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de Carvalho FM, Laux M, Ciapina LP, Gerber AL, Guimarães APC, Kloh VP, Apolinário M, Paes JES, Jonck CR, de Vasconcelos ATR. Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation. Int Microbiol 2024:10.1007/s10123-024-00492-z. [PMID: 38388811 DOI: 10.1007/s10123-024-00492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Mangroves are complex land-sea transition ecosystems whose microbiota are essential for their nutrient recycling and conservation. Brazil is the third-largest estuarine area in the world and "Baía de Todos os Santos" (BTS) is one of the largest bays of the country, with wide anthropogenic exploration. Using a metagenomic approach, we investigated composition and functional adaptability as signatures of the microbiome of pristine and anthropized areas of BTS, including those under petroleum refinery influence. The taxonomic analysis showed dominance of sulfate-reducing Desulfobacteraceae, Rhodobacteraceae, and Flavobacteriaceae. Taxa were significantly diverse between pristine and disturbed areas. Disturbed mangroves showed a notary increase in abundance of halophilic, sulfur-related, and hydrocarbon-degrading genera and a decrease in diatoms compared to pristine area. The metabolic profile of BTS mangroves was correlated with the differentially abundant microbiota. Two ecological scenarios were observed: one marked by functions of central metabolism associated with biomass degradation and another by mechanisms of microbial adaptability to pollution conditions and environmental degradation. Part of the microbiome was distinct and not abundant in Brazilian estuarine soils. The microbiome signature observed in each BTS mangrove reflects how human actions impact the diversity of these ecosystems and also emphasize their role in attempting to restore disturbed mangroves. The microbiome may act as a potential biological indicator of the preservation status of these soils, despite the limitation of soil property conditions. Additionally, our data pointed to metagenomics as an additional tool for environmental assessment and reinforced the need for protective measures for the mangroves under study.
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Affiliation(s)
- Fabíola Marques de Carvalho
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Marcele Laux
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Luciane Prioli Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Ana Paula C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Vinícius Prata Kloh
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Moacir Apolinário
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Jorge Eduardo Santos Paes
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Célio Roberto Jonck
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil.
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Mahmoudi N, Wilhelm RC. Can we manage microbial systems to enhance carbon storage? Environ Microbiol 2023; 25:3011-3018. [PMID: 37431673 DOI: 10.1111/1462-2920.16462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, Quebec, Canada
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana, USA
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Chen Y, Li W, Shi K, Fang Z, Yang Y, Zhang R. Isolation and characterization of a novel phage belonging to a new genus against Vibrio parahaemolyticus. Virol J 2023; 20:81. [PMID: 37127579 PMCID: PMC10152775 DOI: 10.1186/s12985-023-02036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. METHODS A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. RESULTS R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. CONCLUSIONS In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.
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Affiliation(s)
- Yubing Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Wenqing Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Keming Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zheng Fang
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China.
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d’Acapito A, Roret T, Zarkadas E, Mocaër PY, Lelchat F, Baudoux AC, Schoehn G, Neumann E. Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM. J Virol 2023; 97:e0024823. [PMID: 36943070 PMCID: PMC10134823 DOI: 10.1128/jvi.00248-23] [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: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/23/2023] Open
Abstract
Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina virus 1 (Carin-1) is a member of the Podoviridae family infecting the γ-protoabacteria C. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of de-novo manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. IMPORTANCE Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem.
