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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; 27:1485-1500. [PMID: 38388811 PMCID: PMC11452435 DOI: 10.1007/s10123-024-00492-z] [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: 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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Al-Tarshi M, Dobretsov S, Al-Belushi M. Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats. Microorganisms 2024; 12:1561. [PMID: 39203403 PMCID: PMC11356523 DOI: 10.3390/microorganisms12081561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/29/2024] [Accepted: 07/18/2024] [Indexed: 09/03/2024] Open
Abstract
Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.
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Affiliation(s)
- Muna Al-Tarshi
- Marine Conservation Department, DG of Nature Conservation, Environment Authority, P.O. Box 323, Muscat 100, Oman
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123 P.O. Box 34, Muscat 123, Oman;
| | - Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123 P.O. Box 34, Muscat 123, Oman;
- UNESCO Chair in Marine Biotechnology, Sultan Qaboos University, Al Khoud 123 P.O. Box 50, Muscat 123, Oman
| | - Mohammed Al-Belushi
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123 P.O. Box 34, Muscat 123, Oman;
- Central Laboratory for Food Safety, Food Safety and Quality Center, Ministry of Agricultural, Fisheries Wealth & Water Resources, P.O. Box 3094, Airport Central Post, Muscat 111, Oman
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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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Sánchez-Gallego J, Atencio L, Pérez J, Dupuy O, Díaz-Ferguson E, Godoy-Vitorino F. Assessment of Vibrio populations in a transect of Rhizophora mangle in Punta Galeta, Panamá: culture-dependent analyses reveal biotechnological applications. REV BIOL TROP 2023; 71:e50983. [PMID: 39175646 PMCID: PMC11340860 DOI: 10.15517/rev.biol.trop..v71i1.50983] [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] [Indexed: 08/24/2024] Open
Abstract
Introduction Rhizophora mangle is considered an ecological niche for microorganisms with potentially novel and complex degrading enzymes. Objective To characterize Vibrio populations using culture-dependent methods, using samples collected from sediments and water along a red mangrove transect composed of three sites. Methods Strains were characterized according to their distribution, capacity to degrade of organic matter and other environmental parameters. Additionally the sequence diversity was assessed using 16S rRNA sequencing. Results Bacterial densities were strongly associated with temperature and salinity. A total of 87 good-quality sequences representing the isolates from the three sites, were binned into eight OTUs (Operational taxonomic units). Taxonomic assignment indicated that the dominant members were Vibrionaceae. Beta diversity analyses showed that bacterial communities clustered by sample source rather than spatial distribution, and that alpha diversity was found to be higher in water than in sediment. Three percent of the strains from water samples could degrade carboxyl-methyl cellulose with the smallest enzymatic indexes compared to 4 % of the strains from sediment samples that showed the highest enzymatic indexes. Two strains identified as Vibrio agarivorans degraded cellulose and agarose, producing the highest enzymatic indexes. Conclusions We found higher bacterial densities and diversity in the bacterial communities of the water samples compared to the sediment, with different OTUs including those similar to Ferrimonas, Providencia, or Shewanella which were not isolated in the sediment. Vibrio OTUs were shown to degrade cellulose in both sample types. The results of this study highlight the importance of red mangroves as Vibrio habitats and as reservoirs of potential enzyme sources with biotechnological applications.
