Christopher R Chalmers
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Mark J Buller
- Biophysics and Biomedical Modeling Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - John P Florian
- Navy Experimental Diving Unit (NEDU), Panama City, Florida, USA
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25
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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26
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Kirstein IV, Wichels A, Krohne G, Gerdts G. Mature biofilm communities on synthetic polymers in seawater - Specific or general? MARINE ENVIRONMENTAL RESEARCH 2018; 142:147-154. [PMID: 30337052 DOI: 10.1016/j.marenvres.2018.09.028] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/28/2018] [Accepted: 09/30/2018] [Indexed: 05/19/2023]
Abstract
To understand the ecological impacts of the "Plastisphere", those microbes need to be identified that preferentially colonize and interact with synthetic polymer surfaces, as opposed to general surface colonizers. It was hypothesized that the microbial biofilm composition varies distinctly between different substrates. A long-term incubation experiment was conducted (15month) with nine different synthetic polymer films as substrate as well as glass using a natural seawater flow-through system. To identify colonizing microorganisms, 16S and 18SrRNA gene tag sequencing was performed. The microbial biofilms of these diverse artificial surfaces were visualized via scanning electron microscopy. Biofilm communities attached to synthetic polymers are distinct from glass associated biofilms; apparently a more general marine biofilm core community serves as shared core among all synthetic polymers rather than a specific synthetic polymer community. Nevertheless, characteristic and discriminatory taxa of significantly different biofilm communities were identified, indicating their specificity to a given substrate.
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Affiliation(s)
- Inga V Kirstein
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
| | - Antje Wichels
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Georg Krohne
- University of Würzburg, Biocenter, Imaging Core Facility, Würzburg, Germany
| | - Gunnar Gerdts
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
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27
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Bižić-Ionescu M, Ionescu D, Grossart HP. Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems. Front Microbiol 2018; 9:2569. [PMID: 30416497 PMCID: PMC6212488 DOI: 10.3389/fmicb.2018.02569] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/08/2018] [Indexed: 12/15/2022] Open
Abstract
The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.
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Affiliation(s)
- Mina Bižić-Ionescu
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Danny Ionescu
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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28
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Sharma S, Grewal S, Vakhlu J. Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K). Arch Microbiol 2018; 200:1333-1343. [PMID: 29974156 DOI: 10.1007/s00203-018-1549-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/25/2018] [Accepted: 06/30/2018] [Indexed: 11/26/2022]
Abstract
Clay therapy for skin disease treatment is an ancient practice popular worldwide as a cheap alternative to pharmaceutical products. Effectiveness of clay against skin problems has been linked to its mineral composition and to microbial activity. The clay-water paste of a holy shrine Chamliyal in the Jammu region of J&K, India is used as an ointment to treat different skin disorders particularly psoriasis. Using the 16 SrDNA amplicon pyrosequencing and whole-metagenome direct shotgun Illumina sequencing, microbial phylogeny and potential metabolic functions were catalogued for Chamliyal's clay. Microbial diversity profile of the Chamliyal's clay is similar to other medicinal clays, particularly Dead Sea; there is some uniqueness as well. Although Proteobacteria, Actinomycetes and Firmicutes are common inhabitants of all the clay types, sulphur- and iron-reducing bacteria like Deferribacterales are particular to clays used for skin healing. In the present study it is proposed that healing properties of clay may be due to the microbes and microbial genes associated with metabolism of minerals like iron and sulphur, that lead to mineral acquisition in the Chamliyal's clay.
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Affiliation(s)
- Sakshi Sharma
- School of Biotechnology, University of Jammu, Jammu, J&K, 180006, India
| | - Simmi Grewal
- School of Biotechnology, University of Jammu, Jammu, J&K, 180006, India
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, Jammu, J&K, 180006, India.
