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Das BK, Chakraborty HJ, Kumar V, Rout AK, Patra B, Das SK, Behera BK. Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles. Sci Rep 2024; 14:16218. [PMID: 39003345 PMCID: PMC11246455 DOI: 10.1038/s41598-024-67240-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.
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Affiliation(s)
- Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.
| | - Hirak Jyoti Chakraborty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Vikash Kumar
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Ajaya Kumar Rout
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Biswanath Patra
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Sanjoy Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Bijay Kumar Behera
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
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Mondal S, Biswas B, Chowdhury R, Sengupta R, Mandal A, Kotal HN, Giri CK, Ghosh A, Saha S, Begam MM, Mukherjee C, Das I, Basak SK, Mitra Ghosh M, Ray K. Estuarine mangrove niches select cultivable heterotrophic diazotrophs with diverse metabolic potentials-a prospective cross-dialog for functional diazotrophy. Front Microbiol 2024; 15:1324188. [PMID: 38873137 PMCID: PMC11174608 DOI: 10.3389/fmicb.2024.1324188] [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: 10/19/2023] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Biological nitrogen fixation (BNF), an unparalleled metabolic novelty among living microorganisms on earth, globally contributes ~88-101 Tg N year-1 to natural ecosystems, ~56% sourced from symbiotic BNF while ~22-45% derived from free-living nitrogen fixers (FLNF). The success of symbiotic BNF is largely dependent on its interaction with host-plant, however ubiquitous environmental heterotrophic FLNFs face many limitations in their immediate ecological niches to sustain unhindered BNF. The autotrophic FLNFs like cyanobacteria and oceanic heterotrophic diazotrophs have been well studied about their contrivances acclimated/adapted by these organisms to outwit the environmental constraints for functional diazotrophy. However, FLNF heterotrophs face more adversity in executing BNF under stressful estuarine/marine/aquatic habitats. Methods In this study a large-scale cultivation-dependent investigation was accomplished with 190 NCBI accessioned and 45 non-accessioned heterotrophic FLNF cultivable bacterial isolates (total 235) from halophilic estuarine intertidal mangrove niches of Indian Sundarbans, a Ramsar site and UNESCO proclaimed World Heritage Site. Assuming ~1% culturability of the microbial community, the respective niches were also studied for representing actual bacterial diversity via cultivation-independent next-generation sequencing of V3-V4 rRNA regions. Results Both the studies revealed a higher abundance of culturable Gammaproteobacteria followed by Firmicutes, the majority of 235 FLNFs studied belonging to these two classes. The FLNFs displayed comparable selection potential in media for free nitrogen fixers and iron-oxidizing bacteria, linking diazotrophy with iron oxidation, siderophore production, phosphorus solubilization, phosphorus uptake and accumulation as well as denitrification. Discussion This observation validated the hypothesis that under extreme estuarine mangrove niches, diazotrophs are naturally selected as a specialized multidimensional entity, to expedite BNF and survive. Earlier metagenome data from mangrove niches demonstrated a microbial metabolic coupling among C, N, P, S, and Fe cycling in mangrove sediments, as an adaptive trait, evident with the co-abundant respective functional genes, which corroborates our findings in cultivation mode for multiple interrelated metabolic potential facilitating BNF in a challenging intertidal mangrove environment.
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Affiliation(s)
- Sumana Mondal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Biswajit Biswas
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, India
| | - Rajojit Chowdhury
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Sree Chaitanya College, Habra, India
| | - Rudranil Sengupta
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anup Mandal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Hemendra Nath Kotal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Chayan Kumar Giri
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anjali Ghosh
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Subhajit Saha
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Mst Momtaj Begam
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Kalimpong College, Darjeeling, India
| | - Chandan Mukherjee
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- School of Biological and Life Sciences, Galgotias University, Greater Noida, India
| | - Ipsita Das
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | | | | | - Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
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Ramakodi MP. Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data. FEMS Microbiol Lett 2024; 371:fnae009. [PMID: 38305133 DOI: 10.1093/femsle/fnae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/16/2024] [Accepted: 01/31/2024] [Indexed: 02/03/2024] Open
Abstract
A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.
