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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2024; 69:595-612. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [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: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Wissner JL, Parada-Fabián JC, Márquez-Velázquez NA, Escobedo-Hinojosa W, Gaudêncio SP, Prieto-Davó A. Diversity and Bioprospection of Gram-positive Bacteria Derived from a Mayan Sinkhole. MICROBIAL ECOLOGY 2024; 87:77. [PMID: 38806738 PMCID: PMC11133088 DOI: 10.1007/s00248-024-02392-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Water-filled sinkholes known locally as cenotes, found on the Yucatán Peninsula, have remarkable biodiversity. The primary objective of this study was to explore the biotechnological potential of Gram-positive cultivable bacteria obtained from sediment samples collected at the coastal cenote Pol-Ac in Yucatán, Mexico. Specifically, the investigation aimed to assess production of hydrolytic enzymes and antimicrobial compounds. 16 S rRNA gene sequencing led to the identification of 49 Gram-positive bacterial isolates belonging to the phyla Bacillota (n = 29) and Actinomycetota (n = 20) divided into the common genera Bacillus and Streptomyces, as well as the genera Virgibacillus, Halobacillus, Metabacillus, Solibacillus, Neobacillus, Rossellomorea, Nocardiopsis and Corynebacterium. With growth at 55ºC, 21 of the 49 strains were classified as moderately thermotolerant. All strains were classified as halotolerant and 24 were dependent on marine water for growth. Screening for six extracellular hydrolytic enzymes revealed gelatinase, amylase, lipase, cellulase, protease and chitinase activities in 93.9%, 67.3%, 63.3%, 59.2%, 59.2% and 38.8%, of isolated strains, respectively. The genes for polyketide synthases type I, were detected in 24 of the strains. Of 18 strains that achieved > 25% inhibition of growth in the bacterial pathogen Staphylococcus aureus ATCC 6538, 4 also inhibited growth in Escherichia coli ATCC 35,218. Isolates Streptomyces sp. NCA_378 and Bacillus sp. NCA_374 demonstrated 50-75% growth inhibition against at least one of the two pathogens tested, along with significant enzymatic activity across all six extracellular enzymes. This is the first comprehensive report on the biotechnological potential of Gram-positive bacteria isolated from sediments in the cenotes of the Yucatán Peninsula.
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Affiliation(s)
- Julian L Wissner
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Sisal, Yucatán, 97356, México
| | - José Carlos Parada-Fabián
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Sisal, Yucatán, 97356, México
| | - Norma Angélica Márquez-Velázquez
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Sisal, Yucatán, 97356, México
| | - Wendy Escobedo-Hinojosa
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Sisal, Yucatán, 97356, México
| | - Susana P Gaudêncio
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA Faculty of Sciences and Technology, NOVA University of Lisbon, Lisbon, 2819-516, Portugal
- Applied Molecular Biosciences Unit, Chemistry and Life Sciences Departments, NOVA Faculty of Sciences and Technology, UCIBIO, NOVA University of Lisbon, Lisbon, 2819-516, Portugal
| | - Alejandra Prieto-Davó
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, Sisal, Yucatán, 97356, México.
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Guillén-Chable F, Valdez Iuit JO, Avila Castro LA, Rosas C, Merino E, Rodríguez-Escamilla Z, Martínez-Núñez MA. Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast. PLoS One 2024; 19:e0301642. [PMID: 38683832 PMCID: PMC11057721 DOI: 10.1371/journal.pone.0301642] [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: 11/30/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
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Affiliation(s)
- Francisco Guillén-Chable
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Johnny Omar Valdez Iuit
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | | | - Carlos Rosas
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Enrique Merino
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Zuemy Rodríguez-Escamilla
- Facultad de Sistemas Biológicos e Innovación Tecnológica, Universidad Autónoma "Benito Juárez" de Oaxaca, Oaxaca de Juárez, Oaxaca, México
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Du H, Pan J, Zhang C, Yang X, Wang C, Lin X, Li J, Liu W, Zhou H, Yu X, Mo S, Zhang G, Zhao G, Qu W, Jiang C, Tian Y, He Z, Liu Y, Li M. Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America. Microbiol Spectr 2023; 11:e0157723. [PMID: 37668400 PMCID: PMC10580968 DOI: 10.1128/spectrum.01577-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/19/2023] [Indexed: 09/06/2023] Open
Abstract
As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.
