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Bahadur A, Zhang L, Guo W, Sajjad W, Ilahi N, Banerjee A, Faisal S, Usman M, Chen T, Zhang W. Temperature-dependent transformation of microbial community: A systematic approach to analyzing functional microbes and biogas production. ENVIRONMENTAL RESEARCH 2024; 249:118351. [PMID: 38331158 DOI: 10.1016/j.envres.2024.118351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 12/24/2023] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
The stability and effectiveness of the anaerobic digestion (AD) system are significantly influenced by temperature. While majority research has focused on the composition of the microbial community in the AD process, the relationships between functional gene profile deduced from gene expression at different temperatures have received less attention. The current study investigates the AD process of potato peel waste and explores the association between biogas production and microbial gene expression at 15, 25, and 35 °C through metatranscriptomic analysis. The production of total biogas decreased with temperature at 15 °C (19.94 mL/g VS), however, it increased at 35 °C (269.50 mL/g VS). The relative abundance of Petrimonas, Clostridium, Aminobacterium, Methanobacterium, Methanothrix, and Methanosarcina were most dominant in the AD system at different temperatures. At the functional pathways level 3, α-diversity indices, including Evenness (Y = 5.85x + 8.85; R2 = 0.56), Simpson (Y = 2.20x + 2.09; R2 = 0.33), and Shannon index (Y = 1.11x + 4.64; R2 = 0.59), revealed a linear and negative correlation with biogas production. Based on KEGG level 3, several dominant functional pathways associated with Oxidative phosphorylation (ko00190) (25.09, 24.25, 24.04%), methane metabolism (ko00680) (30.58, 32.13, and 32.89%), and Carbon fixation pathways in prokaryotes (ko00720) (27.07, 26.47, and 26.29%), were identified at 15 °C, 25 °C and 35 °C. The regulation of biogas production by temperature possibly occurs through enhancement of central function pathways while decreasing the diversity of functional pathways. Therefore, the methanogenesis and associated processes received the majority of cellular resources and activities, thereby improving the effectiveness of substrate conversion to biogas. The findings of this study illustrated the crucial role of central function pathways in the effective functioning of these systems.
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Affiliation(s)
- Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Cryosphere and Eco-Environment Research Station of Shule River Headwaters, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lu Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Guo
- Lanzhou Xinrong Environmental Energy Engineering Technology Co. Ltd. Lanzhou 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Shah Faisal
- Department of Environmental Engineering, School of Architecture and Civil Engineering, Chengdu University, Chengdu 610106, China
| | - Muhammad Usman
- State Key Laboratory of Grassland Agroecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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2
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Bender L, Preis E, Engelhardt KH, Amin MU, Ayoub AM, Librizzi D, Roschenko V, Schulze J, Yousefi BH, Schaefer J, Bakowsky U. In vitro and in ovo photodynamic efficacy of nebulized curcumin-loaded tetraether lipid liposomes prepared by DC as stable drug delivery system. Eur J Pharm Sci 2024; 196:106748. [PMID: 38471594 DOI: 10.1016/j.ejps.2024.106748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Lung cancer is one of the most common causes of high mortality worldwide. Current treatment strategies, e.g., surgery, radiotherapy, chemotherapy, and immunotherapy, insufficiently affect the overall outcome. In this study, we used curcumin as a natural photosensitizer in photodynamic therapy and encapsulated it in liposomes consisting of stabilizing tetraether lipids aiming for a pulmonary drug delivery system against lung cancer. The liposomes with either hydrolyzed glycerol-dialkyl-glycerol tetraether (hGDGT) in different ratios or hydrolyzed glycerol-dialkyl-nonitol tetraether (hGDNT) were prepared by dual centrifugation (DC), an innovative method for liposome preparation. The liposomes' physicochemical characteristics before and after nebulization and other nebulization characteristics confirmed their suitability. Morphological characterization using atomic force and transmission electron microscopy showed proper vesicular structures indicative of liposomes. Qualitative and quantitative uptake of the curcumin-loaded liposomes in lung adenocarcinoma (A549) cells was visualized and proven. Phototoxic effects of the liposomes were detected on A549 cells, showing decreased cell viability. The generation of reactive oxygen species required for PDT and disruption of mitochondrial membrane potential were confirmed. Moreover, the chorioallantoic membrane (CAM) model was used to further evaluate biocompatibility and photodynamic efficacy in a 3D cell culture context. Photodynamic efficacy was assessed by PET/CT after nebulization of the liposomes onto the xenografted tumors on the CAM with subsequent irradiation. The physicochemical properties and the efficacy of tetraether lipid liposomes encapsulating curcumin, especially liposomes containing hGDNT, in 2D and 3D cell cultures seem promising for future PDT usage against lung cancer.
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Affiliation(s)
- Lena Bender
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Eduard Preis
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Konrad H Engelhardt
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Muhammad Umair Amin
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Abdallah M Ayoub
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Damiano Librizzi
- Center for Tumor Biology and Immunology (ZTI), Core Facility Molecular Imaging, Department of Nuclear Medicine, University of Marburg, Hans-Meerwein-Str. 3, Marburg 35043, Germany
| | - Valeri Roschenko
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Jan Schulze
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Behrooz H Yousefi
- Center for Tumor Biology and Immunology (ZTI), Core Facility Molecular Imaging, Department of Nuclear Medicine, University of Marburg, Hans-Meerwein-Str. 3, Marburg 35043, Germany
| | - Jens Schaefer
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany
| | - Udo Bakowsky
- Department of Pharmaceutics and Biopharmaceutics, University of Marburg, Robert-Koch-Str. 4, Marburg 35037, Germany.