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Affiliation(s)
- Joel Sánchez-Gallego
- Facultad de Ciencias de la Salud-William Gorgas, Universidad Latina de Panamá, Panamá
- Estación Científica Coiba (COIBA-AIP), Clayton, Ciudad del Saber, Panamá
| | - Librada Atencio
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama
| | - Jacinto Pérez
- Facultad de Ciencias de la Salud-William Gorgas, Universidad Latina de Panamá, Panamá
| | - Omar Dupuy
- Facultad de Ciencias de la Salud-William Gorgas, Universidad Latina de Panamá, Panamá
| | | | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, Microbiome Laboratory, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico, USA
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Insights into Bacterial Communities and Diversity of Mangrove Forest Soils along the Upper Gulf of Thailand in Response to Environmental Factors. BIOLOGY 2022; 11:biology11121787. [PMID: 36552296 PMCID: PMC9775068 DOI: 10.3390/biology11121787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
The comprehensive data for the dynamic adaptation of bacterial community structure in response to environmental factors is important for the maintenance of the mangrove ecosystem. This aspect was investigated with soils and surface water from six mangrove forests in six provinces along the Upper Gulf of Thailand shoreline. Mangrove soils were variable with respect to pH (acidic to slightly alkaline) and had low amounts of organic matter (OM). Illumina next-generation sequencing attested that the number of observed species as well as the bacterial diversity and richness among all sites were not significantly different. The gamma-, alpha-Proteobacteria, Desulfobacteria, Bacteroidia, Anaerolineae, Bathyarchaeia, Acidobacteriae, Nitrososphaeria, Clostridia, and Thermoplasmata were more abundant bacterial classes present in all sites. Soil OM was the major factor that mostly modulated the bacterial community structure, while salinity influenced the number of observed species and bacterial richness. These results provide informative data on the bacterial community, in response to both environmental factors and heavy metal pollutants, that is prominent for sustainable development and management of mangrove forests.
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Lyu L, He Y, Dong C, Li G, Wei G, Shao Z, Zhang S. Characterization of chlorinated paraffin-degrading bacteria from marine estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129699. [PMID: 35963094 DOI: 10.1016/j.jhazmat.2022.129699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
This study explored chlorinated paraffin (CP)-degrading bacteria from the marine environment. Aequorivita, Denitromonas, Parvibaculum, Pseudomonas and Ignavibacterium were selected as the dominant genera after enrichment with chlorinated paraffin 52 (CP52) as the sole carbon source. Eight strains were identified as CP degraders, including Pseudomonas sp. NG6 and NF2, Erythrobacter sp. NG3, Castellaniella sp. NF6, Kordiimonas sp. NE3, Zunongwangia sp. NF12, Zunongwangia sp. NH1 and Chryseoglobus sp. NF13, and their degradation efficiencies ranged from 6.4% to 19.0%. In addition to Pseudomonas, the other six genera of bacteria were first reported to have the degradation ability of CPs. Bacterial categories, carbon-chain lengths and chlorination degrees were three crucial factors affecting the degradation efficiencies of CPs, with their influential ability of chlorinated degrees > bacterial categories > carbon-chain lengths. CP degradation can be performed by producing chlorinated alcohols, chlorinated olefins, dechlorinated alcohols and lower chlorinated CPs. This study will provide valuable information on CP biotransformation and targeted bacterial resources for studying the transformation processes of specific CPs in marine environments.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yufei He
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chunming Dong
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guizhen Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guangshan Wei
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China.
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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da Silva H, Oliveira TMP, Sabino EC, Alonso DP, Sallum MAM. Bacterial diversity in Haemagogus leucocelaenus (Diptera: Culicidae) from Vale do Ribeira, São Paulo, Brazil. BMC Microbiol 2022; 22:161. [PMID: 35733096 PMCID: PMC9215073 DOI: 10.1186/s12866-022-02571-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/06/2022] [Indexed: 01/29/2023] Open
Abstract
INTRODUCTION Mosquitoes (Diptera: Culicidae) are vectors that transmit numerous pathogens to humans and other vertebrates. Haemagogus leucocelaenus is a mosquito associated with transmission of yellow fever virus. The insect gut harbors a variety of microorganisms that can live and multiply within it, thus contributing to digestion, nutrition, and development of its host. The composition of bacterial communities in mosquitoes can be influenced by both biotic and abiotic factors. The goal of this study was to investigate the bacterial diversity of Hg. leucocelaenus and verify the differences between the bacterial communities in Hg. leucocelaenus from three different locations in the Atlantic tropical rain forest and southeastern state of São Paulo State, Brazil. RESULTS The phylum Proteobacteria was found in mosquitoes collected from the three selected study sites. More than 50% of the contigs belong to Wolbachia, followed by 5% Swaminathania, and 3% Acinetobacter. The genus Serratia was found in samples from two locations. CONCLUSIONS Wolbachia was reported for the first time in this species and may indicates that the vector competence of the populations of the species can vary along its geographical distribution area. The presence of Serratia might facilitate viral invasion caused by the disruption of the midgut barrier via action of the SmEnhancin protein, which digests the mucins present in the intestinal epithelium.