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Affiliation(s)
- Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xilan Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Cheng Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinhui Li
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Wan Liu
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Haokui Zhou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoli Yu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Shuming Mo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Guoqing Zhang
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Guoping Zhao
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Chengjian Jiang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Costa GMD, Costa SS, Baraúna RA, Castilho BP, Pinheiro IC, Silva A, Schaan AP, Ribeiro-Dos-Santos Â, Graças DAD. Effects of Degradation on Microbial Communities of an Amazonian Mangrove. Microorganisms 2023; 11:1389. [PMID: 37374891 DOI: 10.3390/microorganisms11061389] [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: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy an area of 9000 km2, corresponding to 70% of the mangroves in Brazil, on which studies of microbial biodiversity are extremely scarce. The present study aimed to determine changes in microbial community structure along the PA-458 highway, which fragmented a mangrove zone. Mangrove samples were collected from three zones, (i) degraded, (ii) in the process of recovery, and (iii) preserved. Total DNA was extracted and submitted for 16S rDNA amplification and sequencing on an MiSeq platform. Subsequently, reads were processed for quality control and biodiversity analyses. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all three mangrove locations, but in significantly different proportions. We observed a considerable reduction in diversity in the degraded zone. Important genera involved in sulfur, carbon, and nitrogen metabolism were absent or dramatically reduced in this zone. Our results show that human impact in the mangrove areas, caused by the construction of the PA-458 highway, has resulted in a loss of biodiversity.
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Affiliation(s)
- Gleyciane Machado da Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Sávio Souza Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Rafael Azevedo Baraúna
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Bruno Pureza Castilho
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Izabel Cruz Pinheiro
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Artur Silva
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ana Paula Schaan
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Diego Assis das Graças
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
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Moopantakath J, Imchen M, Anju VT, Busi S, Dyavaiah M, Martínez-Espinosa RM, Kumavath R. Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications. Front Microbiol 2023; 14:1113540. [PMID: 37065149 PMCID: PMC10102575 DOI: 10.3389/fmicb.2023.1113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - V. T. Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- Rosa María Martínez-Espinosa,
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- *Correspondence: Ranjith Kumavath, ,
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Vijayan J, Nathan VK, Ammini P, Ammanamveetil AMH. Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28383-28406. [PMID: 36680718 PMCID: PMC9862233 DOI: 10.1007/s11356-023-25195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/04/2023] [Indexed: 04/16/2023]
Abstract
Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.
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Affiliation(s)
- Jasna Vijayan
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India.
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, Sastra Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamilnadu, India
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, Kerala, India
| | - Abdulla Mohamed Hatha Ammanamveetil
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682 016, Kerala, India
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9
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Gómez-Acata ES, Teutli C, Falcón LI, García-Maldonado JQ, Prieto-Davó A, Yanez-Montalvo A, Cadena S, Chiappa-Carrara X, Herrera-Silveira JA. Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico. PeerJ 2023; 11:e14587. [PMID: 36785710 PMCID: PMC9921989 DOI: 10.7717/peerj.14587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/28/2022] [Indexed: 02/11/2023] Open
Abstract
Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.
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Affiliation(s)
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México
| | | | - José Q. García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | | | | | - Santiago Cadena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Xavier Chiappa-Carrara
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Unidad Multidisciplinaria de Docencia e Investigación, Unidad Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Jorge A. Herrera-Silveira
- Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México,Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
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10
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Rai A, Saha SP, Manvar T, Bhattacharjee A. A shotgun approach to explore the bacterial diversity and a brief insight into the glycoside hydrolases of Samiti lake located in the Eastern Himalayas. J Genet Eng Biotechnol 2022; 20:162. [PMID: 36469176 PMCID: PMC9723087 DOI: 10.1186/s43141-022-00444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Himalayas have always been an enigma and, being biodiversity hotspots, are considered extremely important from an ecological point of view. Recent advances in studies regarding high-altitude lakes have garnered relevant importance as these habitats could harbor potential psychrophilic and psychrotrophic microbes with bio-prospective applications. Contemplating the above scenario, the present study has been undertaken to understand the diversity and the functional capacities of the microbes thriving in this lake. RESULTS In our present study on Samiti Lake, the abundance of Proteobacteria as the major phylum was seen in both the soil and water samples. Incase of the ABSLW (water) and ABS1 (soil) sample, 148,066 and 239,754 predicted genes, were taken for functional analysis. The KEGG analysis showed that ABSLW and ABS1 had 122,911 and 160,268, genes assigned to KO terms respectively. Whereas in case of COG functional analysis, 104,334 and 130,191 genes were assigned to different COG classes for ABSLW and ABS1 respectively. Further, on studying the glycoside hydrolases, an abundance of GH13, GH2, GH3, GH43, and GH23 in both the soil and water samples were seen. CONCLUSION Our study has provided a comprehensive report about the bacterial diversity and functional capacities of microbes thriving in Samiti Lake. It has also thrown some light on the occurrence of glycoside hydrolases in this region, as they have numerous biotechnological applications in different sectors.