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3
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Schiller H, Hong Y, Kouassi J, Rados T, Kwak J, DiLucido A, Safer D, Marchfelder A, Pfeiffer F, Bisson A, Schulze S, Pohlschroder M. Identification of structural and regulatory cell-shape determinants in Haloferax volcanii. Nat Commun 2024; 15:1414. [PMID: 38360755 PMCID: PMC10869688 DOI: 10.1038/s41467-024-45196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative proteomics, genetics, and live-cell imaging to identify mutants that only form rods or disks. We compared the proteomes of the mutants with wild-type cells across growth phases, thereby distinguishing between protein abundance changes specific to cell shape and those related to growth phases. The results identified a diverse set of proteins, including predicted transporters, transducers, signaling components, and transcriptional regulators, as important for cell-shape determination. Through phenotypic characterization of deletion strains, we established that rod-determining factor A (RdfA) and disk-determining factor A (DdfA) are required for the formation of rods and disks, respectively. We also identified structural proteins, including an actin homolog that plays a role in disk-shape morphogenesis, which we named volactin. Using live-cell imaging, we determined volactin's cellular localization and showed its dynamic polymerization and depolymerization. Our results provide insights into archaeal cell-shape determination, with possible implications for understanding the evolution of cell morphology regulation across domains.
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Affiliation(s)
- Heather Schiller
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Yirui Hong
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Joshua Kouassi
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Theopi Rados
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Jasmin Kwak
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA
| | - Anthony DiLucido
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA
| | - Daniel Safer
- University of Pennsylvania, Department of Physiology, Philadelphia, PA, 19104, USA
| | | | - Friedhelm Pfeiffer
- Biology II, Ulm University, 89069, Ulm, Germany
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Alexandre Bisson
- Brandeis University, Department of Biology, Waltham, MA, 02453, USA.
| | - Stefan Schulze
- University of Pennsylvania, Department of Biology, Philadelphia, PA, 19104, USA.
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, 14623, USA.
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4
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Valdez S, de la Vega FV, Pairazaman O, Castellanos R, Esparza M. Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru. Braz J Microbiol 2023; 54:2927-2937. [PMID: 37801222 PMCID: PMC10689642 DOI: 10.1007/s42770-023-01117-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/23/2023] [Indexed: 10/07/2023] Open
Abstract
Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.
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Affiliation(s)
- Silvia Valdez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional Jorge Basadre Grohmann, Tacna, Perú
| | - Fabián Veliz de la Vega
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaiso-Chile Av. Brasil 2085, Valparaíso, Chile.
| | - Omar Pairazaman
- Laboratorio Regional de Salud Pública (Diresa), Cajamarca, Perú
| | - Roberto Castellanos
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional Jorge Basadre Grohmann, Tacna, Perú
| | - Mario Esparza
- Universidad Privada Antenor Orrego, Facultad de Medicina Humana, Laboratorio de Genética, Reproducción y Biología Molecular, Trujillo, Perú
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5
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Notaro A, Zaretsky M, Molinaro A, De Castro C, Eichler J. N-glycosylation in Archaea: Unusual sugars and unique modifications. Carbohydr Res 2023; 534:108963. [PMID: 37890267 DOI: 10.1016/j.carres.2023.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
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6
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Medina-Chávez NO, Viladomat-Jasso M, Zarza E, Islas-Robles A, Valdivia-Anistro J, Thalasso-Siret F, Eguiarte LE, Olmedo-Álvarez G, Souza V, De la Torre-Zavala S. A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico. ASTROBIOLOGY 2023; 23:796-811. [PMID: 37279013 DOI: 10.1089/ast.2021.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.
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Affiliation(s)
- Nahui-Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
| | | | - Eugenia Zarza
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur, Tapachula, Mexico
- Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Africa Islas-Robles
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Jorge Valdivia-Anistro
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, Facultad de Estudios Superiores Zaragoza, UNAM, Ciudad de México, México
| | - Frédéric Thalasso-Siret
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Susana De la Torre-Zavala
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
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7
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [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: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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8
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Mapelli-Brahm P, Gómez-Villegas P, Gonda ML, León-Vaz A, León R, Mildenberger J, Rebours C, Saravia V, Vero S, Vila E, Meléndez-Martínez AJ. Microalgae, Seaweeds and Aquatic Bacteria, Archaea, and Yeasts: Sources of Carotenoids with Potential Antioxidant and Anti-Inflammatory Health-Promoting Actions in the Sustainability Era. Mar Drugs 2023; 21:340. [PMID: 37367666 DOI: 10.3390/md21060340] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.
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Affiliation(s)
- Paula Mapelli-Brahm
- Food Colour and Quality Laboratory, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Patricia Gómez-Villegas
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 21071 Huelva, Spain
| | - Mariana Lourdes Gonda
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Gral Flores 2124, Montevideo 11800, Uruguay
| | - Antonio León-Vaz
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 21071 Huelva, Spain
| | - Rosa León
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 21071 Huelva, Spain
| | | | | | - Verónica Saravia
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de la República, Montevideo 11300, Uruguay
| | - Silvana Vero
- Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Gral Flores 2124, Montevideo 11800, Uruguay
| | - Eugenia Vila
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de la República, Montevideo 11300, Uruguay
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9
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Noyer M, Bernard M, Verneau O, Palacios C. Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49685-49702. [PMID: 36780079 DOI: 10.1007/s11356-023-25637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/14/2023]
Abstract
Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.
