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Chaudhary DK, Seo D, Han S, Hong Y. Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect. MARINE POLLUTION BULLETIN 2024; 202:116300. [PMID: 38555803 DOI: 10.1016/j.marpolbul.2024.116300] [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: 10/30/2023] [Revised: 02/23/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - DongGyun Seo
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Gwangju 61005, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City 30019, Republic of Korea.
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2
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Alcamán-Arias ME, Cifuentes-Anticevic J, Castillo-Inaipil W, Farías L, Sanhueza C, Fernández-Gómez B, Verdugo J, Abarzua L, Ridley C, Tamayo-Leiva J, Díez B. Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula. Microorganisms 2022; 10:microorganisms10061140. [PMID: 35744658 PMCID: PMC9227844 DOI: 10.3390/microorganisms10061140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.
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Affiliation(s)
- María E. Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Jerónimo Cifuentes-Anticevic
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Wilson Castillo-Inaipil
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
| | - Cynthia Sanhueza
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Beatriz Fernández-Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas, Spain
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Leslie Abarzua
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
| | - Christina Ridley
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Javier Tamayo-Leiva
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
- Correspondence:
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3
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Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
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Rapp JZ, Sullivan MB, Deming JW. Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol 2021; 12:701186. [PMID: 34367102 PMCID: PMC8339730 DOI: 10.3389/fmicb.2021.701186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.
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Affiliation(s)
- Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States.,Department of Microbiology, Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States.,Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
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5
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von Friesen LW, Riemann L. Nitrogen Fixation in a Changing Arctic Ocean: An Overlooked Source of Nitrogen? Front Microbiol 2021; 11:596426. [PMID: 33391213 PMCID: PMC7775723 DOI: 10.3389/fmicb.2020.596426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans – challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean – with the aim of guiding and encouraging future research on nitrogen fixation in this region.
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Affiliation(s)
- Lisa W von Friesen
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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6
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Mortazavi R, Attiya S, Ariya PA. Diversity of metals and metal-interactive bacterial populations in different types of Arctic snow and frost flowers: Implications on snow freeze-melt processes in a changing climate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:277-289. [PMID: 31288118 DOI: 10.1016/j.scitotenv.2019.06.350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/22/2019] [Accepted: 06/22/2019] [Indexed: 06/09/2023]
Abstract
Arctic snow has been shown to be a reactive interface for key physical, chemical, and microbiological processes, affecting the Arctic's oxidation, biodiversity, radiation, and climate. To explore the potential links between snow-borne metal contaminants and metal-interactive bacteria, to freezing/melting processes, we performed concurrent chemical characterization, genomic, and morphological analysis of five different Arctic snowpack (accumulated, blowing, fresh falling, surface hoar, and wind pack snow) and frost flower in Utqiaġvik (Barrow), Alaska, using Montreal urban snow as reference. Several complementary analytical techniques, including triple quad ICP-MS/MS along with various chromatography techniques, thermal ionization mass spectrometer (TIMS), high-resolution transition electron microscopy with electron dispersive X-ray spectroscopy (HR-TEM/EDS), and next generation sequencing (NGS), were deployed. Distinct metal composition and bacterial distribution among samples were observed. The concentration of 27 different transition, post-transition, rare, and radioactive metals were determined in molten snow and frost flower, as well as filtered samples. The range of three highest detected metal concentrations among samples were: Hg (3.294-134.485 μg/L), Fe (0.719-34.469 μg/L), and Sr (1.676-19,297.000 μg/L). NGS analysis led to the identification of metal interacting bacteria in all types of snow and frost flowers in the Arctic (blowing snow (1239), surface hoar snow (2243), windpack (2431), frost flowers (1440)), and Montreal urban snow (5498)) with specific bacterial genera such as: Acinetobacter, Arcenicella, Azospirillum (surface hoar snow), Arthrobacter, Paenibacillus (blowing snow), and Cycloclasticus, OM182 clade (frost flower). Several types of bacteria with confirmed or associated ice nucleation activity were observed in different types of snow, and frost flower including Pseudomonas genera (e.g., Pseudomonas fluorescens), Flavobacterium, Corynebacterium, and Pseudoxanthomonas. The implications of the above findings to snow-air interactions including nanoparticles, namely during melting and freezing cycles, and to probe the impact of various natural and anthropogenic activities are herein discussed.
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Affiliation(s)
- Roya Mortazavi
- Department of Atmospheric and Oceanic Sciences, McGill University, Montreal, Canada
| | - Said Attiya
- Faculty of Medicine, McGill University & Génome Québec, Montreal, Canada
| | - Parisa A Ariya
- Department of Atmospheric and Oceanic Sciences, McGill University, Montreal, Canada; Department of Chemistry, McGill University, Montreal, Canada.