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29
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Cuadrat RRC, Ionescu D, Dávila AMR, Grossart HP. Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. Front Microbiol 2018. [PMID: 29515540 PMCID: PMC5826242 DOI: 10.3389/fmicb.2018.00251] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
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Affiliation(s)
- Rafael R C Cuadrat
- Bioinformatics Core Facility, Max Plank Institute for Biology of Ageing, Köln, Germany.,Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Danny Ionescu
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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30
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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31
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Al-Karablieh N. Antimicrobial Activity of Bacillus Persicus 24-DSM Isolated from Dead Sea Mud. Open Microbiol J 2018; 11:372-383. [PMID: 29399218 PMCID: PMC5759096 DOI: 10.2174/1874285801711010372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 11/22/2022] Open
Abstract
Intorduction: Dead Sea is a hypersaline lake with 34% salinity, gains its name due to the absence of any living macroscopic creatures. Despite the extreme hypersaline environment, it is a unique ecosystem for various halophilic microorganisms adapted to this environment. Aims & Objectives: Halophilic microorganisms are known for various potential biotechnological applications, the purpose of the current research is isolation and screening of halophilic bacteria from Dead Sea mud for potential antimicrobial applications. Methods & Materials: Screening for antagonistic bacteria was conducted by bacterial isolation from Dead Sea mud samples and agar plate antagonistic assay. The potential antagonistic isolates were subjected to biochemical characterization and identification by 16S-rRNA sequencing. Among the collected isolates, four isolates showed potential antagonistic activity against Bacillus subtilis 6633 and Escherichia coli 8739. The most active isolate (24-DSM) was subjected for antagonistic activity and minimal inhibitory concentration against different gram positive and negative bacterial strains after cultivation in different salt concentration media. Results: The results of 16S-rRNA analysis revealed that 24-DSM is very closely related to Bacillus persicus strain B48, which was isolated from hypersaline lake in Iran. Conclusion: Therefore, the isolate 24-DSM is assigned as a new strain of B. persicusi isolated from the Dead Sea mud. B. persicusi 24-DSM showed higher antimicrobial activity, when it was cultivated with saline medium, against all tested bacterial strains, where the most sensitive bacterial strain was Corynebacterium diphtheria 51696.
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Affiliation(s)
- Nehaya Al-Karablieh
- Hamdi mango center for scientific research, The University of Jordan, Amman, Jordan
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32
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Cabral BCA, Hoffmann L, Budowle B, Ürményi TP, Moura-Neto RS, Azevedo SMFO, Silva R. Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir. Microbiologyopen 2018; 7:e00523. [PMID: 29380948 PMCID: PMC5911997 DOI: 10.1002/mbo3.523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/18/2017] [Accepted: 06/27/2017] [Indexed: 11/18/2022] Open
Abstract
Our comprehension of the dynamics and diversity of freshwater planktonic bacterial communities is far from complete concerning the Brazilian Amazonian region. Therefore, reference studies are urgently needed. We mapped bacterial communities present in the planktonic communities of a freshwater artificial reservoir located in the western Amazonian basin. Two samples were obtained from rainy and dry seasons, the periods during which water quality and plankton diversity undergo the most significant changes. Hypervariable 16S rRNA and shotgun sequencing were performed to describe the first reference of a microbial community in an Amazonian lentic system. Microbial composition consisted mainly of Betaproteobacteria, Cyanobacteria, Alphaproteobacteria, and Actinobacteria in the dry period. The bacteria distribution in the rainy period was notably absent of Cyanobacteria. Microcystis was observed in the dry period in which the gene cluster for cyanotoxins was found. Iron acquisition gene group was higher in the sample from the rainy season. This work mapped the first inventory of the planktonic microbial community of a large water reservoir in the Amazon, providing a reference for future functional studies and determining other communities and how they interact.