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Affiliation(s)
- Aditi Rai
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Toral Manvar
- Xcelris Labs Ltd, Ahmedabad, Gujarat 380006 India
| | - Arindam Bhattacharjee
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
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11
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Liu GH, Liu DQ, Wang P, Chen QQ, Che JM, Wang JP, Li WJ, Zhou SG. Temperature drives the assembly of Bacillus community in mangrove ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157496. [PMID: 35870580 DOI: 10.1016/j.scitotenv.2022.157496] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO3-N and NH4-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Ding-Qi Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qian-Qian Chen
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jian-Mei Che
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province 350002, PR China.
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12
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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13
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Sepúlveda-Correa A, Daza-Giraldo LV, Polanía J, Arenas NE, Muñoz-García A, Sandoval-Figueredo AV, Vanegas J. Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities. MARINE POLLUTION BULLETIN 2021; 171:112740. [PMID: 34304060 DOI: 10.1016/j.marpolbul.2021.112740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.
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Affiliation(s)
| | | | - Jaime Polanía
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | - Nelson E Arenas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia
| | | | | | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
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14
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Sharma R, Kumar A, Singh N, Sharma K. 16S rRNA gene profiling of rhizospheric microbial community of Eichhornia crassipes. Mol Biol Rep 2021; 48:4055-4064. [PMID: 34021896 DOI: 10.1007/s11033-021-06413-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 05/15/2021] [Indexed: 10/21/2022]
Abstract
The rhizosphere of a plant is an important interface for the plant-microbe interaction that plays a significant role in the uptake and removal of heavy metal from contaminated sites. Eichhornia crassipes is a free-floating macrophyte and a well-known metal hyperaccumulator. It is a promising plant, which harbors a diverse microbial community in its rhizosphere. Therefore it is hypothesized that it can be a good habitat for microorganisms that supports plant growth and increases its phytoremediation potential. The rhizospheric DNA was extracted from the procured plant samples. The library was prepared and sequenced using the Illumina platform. 16S rRNA data from the Next Generation Sequencing (NGS) platform was analyzed using the QIIME software package. Alpha diversity was estimated from statistical indices i.e. Shannon index, Chao1 index, and observed species. The rarefaction plots, rank abundance curve, krona graph, and heat map were generated to study the rhizospheric community in detail. Metagenome consisted of 225,408 flash reads, 185,008 non-chimeric sequences with 17,578 Operational Taxonomic Units (OTU's), and 4622 OTU's without singletons. The data of present study are available at NCBI Bioproject (PRJNA631882). The taxonomic analysis of OTU's showed that the sequences belonged to major Phyla revealing the dominance of Proteobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia. The most abundant Genera in the sampled rhizosphere recorded were Thiothrix and Flavobacterium.
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Affiliation(s)
- Ruchi Sharma
- Department of Microbiology, Mewar University, Chittorgarh, Rajasthan, India.