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Affiliation(s)
| | - Thomas Roret
- Station Biologique de Roscoff (SBR), CNRS FR2424, Sorbonne Université, Roscoff, France
| | | | - Pierre-Yves Mocaër
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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Visnapuu A, Van der Gucht M, Wagemans J, Lavigne R. Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies. Viruses 2022; 14:v14051057. [PMID: 35632801 PMCID: PMC9145820 DOI: 10.3390/v14051057] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/19/2022] Open
Abstract
The bacterial biofilm constitutes a complex environment that endows the bacterial community within with an ability to cope with biotic and abiotic stresses. Considering the interaction with bacterial viruses, these biofilms contain intrinsic defense mechanisms that protect against phage predation; these mechanisms are driven by physical, structural, and metabolic properties or governed by environment-induced mutations and bacterial diversity. In this regard, horizontal gene transfer can also be a driver of biofilm diversity and some (pro)phages can function as temporary allies in biofilm development. Conversely, as bacterial predators, phages have developed counter mechanisms to overcome the biofilm barrier. We highlight how these natural systems have previously inspired new antibiofilm design strategies, e.g., by utilizing exopolysaccharide degrading enzymes and peptidoglycan hydrolases. Next, we propose new potential approaches including phage-encoded DNases to target extracellular DNA, as well as phage-mediated inhibitors of cellular communication; these examples illustrate the relevance and importance of research aiming to elucidate novel antibiofilm mechanisms contained within the vast set of unknown ORFs from phages.
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Chen X, Wei W, Xiao X, Wallace D, Hu C, Zhang L, Batt J, Liu J, Gonsior M, Zhang Y, LaRoche J, Hill P, Xu D, Wang J, Jiao N, Zhang R. Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment. ENVIRONMENT INTERNATIONAL 2022; 158:106950. [PMID: 34715430 DOI: 10.1016/j.envint.2021.106950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L-1 d-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L-1 d-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L-1 d-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Douglas Wallace
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Lianbao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - John Batt
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jihua Liu
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, PR China
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD 20688, United States
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Julie LaRoche
- Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China; Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Paul Hill
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, 361102 Xiamen, PR China; Joint Lab for Ocean Research and Education (LORE) of Dalhousie University, Canada, and Shandong University and Xiamen University, PR China.
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Beyer CD, Thavalingam S, Guseva T, Schardt L, Zimmermann R, Werner C, Dietze P, Bandow JE, Metzler-Nolte N, Rosenhahn A. Zwitterionic Peptides Reduce Accumulation of Marine and Freshwater Biofilm Formers. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49682-49691. [PMID: 34663068 DOI: 10.1021/acsami.1c13459] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Zwitterionic peptides are facile low-fouling compounds for environmental applications as they are biocompatible and fully biodegradable as their degradation products are just amino acids. Here, a set of histidine (H) and glutamic acid (E), as well as lysine (K) and glutamic acid (E) based peptide sequences with zwitterionic properties were synthesized. Both oligopeptides (KE)4K and (HE)4H were synthesized in d and l configurations to test their ability to resist the nonspecific adsorption of the proteins lysozyme and fibrinogen. The coatings were additionally tested against the attachment of the marine organisms Navicula perminuta and Cobetia marina as well as the freshwater bacterium Pseudomonas fluorescens on the developed coatings. While the peptides containing lysine performed better in protein resistance assays and against freshwater bacteria, the sequences containing histidine were generally more resistant against marine organisms. The contribution of amino acid-intrinsic properties such as side chain pKa values and hydrophobicity, as well as external parameters such as pH and salinity of fresh water and seawater on the resistance of the coatings is discussed. In this way, a detailed picture emerges as to which zwitterionic sequences show advantages in future generations of biocompatible, sustainable, and nontoxic fouling release coatings.