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Affiliation(s)
- Bianca C A Cabral
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luísa Hoffmann
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, TX, USA.,Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turán P Ürményi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo S Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sandra M F O Azevedo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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33
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Surface modifications for phase change cooling applications via crenarchaeon Sulfolobus solfataricus P2 bio-coatings. Sci Rep 2017; 7:17891. [PMID: 29263395 PMCID: PMC5738355 DOI: 10.1038/s41598-017-18192-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022] Open
Abstract
Due to its high heat removal capability and exploitation of latent heat, boiling is considered to be one of the most effective cooling methods in industry. Surface structure and wettability are two factors imposing boiling phenomena. Here, we propose an effective and facile method for surface enhancement via crenarchaeon Sulfolobus Solfataricus P2 bio-coatings. The positive effects of such surfaces of bio-coatings were assessed, and enhancements in heat transfer and cooling were obtained. Visualization was also performed, and bubble dynamics of generated bubbles and vapor columns from the tested surfaces with bio-coatings are here presented. Superior performance in terms of boiling heat transfer and cooling was reached with the use of crenarchaeon Sulfolobus Solfataricus P2 coated surfaces. Thus, this study clearly demonstrates the potential of futuristic surfaces with bio-coatings to achieve substantial energy saving and efficiency.
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Paliaga P, Korlević M, Ivančić I, Najdek M. Limited influence of primary treated sewage waters on bacterial abundance, production and community composition in coastal seawaters. MARINE ENVIRONMENTAL RESEARCH 2017; 131:215-226. [PMID: 29032852 DOI: 10.1016/j.marenvres.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
The response of bacteria in terms of abundance, production and community structure to changes induced by the discharge of primary treated sewage waters was investigated combining microbiological, chemical and molecular tools. The primary treatment did not affect substantially the bacterial community structure in wastewaters and did not reduce the concentrations of fecal indicators. The spatial distribution of the sewage plume was governed by vertical stratification and currents. Bacterial abundance and production in the sea receiving waste waters depended predominantly on environmental conditions. In the waters with the highest concentration of fecal pollution indicators the bacterial community was characterized by allochthonous bacteria belonging to Epsilonproteobacteria, Firmicutes, Gammaproteobacteria and Bacteroidetes. The latter two taxa were also present in unpolluted waters but had a different structure, typical for oligotrophic environments. Although the impact of primary treated sewage waters was limited, a sanitary risk persisted due to the relevant presence of potentially pathogenic bacteria.
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Affiliation(s)
- Paolo Paliaga
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Ingrid Ivančić
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
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Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum. Nat Commun 2017; 8:455. [PMID: 28878209 PMCID: PMC5587575 DOI: 10.1038/s41467-017-00342-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown. Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluorescence in situ hybridization, to show that individual cells of Achromatium oxaliferum, the world’s biggest known freshwater bacterium, harbor genetic diversity typical of whole bacterial communities. The cells contain tens of transposable elements, which likely cause the unprecedented diversity that we observe in the sequence and synteny of genes. Given the high within-cell diversity of the usually conserved 16S ribosomal RNA gene, we suggest that gene conversion occurs in multiple, separated genomic hotspots. The ribosomal RNA distribution inside the cells hints to spatially differential gene expression. We also suggest that intracellular gene transfer may lead to extensive gene reshuffling and increased diversity. The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.
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Heim C, Quéric NV, Ionescu D, Schäfer N, Reitner J. Frutexites-like structures formed by iron oxidizing biofilms in the continental subsurface (Äspö Hard Rock Laboratory, Sweden). PLoS One 2017; 12:e0177542. [PMID: 28542238 PMCID: PMC5438144 DOI: 10.1371/journal.pone.0177542] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 04/29/2017] [Indexed: 11/24/2022] Open
Abstract
Stromatolitic iron-rich structures have been reported from many ancient environments and are often described as Frutexites, a cryptic microfossil. Although microbial formation of such structures is likely, a clear relation to a microbial precursor is lacking so far. Here we report recent iron oxidizing biofilms which resemble the ancient Frutexites structures. The living Frutexites-like biofilms were sampled at 160 m depth in the Äspö Hard Rock Laboratory in Sweden. Investigations using microscopy, 454 pyrosequencing, FISH, Raman spectroscopy, biomarker and trace element analysis allowed a detailed view of the structural components of the mineralized biofilm. The most abundant bacterial groups were involved in nitrogen and iron cycling. Furthermore, Archaea are widely distributed in the Frutexites-like biofilm, even though their functional role remains unclear. Biomarker analysis revealed abundant sterols in the biofilm most likely from algal and fungal origins. Our results indicate that the Frutexites-like biofilm was built up by a complex microbial community. The functional role of each community member in the formation of the dendritic structures, as well as their potential relation to fossil Frutexites remains under investigation.