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Affiliation(s)
- Meganathan P Ramakodi
- CSIR-National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, CSIR-IICT Campus, Tarnaka, Hyderabad 500007, India
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Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE, Lee JN, Yeo ZY, Zahn G. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival. ENVIRONMENTAL MICROBIOME 2023; 18:47. [PMID: 37264467 DOI: 10.1186/s40793-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/01/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival. CONCLUSION The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.
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Affiliation(s)
- Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Trevor Millar
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lacee Bowen
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lauren Semon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Zhi Yi Yeo
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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Das I, Chanda A, Akhand A, Hazra S. Carbon Biogeochemistry of the Estuaries Adjoining the Indian Sundarbans Mangrove Ecosystem: A Review. Life (Basel) 2023; 13:life13040863. [PMID: 37109391 PMCID: PMC10141991 DOI: 10.3390/life13040863] [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: 02/09/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
The present study reviewed the carbon-biogeochemistry-related observations concerning CO2 and CH4 dynamics in the estuaries adjoining the Indian Sundarbans mangrove ecosystem. The review focused on the partial pressure of CO2 and CH4 [pCO2(water) and pCH4(water)] and air-water CO2 and CH4 fluxes and their physical, biogeochemical, and hydrological drivers. The riverine-freshwater-rich Hooghly estuary has always exhibited higher CO2 emissions than the marine-water-dominated Sundarbans estuaries. The mangrove sediment porewater and recirculated groundwater were rich in pCO2(water) and pCH4(water), enhancing their load in the adjacent estuaries. Freshwater-seawater admixing, photosynthetically active radiation, primary productivity, and porewater/groundwater input were the principal factors that regulated pCO2(water) and pCH4(water) and their fluxes. Higher chlorophyll-a concentrations, indicating higher primary production, led to the furnishing of more organic substrates that underwent anaerobic degradation to produce CH4 in the water column. The northern Bay of Bengal seawater had a high carbonate buffering capacity that reduced the pCO2(water) and water-to-air CO2 fluxes in the Sundarbans estuaries. Several authors traced the degradation of organic matter to DIC, mainly following the denitrification pathway (and pathways between aerobic respiration and carbonate dissolution). Overall, this review collated the significant findings on the carbon biogeochemistry of Sundarbans estuaries and discussed the areas that require attention in the future.
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Affiliation(s)
- Isha Das
- School of Oceanographic Studies, Jadavpur University, Kolkata 700032, India
| | - Abhra Chanda
- School of Oceanographic Studies, Jadavpur University, Kolkata 700032, India
| | - Anirban Akhand
- Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Sugata Hazra
- School of Oceanographic Studies, Jadavpur University, Kolkata 700032, India
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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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Kopprio GA, Martínez A, Fricke A, Hupfer M, Lara RJ, Graeve M, Gärdes A. Towards the outwelling hypothesis in a Patagonian estuary: First support from lipid markers and bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158670. [PMID: 36099952 DOI: 10.1016/j.scitotenv.2022.158670] [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: 06/24/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Biogeochemical markers in combination with bacterial community composition were studied at two contrasting stations at the Río Negro (RN) estuary to assess the outwelling hypothesis in the Argentinian Patagonia. Inorganic nutrients and dissolved organic matter were exported clearly during the last hours of the ebb at the station Wetland. Moreover, a considerable outwelling of polyunsaturated fatty acids (PUFA), particulates and microalgae was inferred by this combined approach. The exported 22:6(n-3) and 20:5(n-3) contributed very likely to sustain higher trophic levels in the coasts of the Southwest Atlantic. The stable isotopes did not evidence clearly the outwelling; nevertheless, the combination of δ13C with fatty acid bacterial markers indicated organic matter degradation in the sediments. The dominance of Desulfobacterales and Desulfuromonadales suggested sulphate reduction in the sediments, a key mechanism for nutrient outwelling in salt marshes. Marivivens and other Rhodobacterales (Alphaproteobacteria) in the suspended particulate matter were clear indicators of the nutrient outwelling. The colonization of particles according to the island biogeography theory was a good hypothesis to explain the lower bacterial biodiversity at the wetland. The copiotrophic conditions of the RN estuary and particularly at the wetland were deduced also by the dynamic of some Actinobacteria, Bacteroidia and Gammaproteobacteria. This high-resolution snapshot combining isotopic, lipid and bacterial markers offers key pioneer insights into biogeochemical and ecological processes of the RN estuary.