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Affiliation(s)
- Herculano da Silva
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
| | - Ester C. Sabino
- Departamento de Moléstias Infecciosas e Parasitarias, Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Eneas de Carvalho 470, 1º andar, São Paulo, 05403-000 Brazil
| | - Diego Peres Alonso
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
- Biotechnology Institute and Bioscience Institute, Sao Paulo State University (UNESP), Botucatu, 18618-689 Brazil
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Dr. Arnaldo 715, São Paulo, SP 01246-904 Brazil
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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: 25] [Impact Index Per Article: 12.5] [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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Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
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Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure. Molecules 2021; 26:molecules26237332. [PMID: 34885912 PMCID: PMC8658942 DOI: 10.3390/molecules26237332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.
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Yin Y, Yan Z. Variations of soil bacterial diversity and metabolic function with tidal flat elevation gradient in an artificial mangrove wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137385. [PMID: 32092526 DOI: 10.1016/j.scitotenv.2020.137385] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Understanding the sensitivity of soil bacteria to environmental fluctuations can enhance the management of microbial ecosystem services in artificial mangrove wetlands. In this study, the variation in bacterial diversity and metabolic functions in different compartments (bulk soil, rhizosphere soil, and rhizoplane) of the soil and mangrove plant along the tidal elevation gradient was studied in Xiatanwei (Xiamen China) mangrove wetland park, a Kandelia obovata-dominated artificial mangrove stand. With the increase of the tidal flat elevation, the soil pH, total organic matter, and soil moisture contents decreased significantly, while the soil electric conductivity and redox potential increased significantly. The bacterial diversity in the bulk soil and the rhizosphere soil both decreased with the elevation of tidal levels. The relative abundance of the dominant phyla in the bulk and rhizosphere soils decreased with the rise of the tidal flat level. A significant rhizosphere effect was observed in the roots of K. obovata that the rhizosphere soil had higher bacterial diversity and richness than that in the bulk soil nearby. The rhizosphere soil of K. obovata at the low-tidal flat was enriched with the genera Nitrospira and Planctomycetes, which are valuable for the mangrove ecosystem. The Chao1 estimator and Shannon index of the bacterial community in the rhizoplane of K. obovata were much lower than that in the rhizosphere and bulk soils. Results of Biolog-Eco assay show that the bacterial groups in low tidal flat bulk soil had the highest ability in utilizing the carbon sources, which was indicated by the high values of average well color development and the high McIntosh index, and the utilization ability of carbon source decreased with the increase of tidal flat levels. The variation of the soil humidity and Eh jointly shaped the diversity and metabolic function of soil bacterial communities along the tidal flat elevation gradient.
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Affiliation(s)
- Yichen Yin
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Zhongzheng Yan
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China.
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Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s12209-019-00226-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractDiversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient (0–0.4043 g/g) in surface (5–10 cm) and subsurface (35–40 cm) petroleum-contaminated soil samples from the Dagang Oilfield, China. Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods, the bacterial diversity of the soil was studied. Subsequently, the environmental parameters were measured to analyze its relationship with the community variation. Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils, but no differences were observed in different depths of petroleum-contaminated soil. Meanwhile, many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties. Total petroleum hydrocarbon, total organic carbon, and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils. Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.
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Ceccon DM, Faoro H, Lana PDC, Souza EMD, Pedrosa FDO. Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133609. [PMID: 31400683 DOI: 10.1016/j.scitotenv.2019.133609] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/18/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.
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Affiliation(s)
- Denny Marcel Ceccon
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Paulo da Cunha Lana
- Center for Marine Studies, Universidade Federal do Paraná, Pontal do Paraná, Brazil
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Behera P, Mohapatra M, Kim JY, Adhya TK, Pattnaik AK, Rastogi G. Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:3893-3908. [PMID: 30547343 DOI: 10.1007/s11356-018-3927-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, Busan, 46241, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India.
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Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana. Braz J Microbiol 2018; 49:757-769. [PMID: 29866608 PMCID: PMC6175736 DOI: 10.1016/j.bjm.2018.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 02/01/2018] [Accepted: 02/14/2018] [Indexed: 11/23/2022] Open
Abstract
Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.
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