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Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.,Unit. for Environmental Sciences and Management, North-West University, Potchefstroom, ZA-2520, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France. .,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.
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10
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Chen J, Li F, Zhao X, Wang Y, Zhang L, Yan L, Yu L. Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times. Front Microbiol 2022; 13:1024672. [PMID: 36386643 PMCID: PMC9663929 DOI: 10.3389/fmicb.2022.1024672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Fangbing Li
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Xiangwei Zhao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Yang Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Limin Zhang
- Institute of Guizhou Mountain Resources, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Lingbin Yan
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Lifei Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China,*Correspondence: Lifei Yu,
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11
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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12
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Kelly J, Vinogradov E, Robotham A, Tessier L, Logan SM, Jarrell KF. Characterizing the N- and O-linked glycans of the PGF-CTERM sorting domain-containing S-layer protein of Methanoculleus marisnigri. Glycobiology 2022; 32:629-644. [PMID: 35481895 DOI: 10.1093/glycob/cwac019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 01/05/2023] Open
Abstract
The glycosylation of structural proteins is a widespread posttranslational modification in Archaea. Although only a handful of archaeal N-glycan structures have been determined to date, it is evident that the diversity of structures expressed is greater than in the other domains of life. Here, we report on our investigation of the N- and O-glycan modifications expressed by Methanoculleus marisnigri, a mesophilic methanogen from the Order Methanomicrobiales. Unusually, mass spectrometry (MS) analysis of purified archaella revealed no evidence for N- or O-glycosylation of the constituent archaellins, In contrast, the S-layer protein, identified as a PGF-CTERM sorting domain-containing protein encoded by MEMAR_RS02690, is both N- and O-glycosylated. Two N-glycans were identified by NMR and MS analysis: a trisaccharide α-GlcNAc-4-β-GlcNAc3NGaAN-4-β-Glc-Asn where the second residue is 2-N-acetyl, 3-N-glyceryl-glucosamide and a disaccharide β-GlcNAc3NAcAN-4-β-Glc-Asn, where the terminal residue is 2,3 di-N-acetyl-glucosamide. The same trisaccharide was also found N-linked to a type IV pilin. The S-layer protein is also extensively modified in the threonine-rich region near the C-terminus with O-glycans composed exclusively of hexoses. While the S-layer protein has a predicted PGF-CTERM processing site, no evidence of a truncated and lipidated C-terminus, the expected product of processing by an archaeosortase, was found. Finally, NMR also identified a polysaccharide expressed by M. marisnigri and composed of a repeating tetrasaccharide unit of [-2-β-Ribf-3-α-Rha2OMe-3-α-Rha - 2-α-Rha-]. This is the first report of N- and O-glycosylation in an archaeon from the Order Methanomicrobiales.
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Affiliation(s)
- John Kelly
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Evgeny Vinogradov
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Luc Tessier
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Susan M Logan
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Ken F Jarrell
- Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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13
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Gregson BH, Bani A, Steinfield L, Holt D, Whitby C. Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153040. [PMID: 35026246 DOI: 10.1016/j.scitotenv.2022.153040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.
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Affiliation(s)
- Benjamin H Gregson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Alessia Bani
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | | | - Diane Holt
- Center for Enterprise and Entrepreneurship, Leeds University Business School, Leeds LS2 9JT, UK
| | - Corinne Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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14
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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15
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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16
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Fariq A, Yasmin A, Blazier JC, Jannat S. Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing. Biodivers Data J 2021; 9:e68929. [PMID: 34744475 PMCID: PMC8551136 DOI: 10.3897/bdj.9.e68929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms thrive nearly everywhere including extreme environments where few other forms of life can exist. Geochemistry of extreme sites plays a major role in shaping these microbial communities and microbes thriving in such harsh conditions are untapped sources of novel biomolecules. To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. Barcoded amplicon sequencing technique was used to study the microbial communities. Physicochemical analysis of these sites was also conducted to study the dynamics of microbial communities under stressed conditions. Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. Proteobacteria were predominant in saline soil while Firmicutes were most abundant in hot spring sediment. The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. OTUs from genus Alkalibacillus were most abundant in hot spring sediments, whereas Haloarcula were more prevalent in saline soil. Some unidentified sequences were also present at each taxonomic level. Multivariate analysis indicated that electrical conductivity and pH are the major environmental factors involved in modelling microbial communities. This study revealed a poly-extremophilic microbial community in the Murtazaabad hot spring and characterised the unexplored halophilic microbial diversity of saline soil of Pakistan.
