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Esguerra-Rodríguez D, De León-Lorenzana A, Teutli C, Prieto-Davó A, García-Maldonado JQ, Herrera-Silveira J, Falcón LI. Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula. PLoS One 2024; 19:e0307929. [PMID: 39150908 PMCID: PMC11329136 DOI: 10.1371/journal.pone.0307929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/15/2024] [Indexed: 08/18/2024] Open
Abstract
Mangrove forests are fundamental coastal ecosystems for the variety of services they provide, including green-house gas regulation, coastal protection and home to a great biodiversity. Mexico is the fourth country with the largest extension of mangroves of which 60% occurs in the Yucatan Peninsula. Understanding the microbial component of mangrove forests is necessary for their critical roles in biogeochemical cycles, ecosystem health, function and restoration initiatives. Here we study the relation between the microbial community from sediments and the restoration process of mangrove forests, comparing conserved, degraded and restored mangroves along the northern coast of the Yucatan peninsula. Results showed that although each sampling site had a differentiated microbial composition, the taxa belonged predominantly to Proteobacteria (13.2-23.6%), Desulfobacterota (7.6-8.3%) and Chloroflexi (9-15.7%) phyla, and these were similar between rainy and dry seasons. Conserved mangroves showed significantly higher diversity than degraded ones, and restored mangroves recovered their microbial diversity from the degraded state (Dunn test p-value Benjamini-Hochberg adjusted = 0.0034 and 0.0071 respectively). The structure of sediment microbial β-diversity responded significantly to the mangrove conservation status and physicochemical parameters (organic carbon content, redox potential, and salinity). Taxa within Chloroflexota, Desulfobacterota and Thermoplasmatota showed significantly higher abundance in degraded mangrove samples compared to conserved ones. This study can help set a baseline that includes the microbial component in health assessment and restoration strategies of mangrove forests.
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Affiliation(s)
- Daniel Esguerra-Rodríguez
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
| | - Arit De León-Lorenzana
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores Mérida, Universidad Nacional Autónoma de México, Ucú, Yucatán, México
| | - Alejandra Prieto-Davó
- Facultad de Química, Unidad de Química Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - José Q García-Maldonado
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Jorge Herrera-Silveira
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Luisa I Falcón
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
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2
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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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3
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Yi Y, Liu S, Hao Y, Sun Q, Lei X, Wang Y, Wang J, Zhang M, Tang S, Tang Q, Zhang Y, Liu X, Wang Y, Xiao X, Jian H. A systematic analysis of marine lysogens and proviruses. Nat Commun 2023; 14:6013. [PMID: 37758717 PMCID: PMC10533544 DOI: 10.1038/s41467-023-41699-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
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Affiliation(s)
- Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Lei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yecheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingxue Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xipeng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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4
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Roberts AJ, Suttle CA. Pathogens and Passengers: Roles for Crustacean Zooplankton Viruses in the Global Ocean. Microorganisms 2023; 11:microorganisms11041054. [PMID: 37110477 PMCID: PMC10142142 DOI: 10.3390/microorganisms11041054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Viruses infect all living organisms, but the viruses of most marine animals are largely unknown. Crustacean zooplankton are a functional lynchpin in marine food webs, but very few have been interrogated for their associated viruses despite the profound potential effects of viral infection. Nonetheless, it is clear that the diversity of viruses in crustacean zooplankton is enormous, including members of all realms of RNA viruses, as well as single- and double-stranded DNA viruses, in many cases representing deep branches of viral evolution. As there is clear evidence that many of these viruses infect and replicate in zooplankton species, we posit that viral infection is likely responsible for a significant portion of unexplained non-consumptive mortality in this group. In turn, this infection affects food webs and alters biogeochemical cycling. In addition to the direct impacts of infection, zooplankton can vector economically devastating viruses of finfish and other crustaceans. The dissemination of these viruses is facilitated by the movement of zooplankton vertically between epi- and mesopelagic communities through seasonal and diel vertical migration (DVM) and across long distances in ship ballast water. The large potential impact of viruses on crustacean zooplankton emphasises the need to clearly establish the relationships between specific viruses and the zooplankton they infect and investigate disease and mortality for these host-virus pairs. Such data will enable investigations into a link between viral infection and seasonal dynamics of host populations. We are only beginning to uncover the diversity and function of viruses associated with crustacean zooplankton.
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Affiliation(s)
- Alastair J Roberts
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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5
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Zhou Y, Lian Y, Liu T, Jin X, Wang Z, Liu X, Zhou M, Jing D, Yin W, Feng J, Wang H, Zhang D. Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses. ENVIRONMENTAL RESEARCH 2023; 223:115083. [PMID: 36529333 DOI: 10.1016/j.envres.2022.115083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/05/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.
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Affiliation(s)
- Yaqian Zhou
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, PR China
| | - Ying Lian
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Tengxiang Liu
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Xian Jin
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Zhigang Wang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Xin Liu
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Mengling Zhou
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Dan Jing
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Weiwen Yin
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Jiaying Feng
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Heli Wang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, PR China.
| | - Daxin Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, PR China; School of Soil & Water Conservation, Beijing Forestry University, Beijing, 100083, PR China.