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Affiliation(s)
- Christine Heim
- Department of Geobiology, Geoscience Centre, University of Göttingen, Göttingen, Germany
| | - Nadia-Valérie Quéric
- Department of Geobiology, Geoscience Centre, University of Göttingen, Göttingen, Germany
| | - Danny Ionescu
- Leibnitz Institute for Freshwater Ecology and Inland Fisheries, IGB, Experimental Limnology, Stechlin, Germany
| | - Nadine Schäfer
- Department of Geobiology, Geoscience Centre, University of Göttingen, Göttingen, Germany
| | - Joachim Reitner
- Department of Geobiology, Geoscience Centre, University of Göttingen, Göttingen, Germany
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Huhe, Chen X, Hou F, Wu Y, Cheng Y. Bacterial and Fungal Community Structures in Loess Plateau Grasslands with Different Grazing Intensities. Front Microbiol 2017; 8:606. [PMID: 28439265 PMCID: PMC5383705 DOI: 10.3389/fmicb.2017.00606] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/24/2017] [Indexed: 11/13/2022] Open
Abstract
The Loess Plateau of China is one of the most fragile ecosystems worldwide; thus, human production activities need to be conducted very cautiously. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and changes in vegetation and soil physical and chemical properties induced by grazing, in four grasslands with different levels of grazing intensity (0, 2.67, 5.33, and 8.67 sheep/ha) in the semiarid region of the Loess Plateau. The relative abundances of the bacterial community in the grasslands with 2.67 and 5.33 sheep/ha were significantly higher than those in grasslands with 0 and 8.67 sheep/ha, and the fungal diversity was significantly lower for grasslands with 2.67 sheep/ha than for the other grasslands. Redundancy analysis (RDA) showed that plant biomass, nitrate, and total nitrogen have significant effects on bacterial community structure, whereas nitrate and total nitrogen also significantly affect fungal community structure. Variation partitioning showed that soil and plant characteristics influence the bacterial and fungal community structures; these characteristics explained 51.9 and 52.9% of the variation, respectively. Thus, bacterial and fungal community structures are very sensitive to grazing activity and change to different extents with different grazing intensities. Based on our findings, a grazing intensity of about 2.67 sheep/ha is considered the most appropriate in semiarid grassland of the Loess Plateau.
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Affiliation(s)
- Huhe
- Soil Fertilizer and Water-Saving Institute, Gansu Academy of Agricultural SciencesLanzhou, China
- The Ministry of Agriculture in Gansu Province Cultivated Land Conservation and Agricultural Environmental Science Observation Experiment StationsWuwei, China
| | - Xianjiang Chen
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Yanpei Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Yunxiang Cheng
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
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Meyer JM, Baskaran P, Quast C, Susoy V, Rödelsperger C, Glöckner FO, Sommer RJ. Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island. Environ Microbiol 2017; 19:1476-1489. [PMID: 28198090 DOI: 10.1111/1462-2920.13697] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/20/2016] [Accepted: 01/08/2017] [Indexed: 02/06/2023]
Abstract
Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles´ deaths. Surprisingly, new dauers are seen after 11 days, suggesting that some worms return to the dauer stage after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects.