| | - Ajay Kumar
- Department of Biotechnology, Mewar Institute of Management, Vasundhara, Ghaziabad, 201012, Uttar Pradesh, India
| | - Neetu Singh
- Department of Biotechnology, Mewar Institute of Management, Vasundhara, Ghaziabad, 201012, Uttar Pradesh, India
| | - Kritika Sharma
- Department of Biotechnology, Mewar University, Chittorgarh, Rajasthan, India
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15
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Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales. Int J Syst Evol Microbiol 2021; 71:004806. [PMID: 33999795 PMCID: PMC8289202 DOI: 10.1099/ijsem.0.004806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
We isolated a novel strain, R1DC25T, described as Kaustia mangrovi gen. nov. sp. nov. from the sediments of a mangrove forest on the coast of the Red Sea in Saudi Arabia. This isolate is a moderately halophilic, aerobic/facultatively anaerobic Gram-stain-negative bacterium showing optimum growth at between 30 and 40 °C, at a pH of 8.5 and with 3-5 % NaCl. The genome of R1DC25T comprises a circular chromosome that is 4 630 536 bp in length, with a DNA G+C content of 67.3 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis of 120 concatenated single-copy genes revealed that R1DC25T represents a distinct lineage within the family Parvibaculaceae in the order Rhizobiales within the class Alphaproteobacteria. R1DC25T showing 95.8, 95.3 and 94.5 % 16S rRNA gene sequence identity with Rhodoligotrophos appendicifer, Rhodoligotrophos jinshengii and Rhodoligotrophos defluvii, respectively. The predominant quinone was Q-10, and the polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, as well as several distinct aminolipids and lipids. The predominant cellular fatty acids were C19 : 0 cyclo ω8c, a combination of C18 : 1ω7c and/or C18 : 1ω6c and C16 : 0. On the basis of the differences in the phenotypic, physiological and biochemical characteristics from its known relatives and the results of our phylogenetic analyses, R1DC25T (=KCTC 72348T;=JCM 33619T;=NCCB 100699T) is proposed to represent a novel species in a novel genus, and we propose the name Kaustia mangrovi gen. nov., sp. nov. (Kaustia, subjective name derived from the abbreviation KAUST for King Abdullah University of Science and Technology; mangrovi, of a mangrove).
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Affiliation(s)
- Fatmah O. Sefrji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kholoud A. Seferji
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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16
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Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
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17
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Ahmad T, Gupta G, Sharma A, Kaur B, El-Sheikh MA, Alyemeni MN. Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake. PLoS One 2021; 16:e0248116. [PMID: 33764980 PMCID: PMC7993826 DOI: 10.1371/journal.pone.0248116] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 11/23/2022] Open
Abstract
Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).
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Affiliation(s)
- Tawseef Ahmad
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Anshula Sharma
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
| | - Baljinder Kaur
- Department of Biotechnology, Punjabi University Patiala, Punjabi, India
- * E-mail: (BK); (MNA)
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail: (BK); (MNA)
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18
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Mukherji S, Ghosh A, Bhattacharyya C, Mallick I, Bhattacharyya A, Mitra S, Ghosh A. Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110481. [PMID: 32203775 DOI: 10.1016/j.ecoenv.2020.110481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anandita Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Chandrima Bhattacharyya
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Ivy Mallick
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anish Bhattacharyya
- Department of Biochemistry, 35 Ballygunge Circular Road, University of Calcutta, Kolkata, 700019, India
| | - Suparna Mitra
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Thoresby Place, Leeds, LS1 3EX, W. Yorkshire, United Kingdom
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India.
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Secondary metabolites from the mangrove sediment-derived fungus Penicillium pinophilum SCAU037. Fitoterapia 2019; 136:104177. [DOI: 10.1016/j.fitote.2019.104177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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Haldar S, Nazareth SW. Diversity of fungi from mangrove sediments of Goa, India, obtained by metagenomic analysis using Illumina sequencing. 3 Biotech 2019; 9:164. [PMID: 30997301 DOI: 10.1007/s13205-019-1698-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
The fungal composition, abundance and diversity of the mangrove sediments from the Mandovi and Zuari estuaries, Goa, using paired-end Illumina sequencing, hitherto unexplored by a metagenomic approach, indicated that though the types of fungal phyla were similar between the two sediments, the abundance of the species was significantly different between them (p value < 0.005). Basidiomycota and Ascomycota were the two major phyla which were sub-divided into eighteen classes, families, orders, genera and species and one unassigned group in both the sediments. The top five classes observed were Agaricomycetes, Sordariomycetes, Saccharomycetes, Dothideomycetes and Eurotiomycetes from both the sediments. The diversity analysis based on the observed fungal species richness (Chao 1 for Mandovi were 614 and 714.7 while for Zuari were 665 and 771.2) revealed that Zuari sediment was taxonomically rich, indicating these to be potent candidates for bioremediation and a rich repository for biotechnologically important fungi. This is a first report on diversity of fungi from mangrove sediments of Goa using metagenomic studies.
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Affiliation(s)
- Shyamalina Haldar
- Department of Microbiology, Goa University, Taleigao Plateau, Goa 403206 India
| | - Sarita W Nazareth
- Department of Microbiology, Goa University, Taleigao Plateau, Goa 403206 India
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