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Affiliation(s)
- Germán A Kopprio
- Robert Koch Institute, Berlin, Germany; Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany; Instituto Argentino de Oceanografía - Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina.
| | - Ana Martínez
- Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Anna Fricke
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Michael Hupfer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Rubén J Lara
- Instituto Argentino de Oceanografía - Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Martin Graeve
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Astrid Gärdes
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; University of Applied Sciences, Bremerhaven, Germany
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De D, Nayak T, Chowdhury S, Dhal PK. Insights of Host Physiological Parameters and Gut Microbiome of Indian Type 2 Diabetic Patients Visualized via Metagenomics and Machine Learning Approaches. Front Microbiol 2022; 13:914124. [PMID: 35923393 PMCID: PMC9340226 DOI: 10.3389/fmicb.2022.914124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Type 2 diabetes (T2D) is a serious public health issue and may also contribute to modification in the structure of the intestinal microbiota, implying a link between T2D and microbial inhabitants in the digestive tract. This work aimed to develop efficient models for identifying essential physiological markers for improved T2D classification using machine learning algorithms. Using amplicon metagenomic approaches, an effort has also been made to understand the alterations in core gut microbial members in Indian T2D patients with respect to their control normal glucose tolerance (NGT). Our data indicate the level of fasting blood glucose (FBG) and glycated hemoglobin (HbA1c) were the most useful physiological indicators while random forest and support vector machine with RBF Kernel were effective predictions models for identifications of T2D. The dominating gut microbial members Allopreotella, Rikenellaceae RC9 gut group, Haemophilus, Ruminococcus torques group, etc. in Indian T2D patients showed a strong association with both FBG and HbA1c. These members have been reported to have a crucial role in gut barrier breakdown, blood glucose, and lipopolysaccharide level escalation, or as biomarkers. While the dominant NGT microbiota (Akkermansia, Ligilactobacillus, Enterobacter, etc.) in the colon has been shown to influence inflammatory immune responses by acting as an anti-inflammatory agent and maintaining the gut barrier. The topology study of co-occurrence network analysis indicates that changes in network complexity in T2D lead to variations in the different gut microbial members compared to NGT. These studies provide a better understanding of the gut microbial diversity in Indian T2D patients and show the way for the development of valuable diagnostics strategies to improve the prediction and modulation of the T2D along with already established methods.