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Affiliation(s)
- Anila Fariq
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan.,Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
| | - Azra Yasmin
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan
| | - John C Blazier
- Texas A&M Institute of Genome Sciences and SocietyTexas A&M University,, College Station, Texas, United States of America Texas A&M Institute of Genome Sciences and SocietyTexas A&M University, College Station, Texas United States of America
| | - Sammyia Jannat
- Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
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17
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Proteomic perspectives on thermotolerant microbes: an updated review. Mol Biol Rep 2021; 49:629-646. [PMID: 34671903 DOI: 10.1007/s11033-021-06805-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Thermotolerant microbes are a group of microorganisms that survive in elevated temperatures. The thermotolerant microbes, which are found in geothermal heat zones, grow at temperatures of or above 45°C. The proteins present in such microbes are optimally active at these elevated temperatures. Hence, therefore, serves as an advantage in various biotechnological applications. In the last few years, scientists have tried to understand the molecular mechanisms behind the maintenance of the structural integrity of the cell and to study the stability of various thermotolerant proteins at extreme temperatures. Proteomic analysis is the solution for this search. Applying novel proteomic tools determines the proteins involved in the thermostability of microbes at elevated temperatures. METHODS Advanced proteomic techniques like Mass spectrometry, nano-LC-MS, protein microarray, ICAT, iTRAQ, and SILAC could enable the screening and identification of novel thermostable proteins. RESULTS This review provides up-to-date details on the protein signature of various thermotolerant microbes analyzed through advanced proteomic tools concerning relevant research articles. The protein complex composition from various thermotolerant microbes cultured at different temperatures, their structural arrangement, and functional efficiency of the protein was reviewed and reported. CONCLUSION This review provides an overview of thermotolerant microbes, their enzymes, and the proteomic tools implemented to characterize them. This article also reviewed a comprehensive view of the current proteomic approaches for protein profiling in thermotolerant microbes.
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18
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Methanogenesis at High Temperature, High Ionic Strength and Low pH in the Volcanic Area of Dallol, Ethiopia. Microorganisms 2021; 9:microorganisms9061231. [PMID: 34204110 PMCID: PMC8228321 DOI: 10.3390/microorganisms9061231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
The Dallol geothermal area originated as a result of seismic activity and the presence of a shallow underground volcano, both due to the divergence of two tectonic plates. In its ascent, hot water dissolves and drags away the subsurface salts. The temperature of the water that comes out of the chimneys is higher than 100 °C, with a pH close to zero and high mineral concentration. These factors make Dallol a polyextreme environment. So far, nanohaloarchaeas, present in the salts that form the walls of the chimneys, have been the only living beings reported in this extreme environment. Through the use of complementary techniques: culture in microcosms, methane stable isotope signature and hybridization with specific probes, the methanogenic activity in the Dallol area has been assessed. Methane production in microcosms, positive hybridization with the Methanosarcinales probe and the δ13CCH4-values measured, show the existence of extensive methanogenic activity in the hydrogeothermic Dallol system. A methylotrophic pathway, carried out by Methanohalobium and Methanosarcina-like genera, could be the dominant pathway for methane production in this environment.
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19
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Lastauskienė E, Valskys V, Stankevičiūtė J, Kalcienė V, Gėgžna V, Kavoliūnas J, Ružauskas M, Armalytė J. The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition. Front Vet Sci 2021; 8:673756. [PMID: 34113676 PMCID: PMC8186532 DOI: 10.3389/fvets.2021.673756] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/16/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture is a fast-growing animal food sector, and freshwater fish farming is particularly common in Central and Eastern Europe. As the biodiversity of fishery ponds is changed toward fulfilling the industrial needs, precautions should be taken to keep the system sustainable and protect the adjacent environment from possible damage. Due to risk of infectious diseases, antibiotics are used in aquaculture production systems. The constant exposure to antimicrobials can contribute to the rise of antibiotic resistance in aquaculture products and the adjacent ecosystems, with possibility of dissemination to the wider environment as well as between animals and humans. Even though previous studies have found antibiotic resistance genes in the sediments and water of farming ponds, the tendency and direction of spreading is not clear yet. The objective of this project was to evaluate the influence of intensive fish farming on the condition of water bodies used for the aquaculture and the environment, concentrating on the impact of the aquaculture on the surrounding water ecosystems as well as the possibility of transferring the pollutants and antibiotic resistance genes to both environment and the human hosts. Combined measurement of antibiotic and heavy metal contamination, toxicity assessment, microorganism diversity, and the detection of common antibiotic resistance genes was performed in the sediments of one fishery farm ponds as well as sampling points upstream and downstream. All the tested sediment samples did not show significantly elevated heavy metal concentrations and no substantial veterinary antibiotic pollution. From the antibiotic resistance genes tested, the presence of aminoglycoside and β-lactam resistance determinants as well as the presence of integrons could be of concern for the possibility of transfer to humans. However, despite the lack of heavy metal and antibiotic pollution, the sediments showed toxicity, the cause of which should be explored more.
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Affiliation(s)
- Eglė Lastauskienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vaidotas Valskys
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jonita Stankevičiūtė
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginija Kalcienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vilmantas Gėgžna
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justinas Kavoliūnas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Modestas Ružauskas
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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20
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Starke R, Siles JA, Fernandes MLP, Schallert K, Benndorf D, Plaza C, Jehmlich N, Delgado-Baquerizo M, Bastida F. The structure and function of soil archaea across biomes. J Proteomics 2021; 237:104147. [PMID: 33582288 DOI: 10.1016/j.jprot.2021.104147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/02/2023]
Abstract
We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-"omics" approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic.
| | - José A Siles
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia E-30100, Spain
| | - Maysa Lima Parente Fernandes
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Kay Schallert
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Cesar Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006 Madrid, Spain
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Department of Molecular Systems Biology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Sevilla, Spain
| | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia E-30100, Spain
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21
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Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M, Sanvoisin A, Toffin L, Alain K. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Microorganisms 2020; 9:E30. [PMID: 33374130 PMCID: PMC7824343 DOI: 10.3390/microorganisms9010030] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.