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Affiliation(s)
- Jan M Meyer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Praveen Baskaran
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Christian Quast
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Vladislav Susoy
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Christian Rödelsperger
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
| | - Frank O Glöckner
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, 28359, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany
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40
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Perl T, Kis-Papo T, Nevo E. Fungal biodiversity in the hypersaline Dead Sea: extinction and evolution. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Braun B, Schröder J, Knecht H, Szewzyk U. Unraveling the microbial community of a cold groundwater catchment system. WATER RESEARCH 2016; 107:113-126. [PMID: 27837729 DOI: 10.1016/j.watres.2016.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 10/02/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
The abundance, diversity and composition of bacterial communities in water wells with low groundwater temperatures were assessed. The drinking water catchment system, equipped with subsurface groundwater treatment for iron- and manganese removal, is located within a continental influenced veldt landscape type in eastern Russia, close to the border to China. In this study, the bacterial communities in 22 different water wells of the catchment system were analyzed and correlated to operating conditions and environmental factors. The investigated bacterial treated and groundwater populations differed from those in central European groundwater. Large variations between the investigated samples were observed, and DGGE profiles of water samples from the beginning and the end of the abstraction phases revealed two distinct fingerprint clusters with about 82% similarity to each other corresponding to the operation mode of the wells. Sequence data analysis from 454 pyrosequencing indicated Rhodoferax and Gallionella as the most abundant genera within the catchment system. The abundance of the OTU Methylotenera was statistically significant when correlated to the beginning of the abstraction phases, while no indicator OTUs could be determined for the end of the pumping phases. ACK-M1 cluster was proofed as indicator OTU for operating wells, whereas the Gallionella OTUs were correlated with non operating wells. Well operation and resultant oxygen entry could serve as factors that altered the bacterial community structure and composition the most. Quantitative PCR analysis showed that genes related to the iron-reducing Rhodoferax genus were present in nearly all of the samples. This study clearly showed an alteration within the bacterial communities dependent on the operation mode of the water wells.
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Affiliation(s)
- Burga Braun
- Technische Universität Berlin, Department of Environmental Microbiology, Ernst Reuter Platz 1, 10587, Berlin, Germany.
| | - Josephin Schröder
- Technische Universität Berlin, Department of Environmental Microbiology, Ernst Reuter Platz 1, 10587, Berlin, Germany
| | - Henrik Knecht
- University Hospital Schleswig-Holstein, 2(nd) Medical Department, Campus Kiel, Chemnitzstr. 33, 24116, Kiel, Germany
| | - Ulrich Szewzyk
- Technische Universität Berlin, Department of Environmental Microbiology, Ernst Reuter Platz 1, 10587, Berlin, Germany
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42
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Vaksmaa A, Lüke C, van Alen T, Valè G, Lupotto E, Jetten MSM, Ettwig KF. Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil. FEMS Microbiol Ecol 2016; 92:fiw181. [PMID: 27562776 DOI: 10.1093/femsec/fiw181] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2016] [Indexed: 12/23/2022] Open
Abstract
In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 106 to 3.9 × 106 16S rRNA gene copies g-1dw in bulk soil and 0.27 × 106 to 2.8 × 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.
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Affiliation(s)
- A Vaksmaa
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - C Lüke
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - T van Alen
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - G Valè
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - E Lupotto
- CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy
| | - M S M Jetten
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - K F Ettwig
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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Korlević M, Šupraha L, Ljubešić Z, Henderiks J, Ciglenečki I, Dautović J, Orlić S. Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary. Syst Appl Microbiol 2016; 39:398-408. [PMID: 27475818 DOI: 10.1016/j.syapm.2016.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
Abstract
Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 clade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary.
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Affiliation(s)
- M Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - L Šupraha
- Paleobiology, Department of Earth Sciences, Uppsala University, Sweden
| | - Z Ljubešić
- Division of Biology, Faculty of Science, University of Zagreb, Croatia
| | - J Henderiks
- Paleobiology, Department of Earth Sciences, Uppsala University, Sweden
| | - I Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - J Dautović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - S Orlić
- Division of Material Chemistry, Ruđer Bošković Institute, Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, Zagreb, Croatia.