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Affiliation(s)
- Cindy D Beyer
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sugina Thavalingam
- Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Tatiana Guseva
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lisa Schardt
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ralf Zimmermann
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, 01069 Dresden, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, 01069 Dresden, Germany
| | - Pascal Dietze
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Axel Rosenhahn
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
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8
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Blanco-Ameijeiras S, Cabanes DJE, Cable RN, Trimborn S, Jacquet S, Wiegmann S, Völkner C, Lelchat F, Bracher A, Duhaime MB, Hassler CS. Exopolymeric Substances Control Microbial Community Structure and Function by Contributing to both C and Fe Nutrition in Fe-Limited Southern Ocean Provinces. Microorganisms 2020; 8:E1980. [PMID: 33322799 PMCID: PMC7763086 DOI: 10.3390/microorganisms8121980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 11/23/2022] Open
Abstract
Organic ligands such as exopolymeric substances (EPS) are known to form complexes with iron (Fe) and modulate phytoplankton growth. However, the effect of organic ligands on bacterial and viral communities remains largely unknown. Here, we assessed how Fe associated with organic ligands influences phytoplankton, microbial, and viral abundances and their diversity in the Southern Ocean. While the particulate organic carbon (POC) was modulated by Fe chemistry and bioavailability in the Drake Passage, the abundance and diversity of microbes and viruses were not governed by Fe bioavailability. Only following amendments with bacterial EPS did bacterial abundances increase, while phenotypic alpha diversity of bacterial and viral communities decreased. The latter was accompanied by significantly enhanced POC, pointing toward the relief of C limitation or other drivers of the microbial loop. Based on the literature and our findings, we propose a conceptual framework by which EPS may affect phytoplankton, bacteria, and viruses. Given the importance of the Southern Ocean for Earth's climate as well as the prevalence of viruses and their increasingly recognized impact on marine biogeochemistry and C cycling; the role of microbe-virus interactions on primary productivity in the Southern Ocean needs urgent attention.
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Affiliation(s)
- Sonia Blanco-Ameijeiras
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva—Faculty of Science, Boulevard Carl-Vogt 66, 1211 Geneva, Switzerland; (S.B.-A.); (D.J.E.C.); (F.L.); (C.S.H.)
| | - Damien J. E. Cabanes
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva—Faculty of Science, Boulevard Carl-Vogt 66, 1211 Geneva, Switzerland; (S.B.-A.); (D.J.E.C.); (F.L.); (C.S.H.)
| | - Rachel N. Cable
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (R.N.C.); (M.B.D.)
| | - Scarlett Trimborn
- Sections Ecological Chemistry and Physical Oceanography, Alfred Wegener Institute—Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (S.W.); (C.V.); (A.B.)
- Department Marine Botany, University of Bremen, Leobener Strasse NW2-A, 28359 Bremen, Germany
| | - Stéphan Jacquet
- INRAE, UMR CARRTEL, Université Savoie Mont-Blanc, 75bis Avenue de Corzent, 74200 Thonon-les-Bains, France ;
| | - Sonja Wiegmann
- Sections Ecological Chemistry and Physical Oceanography, Alfred Wegener Institute—Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (S.W.); (C.V.); (A.B.)
| | - Christian Völkner
- Sections Ecological Chemistry and Physical Oceanography, Alfred Wegener Institute—Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (S.W.); (C.V.); (A.B.)
| | - Florian Lelchat
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva—Faculty of Science, Boulevard Carl-Vogt 66, 1211 Geneva, Switzerland; (S.B.-A.); (D.J.E.C.); (F.L.); (C.S.H.)
- Leo Viridis, 245 rue René Descartes, 29280 Plouzané, Bretagne, France
| | - Astrid Bracher
- Sections Ecological Chemistry and Physical Oceanography, Alfred Wegener Institute—Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; (S.W.); (C.V.); (A.B.)
- Institute of Environmental Physics, University Bremen, Otto-Hahn-Allee 1, 28359 Bremen, Germany
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (R.N.C.); (M.B.D.)
| | - Christel S. Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva—Faculty of Science, Boulevard Carl-Vogt 66, 1211 Geneva, Switzerland; (S.B.-A.); (D.J.E.C.); (F.L.); (C.S.H.)
- Swiss Polar Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, Waldbauer JR, Coleman ML. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol 2019; 18:21-34. [PMID: 31690825 DOI: 10.1038/s41579-019-0270-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
Ecosystems are controlled by 'bottom-up' (resources) and 'top-down' (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability. In this Review, we discuss recent advances in understanding the biogeochemical impact of viruses, focusing on how metabolic reprogramming of host cells during lytic viral infection alters the flow of energy and nutrients in aquatic ecosystems. Our synthesis revealed several emerging themes. First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain. This Review highlights the need for understanding viral infection dynamics in realistic physiological and environmental contexts to better predict their biogeochemical consequences.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | | | - David M Needham
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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