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Affiliation(s)
- Marc Cozannet
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institute Pasteur, 75015 Paris, France;
| | - Erwan Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Yann Moalic
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Amandine Sanvoisin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Laurent Toffin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
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22
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Zamanpour MK, Kaliappan RS, Rockne KJ. Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110997. [PMID: 32778285 DOI: 10.1016/j.jenvman.2020.110997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/19/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C10 alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.
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Affiliation(s)
| | - Raja Shankar Kaliappan
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Karl John Rockne
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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23
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Thornton KL, Butler JK, Davis SJ, Baxter BK, Wilson LG. Haloarchaea swim slowly for optimal chemotactic efficiency in low nutrient environments. Nat Commun 2020; 11:4453. [PMID: 32901025 PMCID: PMC7478972 DOI: 10.1038/s41467-020-18253-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/05/2020] [Indexed: 01/18/2023] Open
Abstract
Archaea have evolved to survive in some of the most extreme environments on earth. Life in extreme, nutrient-poor conditions gives the opportunity to probe fundamental energy limitations on movement and response to stimuli, two essential markers of living systems. Here we use three-dimensional holographic microscopy and computer simulations to reveal that halophilic archaea achieve chemotaxis with power requirements one hundred-fold lower than common eubacterial model systems. Their swimming direction is stabilised by their flagella (archaella), enhancing directional persistence in a manner similar to that displayed by eubacteria, albeit with a different motility apparatus. Our experiments and simulations reveal that the cells are capable of slow but deterministic chemotaxis up a chemical gradient, in a biased random walk at the thermodynamic limit.
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Affiliation(s)
- Katie L Thornton
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
| | - Jaimi K Butler
- Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT, 84105, USA
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, 1840 South 1300 East, Salt Lake City, UT, 84105, USA
| | - Laurence G Wilson
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK.
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24
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Pedone E, Fiorentino G, Bartolucci S, Limauro D. Enzymatic Antioxidant Signatures in Hyperthermophilic Archaea. Antioxidants (Basel) 2020; 9:antiox9080703. [PMID: 32756530 PMCID: PMC7465337 DOI: 10.3390/antiox9080703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
To fight reactive oxygen species (ROS) produced by both the metabolism and strongly oxidative habitats, hyperthermophilic archaea are equipped with an array of antioxidant enzymes whose role is to protect the biological macromolecules from oxidative damage. The most common ROS, such as superoxide radical (O2-.) and hydrogen peroxide (H2O2), are scavenged by superoxide dismutase, peroxiredoxins, and catalase. These enzymes, together with thioredoxin, protein disulfide oxidoreductase, and thioredoxin reductase, which are involved in redox homeostasis, represent the core of the antioxidant system. In this review, we offer a panorama of progression of knowledge on the antioxidative system in aerobic or microaerobic (hyper)thermophilic archaea and possible industrial applications of these enzymes.
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Affiliation(s)
- Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso universitario Monte S. Angelo, Via Cinthia, 80126 Napoli, Italy; (G.F.); (S.B.)
- Correspondence:
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Huang M, Chai L, Jiang D, Zhang M, Zhao Y, Huang Y. Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:699-707. [PMID: 30092526 DOI: 10.1016/j.scitotenv.2018.07.305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/21/2018] [Accepted: 07/22/2018] [Indexed: 05/15/2023]
Abstract
Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Dalin Jiang
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yanran Zhao
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, Beijing 100871, China.
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26
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Pyzik A, Ciezkowska M, Krawczyk PS, Sobczak A, Drewniak L, Dziembowski A, Lipinski L. Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. Microb Cell Fact 2018; 17:197. [PMID: 30572955 PMCID: PMC6302309 DOI: 10.1186/s12934-018-1043-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways. RESULTS A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated. CONCLUSIONS The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.
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Affiliation(s)
- Adam Pyzik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Martyna Ciezkowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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27
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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28
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Lew S, Glińska-Lewczuk K. Environmental controls on the abundance of methanotrophs and methanogens in peat bog lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1201-1211. [PMID: 30248845 DOI: 10.1016/j.scitotenv.2018.07.141] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The aim of the present study was to identify the factors that influence the composition of methanogens and methanotrophs in the background prokaryotic community in peat bog lakes. We hypothesized that the microbial composition is a function of the physicochemical conditions of the water and a function of depth-dependent oxygen (DO) concentrations. To address this aim, we collected water samples from subsurface and near-bottom layers, representing oxic and anoxic conditions in 4 peat bog lakes in NE Poland. The structure of methanogenic Archaea and methane-oxidizing bacteria (MOB) was determined with double labeled-fluorescence in situ hybridization (DOPE-FISH). The results showed significant differences in Procaryota communities between the oxic (subsurface) and suboxic/anoxic (near-bottom) layers in peat bog lakes (t-test, p < 0.05). The methanogens from the Archaea domain were observed in anoxic periods, while methanotrophs were present regardless of water depth and season. The abundance of methanogens was inversely correlated with DO and CO2. Methanotrophs adapted better to the changing habitat conditions. The nonmetrical multidimensional scaling (NMS) and partial least square regression (PLS-R) models showed that the methanotrophs in subsurface layers are positively associated with temperature, DOC, and TON while negatively associated with pH. The DO availability is not a prerequisite condition for the presence of methanothrophs. The most important factors for MOB at the bottom were CO2 and TON. Due to a significant role of methanotrophs in the control of the methane emission flux rates, there is a need for further research on factors responsible for methanotroph development in peat bog lakes.