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Numberger D, Herlemann DPR, Jürgens K, Dehnhardt G, Schulz-Vogt H. Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina). Microbiologyopen 2016; 5:782-792. [PMID: 27734626 PMCID: PMC5061715 DOI: 10.1002/mbo3.369] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 01/12/2023] Open
Abstract
The gut microbiota has many beneficial effects on host metabolism and health, and its composition is determined by numerous factors. It is also assumed that there was a co‐evolution of mammals and the bacteria inhabiting their gut. Current knowledge of the mammalian gut microbiota mainly derives from studies on humans and terrestrial animals, whereas those on marine mammals are sparse. However, they could provide additional information on influencing factors, such as the role of diet and co‐evolution with the host. In this study, we investigated and compared the bacterial diversity in the feces of five male harbor seals (Phoca vitulina). Because this small population included two half‐brother pairs, each sharing a common father, it allowed an evaluation of the impact of host relatedness or genetic similarity on the gut microbial community. Fresh feces obtained from the seals by an enema were analyzed by fluorescence in situ hybridization and amplicon sequencing of 16S rRNA genes. The results showed that the bacterial communities in the seals' feces mainly consisted of the phyla Firmicutes (19–43%), Bacteroidetes (22–36%), Fusobacteria (18–32%), and Proteobacteria (5–17%) . Twenty‐one bacterial members present in the fecal samples of the five seals contributed an average relative abundance of 93.7 + 8.7% of the total fecal microbial community. Contrary to all expectations based on previous studies a comparison of the fecal community between individual seals showed a higher similarity between unrelated than related individuals.
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Affiliation(s)
- Daniela Numberger
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany. .,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany.
| | - Daniel P R Herlemann
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany.,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany
| | - Guido Dehnhardt
- University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany.,Marine Science Center, Am Yachthafen 3a, Rostock, D-18119, Germany
| | - Heide Schulz-Vogt
- Leibniz Institute for Baltic Sea Research, Seestrasse 15, Rostock, D-18119, Germany.,University of Rostock, Albert-Einstein-Strasse 3, Rostock, D-18059, Germany
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Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME JOURNAL 2016; 10:2447-58. [PMID: 27022994 PMCID: PMC5030689 DOI: 10.1038/ismej.2016.36] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 01/29/2016] [Accepted: 02/07/2016] [Indexed: 11/14/2022]
Abstract
Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.
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46
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Lucas J, Koester I, Wichels A, Niggemann J, Dittmar T, Callies U, Wiltshire KH, Gerdts G. Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level. Front Microbiol 2016; 7:321. [PMID: 27014241 PMCID: PMC4791370 DOI: 10.3389/fmicb.2016.00321] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
Remineralization and transformation of dissolved organic matter (DOM) by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition (BCC) at Helgoland Roads (North Sea) in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of 20 days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom toward the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen (TDN) concentration, temperature, and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of BCC variation.