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6
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Patil MP, Jeong I, Woo HE, Kim JO, Lee DI, Kim K. Natural Variations in the Benthic Environment and Bacterial Communities of Coastal Sediments around Aquaculture Farms in South Korea. Indian J Microbiol 2023; 63:100-105. [PMID: 37188235 PMCID: PMC10172443 DOI: 10.1007/s12088-023-01067-8] [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: 11/22/2022] [Accepted: 02/18/2023] [Indexed: 03/02/2023] Open
Abstract
The aim of this study was to examine the possible seasonal variations in the nutrients (dissolved inorganic nitrogen-DIN and phosphorus) and benthic bacterial communities in marine aquaculture surrounding sediments. The study areas were Geoje, Tongyeong, and Changwon bays in Korea, which are famous for oysters (Magallana gigas), Halocynthia roretzi, and warty sea squirt (Styela clava) farming, respectively. The study sites included semi-enclosed coastal areas with a low seawater exchange rate. Subtidal sediment samples were collected seasonally from the area surrounding the aquacultures between April and December 2020. Seasonal variations in nutrients were observed, with the highest concentration of DIN in August. For phosphorus, site-specific variations were also observed. To investigate the variations in benthic bacterial communities, the advanced technique of 16S rRNA gene amplicon sequencing was applied, and the results indicated a seasonal variation pattern and predominance of Proteobacteria (59.39-69.73%), followed by Bacteroidetes (6.55-12.85%) and Chloroflexi (2.04-4.50%). This study provides a reference for future studies on natural variations in the benthic environment and bacterial communities in the areas surrounding aquacultures. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01067-8.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Ilwon Jeong
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
- School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Dae In Lee
- Marine Environmental Management Division, National Institute of Fisheries Science, Busan, 46083 South Korea
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
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7
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Medina-Contreras D, Arenas F. Are stable isotopes an efficient tool for tracking the effect of anthropogenic activities on mangrove food web structure and function? HYDROBIOLOGIA 2022; 850:1237-1249. [PMID: 36532364 PMCID: PMC9734736 DOI: 10.1007/s10750-022-05086-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Understanding and connecting the impact of anthropogenic activities on mangrove food webs is a research challenge. Has research on the subject been able to find answers using stable isotopes? The present opinion paper analyzed the utility of stable isotopes in tracing the impact of anthropogenic activities on mangrove food webs and if the research questions raised could be answered using these chemical markers. Representative research papers (16) focused on the use of stable isotopes (δ13C, δ15N, δ34S, δ2H, δD,206Pb/207Pb, and 208Pb/207Pb) to evaluate the effect of anthropogenic activities (Sewage discharge, timber harvesting-deforestation, metallurgical activities, hydrological disruption, aquaculture ponds, and urban development) on mangrove food webs were selected. Each article included at least one group of consumers (invertebrate or fish). Publications only focused on water quality or primary producers were not included. Most studies managed to determine the effect of the anthropogenic activities on the food web's stable isotope values. Based on the above, we concluded that these markers are an effective tool to determine affectation patterns on the structure and function of mangrove food webs. The results obtained herein facilitate the correct management of mangroves and their derived resources.
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Affiliation(s)
- Diana Medina-Contreras
- Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional S/N Col. Playa Palo de Santa Rita, Código Postal 23096 La Paz, B.C.S México
| | - Fernando Arenas
- Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional S/N Col. Playa Palo de Santa Rita, Código Postal 23096 La Paz, B.C.S México
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8
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Li S, Li L, Gao Q, Dong S, Shi S. Deep-sea cage culture altered microbial community composition in the sediments of the Yellow Sea Cold Water Mass. MARINE POLLUTION BULLETIN 2022; 183:114081. [PMID: 36067677 DOI: 10.1016/j.marpolbul.2022.114081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Environmental impacts of the first submersible salmonid culture cage, which was launched in the deep-sea of the Yellow Sea Cold Water Mass, were investigated. The temporal and spatial variations of several physicochemical parameters were observed in both the bottom and sediment pore water. Aquaculture activities decreased bacterial richness in the sediment. The dominant phyla Proteobacteria, Desulfobacterota and Acidobacteriota, accounted for 30.42 % of the total bacteria community. Principal component analysis indicated that the bacterial composition in December was different from that in the other three months, and the aquaculture activity affected the distribution of the sediment microbial community in June, August and April. Planctomycetes was selected as biomarkers in the aquaculture area by linear discriminant analysis effect size. Redundancy analysis showed that the biomarkers were positively correlated with temperature and the concentration of nitrite in June, and negatively correlated with the dissolved oxygen in August and April.
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Affiliation(s)
- Shuting Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Li Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266235, PR China.
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266235, PR China
| | - Shuanglin Dong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266235, PR China
| | - Shuai Shi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
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9
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Abstract
Microbial taxonomic marker gene studies using 16S rRNA gene amplicon sequencing provide an understanding of microbial community structure and diversity; however, it can be difficult to infer the functionality of microbes in the ecosystem from these data. Here, we show how to predict metabolism from phylogeny using the paprica pipeline. This approach allows resolution at the strain and species level for select regions on the prokaryotic phylogenetic tree and provides an estimate of gene and metabolic pathway abundance. For complete details on the use and execution of this protocol, please refer to Erazo and Bowman (2021).
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Affiliation(s)
- Natalia G. Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, USA
- Corresponding author
| | - Avishek Dutta
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Jeff S. Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, UC San Diego, La Jolla, CA, USA
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10
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Tavares TCL, Bezerra WM, Normando LRO, Rosado AS, Melo VMM. Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World. Front Microbiol 2021; 12:715991. [PMID: 34512595 PMCID: PMC8427804 DOI: 10.3389/fmicb.2021.715991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.
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Affiliation(s)
| | - Walderly Melgaço Bezerra
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
| | | | - Alexandre Soares Rosado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Vânia Maria Maciel Melo
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
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