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7
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Felföldi T, Márton Z, Szabó A, Mentes A, Bóka K, Márialigeti K, Máthé I, Koncz M, Schumann P, Tóth E. Siculibacillus lacustris gen. nov., sp. nov., a new rosette-forming bacterium isolated from a freshwater crater lake (Lake St. Ana, Romania). Int J Syst Evol Microbiol 2019; 69:1731-1736. [PMID: 30950779 DOI: 10.1099/ijsem.0.003385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new aerobic alphaproteobacterium, strain SA-279T, was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9T (96.4 %) and Ancalomicrobiumadetum NBRC 102456T (94.2 %). Cells of strain SA-279T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279T (=DSM 29840T=JCM 31761T).
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Affiliation(s)
- Tamás Felföldi
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Attila Szabó
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anikó Mentes
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Bóka
- 3Department of Plant Anatomy, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Mihály Koncz
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,†Present address: Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Peter Schumann
- 4Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika Tóth
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
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8
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [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] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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9
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van der Walt AJ, van Goethem MW, Ramond JB, Makhalanyane TP, Reva O, Cowan DA. Assembling metagenomes, one community at a time. BMC Genomics 2017; 18:521. [PMID: 28693474 PMCID: PMC5502489 DOI: 10.1186/s12864-017-3918-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data. RESULTS To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours. CONCLUSIONS We found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.
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Affiliation(s)
- Andries Johannes van der Walt
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.,Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Marc Warwick van Goethem
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Don Arthur Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.
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10
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Gionfriddo CM, Tate MT, Wick RR, Schultz MB, Zemla A, Thelen MP, Schofield R, Krabbenhoft DP, Holt KE, Moreau JW. Microbial mercury methylation in Antarctic sea ice. Nat Microbiol 2016; 1:16127. [PMID: 27670112 DOI: 10.1038/nmicrobiol.2016.127] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/29/2016] [Indexed: 11/09/2022]
Abstract
Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.
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Affiliation(s)
- Caitlin M Gionfriddo
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael T Tate
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Ryan R Wick
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Mark B Schultz
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Adam Zemla
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550 USA
| | - Michael P Thelen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Robyn Schofield
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David P Krabbenhoft
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
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11
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Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region. Polar Biol 2016. [DOI: 10.1007/s00300-016-1921-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Boetius A, Anesio AM, Deming JW, Mikucki JA, Rapp JZ. Microbial ecology of the cryosphere: sea ice and glacial habitats. Nat Rev Microbiol 2015; 13:677-90. [PMID: 26344407 DOI: 10.1038/nrmicro3522] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.
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Affiliation(s)
- Antje Boetius
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Alexandre M Anesio
- Bristol Glaciology Center, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Jody W Deming
- School of Oceanography, Box 357940, University of Washington, Seattle, Washington 98195, USA
| | - Jill A Mikucki
- Department of Biology, 276 Bicentennial Way, Middlebury College, Middlebury, Vermont 05753, USA
| | - Josephine Z Rapp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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13
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Bowman JS, Ducklow HW. Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula. PLoS One 2015; 10:e0135868. [PMID: 26285202 PMCID: PMC4540456 DOI: 10.1371/journal.pone.0135868] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/27/2015] [Indexed: 02/01/2023] Open
Abstract
Taxonomic marker gene studies, such as the 16S rRNA gene, have been used to successfully explore microbial diversity in a variety of marine, terrestrial, and host environments. For some of these environments long term sampling programs are beginning to build a historical record of microbial community structure. Although these 16S rRNA gene datasets do not intrinsically provide information on microbial metabolism or ecosystem function, this information can be developed by identifying metabolisms associated with related, phenotyped strains. Here we introduce the concept of metabolic inference; the systematic prediction of metabolism from phylogeny, and describe a complete pipeline for predicting the metabolic pathways likely to be found in a collection of 16S rRNA gene phylotypes. This framework includes a mechanism for assigning confidence to each metabolic inference that is based on a novel method for evaluating genomic plasticity. We applied this framework to 16S rRNA gene libraries from the West Antarctic Peninsula marine environment, including surface and deep summer samples and surface winter samples. Using statistical methods commonly applied to community ecology data we found that metabolic structure differed between summer surface and winter and deep samples, comparable to an analysis of community structure by 16S rRNA gene phylotypes. While taxonomic variance between samples was primarily driven by low abundance taxa, metabolic variance was attributable to both high and low abundance pathways. This suggests that clades with a high degree of functional redundancy can occupy distinct adjacent niches. Overall our findings demonstrate that inferred metabolism can be used in place of taxonomy to describe the structure of microbial communities. Coupling metabolic inference with targeted metagenomics and an improved collection of completed genomes could be a powerful way to analyze microbial communities in a high-throughput manner that provides direct access to metabolic and ecosystem function.
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Affiliation(s)
- Jeff S. Bowman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, United States of America
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, United States of America
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