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Affiliation(s)
- Sylwia Lew
- University of Warmia and Mazury in Olsztyn, Department of Microbiology and Mycology, Oczapowskiego str. 1a, 10-719 Olsztyn, Poland.
| | - Katarzyna Glińska-Lewczuk
- University of Warmia and Mazury in Olsztyn, Department of Water Resources, Climatology and Environmental Management, Plac Łódzki 2, 10-719 Olsztyn, Poland.
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29
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Seth-Pasricha M, Senn S, Sanman LE, Bogyo M, Nanda V, Bidle KA, Bidle KD. Catalytic linkage between caspase activity and proteostasis in Archaea. Environ Microbiol 2018; 21:286-298. [PMID: 30370585 DOI: 10.1111/1462-2920.14456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 11/29/2022]
Abstract
The model haloarchaeon, Haloferax volcanii possess an extremely high, and highly specific, basal caspase activity in exponentially growing cells that closely resembles caspase-4. This activity is specifically inhibited by the pan-caspase inhibitor, z-VAD-FMK, and has no cross-reactivity with other known protease families. Although it is one of the dominant cellular proteolytic activities in exponentially growing H. volcanii cells, the interactive cellular roles remain unknown and the protein(s) responsible for this activity remain elusive. Here, biochemical purification and in situ trapping with caspase targeted covalent inhibitors combined with genome-enabled proteomics, structural analysis, targeted gene knockouts and treatment with canavanine demonstrated a catalytic linkage between caspase activity and thermosomes, proteasomes and cdc48b, a cell division protein and proteasomal degradation facilitating ATPase, as part of an 'interactase' of stress-related protein complexes with an established link to the unfolded protein response (UPR). Our findings provide novel cellular and biochemical context for the observed caspase activity in Archaea and add new insight to understanding the role of this activity, implicating their possible role in the establishment of protein stress and ER associated degradation pathways in Eukarya.
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Affiliation(s)
- Mansha Seth-Pasricha
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Stefan Senn
- Abteilung für Chemie und Bioanalytik, Universität Salzburg, Salzburg, Austria
| | - Laura E Sanman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Kelly A Bidle
- Department of Biology, Behavioral Neuroscience, and Health Sciences, Rider University, Lawrenceville, NJ, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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30
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Ritschard JS, Amato L, Kumar Y, Müller B, Meile L, Schuppler M. The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese. AIMS Microbiol 2018; 4:622-641. [PMID: 31294238 PMCID: PMC6613336 DOI: 10.3934/microbiol.2018.4.622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/20/2018] [Indexed: 01/05/2023] Open
Abstract
The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.
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Affiliation(s)
- Jasmine S Ritschard
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Lea Amato
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Yadhu Kumar
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Britta Müller
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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31
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Denis A, Martínez-Núñez MA, Tenorio-Salgado S, Perez-Rueda E. Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. Life (Basel) 2018; 8:life8040040. [PMID: 30248960 PMCID: PMC6316755 DOI: 10.3390/life8040040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 01/06/2023] Open
Abstract
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Affiliation(s)
- Antonia Denis
- Facultad de Medicina, Universidad Juárez Autónoma de Tabasco, C.P. 86100, Tabasco, Mexico.
| | - Mario Alberto Martínez-Núñez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, C.P. 97000, Mérida, Yucatán, Mexico.
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, C.P. 97302, Mérida, Yucatán, Mexico.
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Methionine Sulfoxide Reductases of Archaea. Antioxidants (Basel) 2018; 7:antiox7100124. [PMID: 30241308 PMCID: PMC6211008 DOI: 10.3390/antiox7100124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 01/04/2023] Open
Abstract
Methionine sulfoxide reductases are found in all domains of life and are important in reversing the oxidative damage of the free and protein forms of methionine, a sulfur containing amino acid particularly sensitive to reactive oxygen species (ROS). Archaea are microbes of a domain of life distinct from bacteria and eukaryotes. Archaea are well known for their ability to withstand harsh environmental conditions that range from habitats of high ROS, such as hypersaline lakes of intense ultraviolet (UV) radiation and desiccation, to hydrothermal vents of low concentrations of dissolved oxygen at high temperature. Recent evidence reveals the methionine sulfoxide reductases of archaea function not only in the reduction of methionine sulfoxide but also in the ubiquitin-like modification of protein targets during oxidative stress, an association that appears evolutionarily conserved in eukaryotes. Here is reviewed methionine sulfoxide reductases and their distribution and function in archaea.