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Affiliation(s)
- Judith Lucas
- Biological Station Helgoland, Shelf Sea Systems Ecology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
| | - Irina Koester
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg Oldenburg, Germany
| | - Antje Wichels
- Biological Station Helgoland, Shelf Sea Systems Ecology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg Oldenburg, Germany
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg Oldenburg, Germany
| | - Ulrich Callies
- Helmholtz-Zentrum Geesthacht Centre for Materials and Coastal Research, Institute of Coastal Research, Modelling for the Assessment of Coastal Systems Geesthacht, Germany
| | - Karen H Wiltshire
- Biological Station Helgoland, Shelf Sea Systems Ecology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine ResearchHelgoland, Germany; Wattenmeerstation Sylt, Coastal Ecology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine ResearchList/Sylt, Germany
| | - Gunnar Gerdts
- Biological Station Helgoland, Shelf Sea Systems Ecology, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research Helgoland, Germany
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47
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Kottmeier C, Agnon A, Al-Halbouni D, Alpert P, Corsmeier U, Dahm T, Eshel A, Geyer S, Haas M, Holohan E, Kalthoff N, Kishcha P, Krawczyk C, Lati J, Laronne JB, Lott F, Mallast U, Merz R, Metzger J, Mohsen A, Morin E, Nied M, Rödiger T, Salameh E, Sawarieh A, Shannak B, Siebert C, Weber M. New perspectives on interdisciplinary earth science at the Dead Sea: The DESERVE project. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 544:1045-1058. [PMID: 26779955 DOI: 10.1016/j.scitotenv.2015.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
The Dead Sea region has faced substantial environmental challenges in recent decades, including water resource scarcity, ~1m annual decreases in the water level, sinkhole development, ascending-brine freshwater pollution, and seismic disturbance risks. Natural processes are significantly affected by human interference as well as by climate change and tectonic developments over the long term. To get a deep understanding of processes and their interactions, innovative scientific approaches that integrate disciplinary research and education are required. The research project DESERVE (Helmholtz Virtual Institute Dead Sea Research Venue) addresses these challenges in an interdisciplinary approach that includes geophysics, hydrology, and meteorology. The project is implemented by a consortium of scientific institutions in neighboring countries of the Dead Sea (Israel, Jordan, Palestine Territories) and participating German Helmholtz Centres (KIT, GFZ, UFZ). A new monitoring network of meteorological, hydrological, and seismic/geodynamic stations has been established, and extensive field research and numerical simulations have been undertaken. For the first time, innovative measurement and modeling techniques have been applied to the extreme conditions of the Dead Sea and its surroundings. The preliminary results show the potential of these methods. First time ever performed eddy covariance measurements give insight into the governing factors of Dead Sea evaporation. High-resolution bathymetric investigations reveal a strong correlation between submarine springs and neo-tectonic patterns. Based on detailed studies of stratigraphy and borehole information, the extension of the subsurface drainage basin of the Dead Sea is now reliably estimated. Originality has been achieved in monitoring flash floods in an arid basin at its outlet and simultaneously in tributaries, supplemented by spatio-temporal rainfall data. Low-altitude, high resolution photogrammetry, allied to satellite image analysis and to geophysical surveys (e.g. shear-wave reflections) has enabled a more detailed characterization of sinkhole morphology and temporal development and the possible subsurface controls thereon. All the above listed efforts and scientific results take place with the interdisciplinary education of young scientists. They are invited to attend joint thematic workshops and winter schools as well as to participate in field experiments.
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Affiliation(s)
- Christoph Kottmeier
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany.
| | - Amotz Agnon
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Djamil Al-Halbouni
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | | | - Ulrich Corsmeier
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany
| | - Torsten Dahm
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Adam Eshel
- Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Stefan Geyer
- Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
| | - Michael Haas
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Eoghan Holohan
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Norbert Kalthoff
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany
| | | | - Charlotte Krawczyk
- Leibniz Institute for Applied Geophysics (LIAG), Stilleweg 2, 30655 Hannover, Germany
| | | | | | - Friederike Lott
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany
| | - Ulf Mallast
- Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
| | - Ralf Merz
- Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
| | - Jutta Metzger
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany
| | | | - Efrat Morin
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Manuela Nied
- Karlsruhe Institute of Technology, Hermann von Helmholtz Platz 1, Eggenstein-Leopoldshafen, Germany
| | - Tino Rödiger
- Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
| | | | - Ali Sawarieh
- Ministry of Energy and Mineral Resources (MEMR), Amman, Jordan
| | | | - Christian Siebert
- Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Strasse 4, 06120 Halle, Germany
| | - Michael Weber
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany; University of Potsdam, Potsdam, Germany
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48
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Oren A. Life in Hypersaline Environments. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Roger Anderson O. Marine and estuarine natural microbial biofilms: ecological and biogeochemical dimensions. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.3.304] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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50
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Boopathi T, Lee JB, Youn SH, Ki JS. Temporal and spatial dynamics of phytoplankton diversity in the East China Sea near Jeju Island (Korea): A pyrosequencing-based study. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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