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Echeverría-Vega A, Chong G, Serrano AE, Guajardo M, Encalada O, Parro V, Blanco Y, Rivas L, Rose KC, Moreno-Paz M, Luque JA, Cabrol NA, Demergasso CS. Watershed-Induced Limnological and Microbial Status in Two Oligotrophic Andean Lakes Exposed to the Same Climatic Scenario. Front Microbiol 2018; 9:357. [PMID: 29556224 PMCID: PMC5844981 DOI: 10.3389/fmicb.2018.00357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/14/2018] [Indexed: 12/04/2022] Open
Abstract
Laguna Negra and Lo Encañado are two oligotrophic Andean lakes forming part of the system fed by meltwater from distinct glacial tongues of the Echaurren glacier in central Chile, which is in a recession period. The recent increase in temperature and decline in precipitation have led to an increase of glacial meltwater and sediments entering these lakes. Although the lacustrine systems are also hydrogeologically connected, the limnology of the lakes is strongly controlled by the surface processes related to the respective sub-watersheds and hydrology. Watershed characteristics (area and length, slope, lithology, resistance to erosion, among others) affect the chemical and physical characteristics of both lakes (e.g., nutrient concentration and turbidity). We studied physical and chemical variables and performed 16S rRNA amplicon sequencing to determine the specific microbial signature of the lakes. The transparency, temperature, turbidity and concentrations of chlorophyll-a, dissolved organic matter, nutrients and the total number of cells, revealed the different status of both lakes at the time of sampling. The predominant bacterial groups in both lakes were Proteobacteria, Verrucomicrobia, and Bacteroidetes. Interestingly, the contribution of phototrophs was significantly higher in LN compared to LE (13 and 4% respectively) and the major fraction corresponded to Anoxygenic Phototrophs (AP) represented by Chloroflexi, Alpha, and Betaproteobacteria. Multivariate analyses showed that the nutrient levels and the light availability of both lakes, which finally depend on the hydrological characteristics of the respective watersheds, explain the differential community composition/function. The abundance of a diverse photoheterotrophic bacterioplankton community suggests that the ability to utilize solar energy along with organic and inorganic substrates is a key function in these oligotrophic mountain lakes.
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Affiliation(s)
| | - Guillermo Chong
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile
| | - Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mariela Guajardo
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Luis Rivas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Kevin C Rose
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - José A Luque
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Nathalie A Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States.,Space Science Division, NASA Ames Research Center, Moffett Field, CA, United States
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Archaeal community compositions in tilapia pond systems and their influencing factors. World J Microbiol Biotechnol 2018; 34:43. [PMID: 29492679 DOI: 10.1007/s11274-018-2412-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/12/2018] [Indexed: 10/17/2022]
Abstract
Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities' response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.
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Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification. Methods Enzymol 2018; 612:413-442. [DOI: 10.1016/bs.mie.2018.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 2017; 22:1-12. [PMID: 29110088 DOI: 10.1007/s00792-017-0974-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.
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Larsen BB, Miller EC, Rhodes MK, Wiens JJ. Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life. QUARTERLY REVIEW OF BIOLOGY 2017. [DOI: 10.1086/693564] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Rajput A, Kumar M. Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing. Front Microbiol 2017; 8:798. [PMID: 28515720 PMCID: PMC5413776 DOI: 10.3389/fmicb.2017.00798] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/19/2017] [Indexed: 11/13/2022] Open
Abstract
LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site) evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS.
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Affiliation(s)
- Akanksha Rajput
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial ResearchChandigarh, India
| | - Manoj Kumar
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial ResearchChandigarh, India
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Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico. Int J Mol Sci 2017; 18:ijms18040876. [PMID: 28425930 PMCID: PMC5412457 DOI: 10.3390/ijms18040876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 11/25/2022] Open
Abstract
Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), which catalyzes the direct oxidation of glyceraldehyde-3-phosphate to 3-phosphoglycerate omitting adenosine 5′-triphosphate (ATP) formation by substrate-level-phosphorylation via phosphoglycerate kinase. In this study we formulate three hypotheses that could explain functionally why GAPN exists in these Archaea, and then construct and use mathematical models to test these three hypotheses. We used kinetic parameters of enzymes of Sulfolobus solfataricus (S. solfataricus) which is a thermo-acidophilic archaeon that grows optimally between 60 and 90 °C and between pH 2 and 4. For comparison, we used a model of Saccharomyces cerevisiae (S. cerevisiae), an organism that can live at moderate temperatures. We find that both the first hypothesis, i.e., that the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plus phosphoglycerate kinase (PGK) route (the alternative to GAPN) is thermodynamically too much uphill and the third hypothesis, i.e., that GAPDH plus PGK are required to carry the flux in the gluconeogenic direction, are correct. The second hypothesis, i.e., that the GAPDH plus PGK route delivers less than the 1 ATP per pyruvate that is delivered by the GAPN route, is only correct when GAPDH reaction has a high rate and 1,3-bis-phosphoglycerate (BPG) spontaneously degrades to 3PG at a high rate.
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Affiliation(s)
- Yanfei Zhang
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
| | - Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Stellenbosch 7602, South Africa.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environment Research (CWE), University Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany.
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK.
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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Eichler J, Guan Z. Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:589-599. [PMID: 28330764 DOI: 10.1016/j.bbalip.2017.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 11/28/2022]
Abstract
N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84105, Israel.
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Genetic technologies for extremely thermophilic microorganisms of Sulfolobus, the only genetically tractable genus of crenarchaea. SCIENCE CHINA-LIFE SCIENCES 2017; 60:370-385. [DOI: 10.1007/s11427-016-0355-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/18/2016] [Indexed: 12/26/2022]
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Transfection Studies with Colloidal Systems Containing Highly Purified Bipolar Tetraether Lipids from Sulfolobus acidocaldarius. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:8047149. [PMID: 28239294 PMCID: PMC5292391 DOI: 10.1155/2017/8047149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/04/2016] [Accepted: 12/22/2016] [Indexed: 11/18/2022]
Abstract
Lipid vectors are commonly used to facilitate the transfer of nucleic acids into mammalian cells. In this study, two fractions of tetraether lipids from the archaea Sulfolobus acidocaldarius were extracted and purified using different methods. The purified lipid fractions polar lipid fraction E (PLFE) and hydrolysed glycerol-dialkyl-nonitol tetraether (hGDNT) differ in their structures, charge, size, and miscibility from conventional lipids. Liposomes were prepared by mixing tetraether lipids with cholesterol (CH) and 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) resulting in stable vectors for gene delivery. Lipoplexes were prepared by complexation of liposomes with a luciferase expressing plasmid (pCMV-luc) at certain nitrogen-to-phosphorus (N/P) ratios and optimised for the transient transfection of ovarian adenocarcinoma cells (SK-OV-3). Complexation efficacy was investigated by gel-red fluorescence assay. Biophysical properties, like size, surface charge, and morphology, were investigated by differential light scattering (DLS), atomic force microscopy (AFM), and scanning electron microscopy (Cryo-SEM), respectively, revealing structural differences between liposomes and lipoplexes. A range of stable transfecting agents containing tetraether lipids were obtained by incorporating 5 mol% of tetraether lipids. Lipoplexes showed a decrease in free gel-red with increasing N/P ratios indicating efficient incorporation of plasmid DNA (pDNA) and remarkable stability. Transfection experiments of the lipoplexes revealed successful and superior transfection of SK-OV-3 cell line compared to the commercially available DOTAP and branched polyethyleneimine (25 kDa bPEI).
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44
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Transcription Factor-Mediated Gene Regulation in Archaea. RNA METABOLISM AND GENE EXPRESSION IN ARCHAEA 2017. [DOI: 10.1007/978-3-319-65795-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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45
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Levin GV, Straat PA. The Case for Extant Life on Mars and Its Possible Detection by the Viking Labeled Release Experiment. ASTROBIOLOGY 2016; 16:798-810. [PMID: 27626510 PMCID: PMC6445182 DOI: 10.1089/ast.2015.1464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The 1976 Viking Labeled Release (LR) experiment was positive for extant microbial life on the surface of Mars. Experiments on both Viking landers, 4000 miles apart, yielded similar, repeatable, positive responses. While the authors eventually concluded that the experiment detected martian life, this was and remains a highly controversial conclusion. Many believe that the martian environment is inimical to life and the LR responses were nonbiological, attributed to an as-yet-unidentified oxidant (or oxidants) in the martian soil. Unfortunately, no further metabolic experiments have been conducted on Mars. Instead, follow-on missions have sought to define the martian environment, mostly searching for signs of water. These missions have collected considerable data regarding Mars as a habitat, both past and present. The purpose of this article is to consider recent findings about martian water, methane, and organics that impact the case for extant life on Mars. Further, the biological explanation of the LR and recent nonbiological hypotheses are evaluated. It is concluded that extant life is a strong possibility, that abiotic interpretations of the LR data are not conclusive, and that, even setting our conclusion aside, biology should still be considered as an explanation for the LR experiment. Because of possible contamination of Mars by terrestrial microbes after Viking, we note that the LR data are the only data we will ever have on biologically pristine martian samples. Key Words: Extant life on Mars-Viking Labeled Release experiment-Astrobiology-Extraterrestrial life-Mars. Astrobiology 16, 798-810.
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Watling HR, Collinson DM, Corbett MK, Shiers DW, Kaksonen AH, Watkin EL. Saline-water bioleaching of chalcopyrite with thermophilic, iron(II)- and sulfur-oxidizing microorganisms. Res Microbiol 2016; 167:546-54. [DOI: 10.1016/j.resmic.2016.05.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
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47
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Parikka KJ, Le Romancer M, Wauters N, Jacquet S. Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems. Biol Rev Camb Philos Soc 2016; 92:1081-1100. [DOI: 10.1111/brv.12271] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Kaarle J. Parikka
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
- LabMCT, Belgian Department of Defense; Queen Astrid Military Hospital; Brussels 1120 Belgium
| | - Marc Le Romancer
- Laboratory of Microbiology of Extreme Environments; lnstitut Universitaire Européen de la Mer; Plouzané 29280 France
| | - Nina Wauters
- Biological Evolution and Ecology; Université Libre de Bruxelles; Brussels 1050 Belgium
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Liu Y, Priscu JC, Xiong J, Conrad R, Vick-Majors T, Chu H, Hou J. Salinity drives archaeal distribution patterns in high altitude lake sediments on the Tibetan Plateau. FEMS Microbiol Ecol 2016; 92:fiw033. [DOI: 10.1093/femsec/fiw033] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 2016; 100:4685-98. [PMID: 26810199 DOI: 10.1007/s00253-016-7318-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.
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Schneider D, Engelhaupt M, Allen K, Kurniawan S, Krashevska V, Heinemann M, Nacke H, Wijayanti M, Meryandini A, Corre MD, Scheu S, Daniel R. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia). Front Microbiol 2015; 6:1339. [PMID: 26696965 PMCID: PMC4672069 DOI: 10.3389/fmicb.2015.01339] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/16/2015] [Indexed: 12/04/2022] Open
Abstract
Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.
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Affiliation(s)
- Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Kara Allen
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany
| | - Syahrul Kurniawan
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany ; Department of Soil Science, Faculty of Agriculture, University of Brawijaya Malang, Indonesia
| | - Valentyna Krashevska
- Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Heiko Nacke
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University Bogor, Indonesia
| | - Marife D Corre
- Soil Science of Tropical and Subtropical Ecosystems, Buesgen Institute, Georg-August University Göttingen, Germany
| | - Stefan Scheu
- Animal Ecology, J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August University Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Germany
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