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Affiliation(s)
- Debjit De
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Subhankar Chowdhury
- Department of Endocrinology, Institute of Post Graduate Medical Education and Research (IPGMER) and SSKM Hospital, Kolkata, India
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
- *Correspondence: Paltu Kumar Dhal
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Chen Y, Wang H, Gao X, Li X, Dong S, Zhou H, Tan Z. COD/TN ratios shift the microbial community assembly of a pilot-scale shortcut nitrification-denitrification process for biogas slurry treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:49335-49345. [PMID: 35220533 DOI: 10.1007/s11356-022-19285-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
In this study, effects of carbon to nitrogen (COD/TN) ratios of biogas slurry on shortcut nitrification-denitrification in a pilot-scale integrated fixed film activated sludge (IFAS) system were investigated. Lowering the COD/TN ratio from 11.7 to 6.2 exerted a negative impact on shortcut nitrification-denitrification performance. Accordingly, the NH3-N and TN removal rates decreased from 94.4 to 91.2% and 92.3 to 85.9%, respectively. The dynamics of microbial assembly was analyzed by MiSeq sequencing, and the denitrifying functional genes were quantified by qPCR. The results showed that ammonia oxidizing bacteria and amoA gene were more abundant on the biofilm of oxic tank, indicating they play a key role in NH3-N removal. Autotrophic, endogenous, and fast heterotrophic kinetics denitrifiers were coexisted and enriched in the IFAS system with a decreasing of COD/TN ratio. TN removal was mainly affected by denitrifiers (including Arenimonas, Acidovorax, and Thaurea) harboring narG and nirS genes. Canonical correspondence analysis proved that COD/TN ratio was the most critical factor driving the succession of microbial community. Dissolved oxygen (DO) and pH were found positively correlated with denitrifiers at low COD/TN ratio conditions. As a result, NH3-N and TN removal were effectively enhanced when the DO level in the oxic tank of IFAS system was increased to 1.0-3.0 mg/L.
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Affiliation(s)
- Yangwu Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huan Wang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Xingdong Gao
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xin Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shiyang Dong
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Houzhen Zhou
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhouliang Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Quintanilla E, Rodrigues CF, Henriques I, Hilário A. Microbial Associations of Abyssal Gorgonians and Anemones (>4,000 m Depth) at the Clarion-Clipperton Fracture Zone. Front Microbiol 2022; 13:828469. [PMID: 35432234 PMCID: PMC9006452 DOI: 10.3389/fmicb.2022.828469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/18/2022] [Indexed: 01/04/2023] Open
Abstract
Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.
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Affiliation(s)
- Elena Quintanilla
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Clara F. Rodrigues
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal
| | - Ana Hilário
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Aveiro, Portugal
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Kunda P, Mukherjee A, Dhal PK. Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India. World J Microbiol Biotechnol 2021; 37:184. [PMID: 34580777 DOI: 10.1007/s11274-021-03153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.
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Affiliation(s)
- Pranamita Kunda
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India
- Agricultural and Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, Giridih, Jharkhand, India
| | - Abhishek Mukherjee
- Agricultural and Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, Giridih, Jharkhand, India
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India.
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Tyagi I, Tyagi K, Bhutiani R, Chandra K, Kumar V. Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42372-42386. [PMID: 33813698 DOI: 10.1007/s11356-021-13756-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
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Affiliation(s)
- Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Rakesh Bhutiani
- Department of Environmental Sciences, Gurukul Kangri Vishwavidyalaya, Haridwar, 249404, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, 700053, India.
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Zhang ZF, Pan J, Pan YP, Li M. Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments. mSystems 2021; 6:e0138120. [PMID: 34128692 PMCID: PMC8269266 DOI: 10.1128/msystems.01381-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.
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Affiliation(s)
- Zhi-Feng Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Mamangkey J, Suryanto D, Munir E, Mustopa AZ, Sibero MT, Mendes LW, Hartanto A, Taniwan S, Ek-Ramos MJ, Harahap A, Verma A, Trihatmoko E, Putranto WS, Pardosi L, Rudia LOAP. Isolation and enzyme bioprospection of bacteria associated to Bruguiera cylindrica, a mangrove plant of North Sumatra, Indonesia. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00617. [PMID: 34026573 PMCID: PMC8121877 DOI: 10.1016/j.btre.2021.e00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/05/2020] [Accepted: 04/08/2021] [Indexed: 11/30/2022]
Abstract
Mangrove-associated bacteria are of industrial interest due to their diverse and versatile enzyme properties. This study investigates the culturable bacteria from a wide range of habitat in a Bruguiera cylindrica mangrove ecosystem in North Sumatra. Screening of extracellular hydrolytic enzymes showed multiple potential traits in amylase, cellulase, chitinase, phosphatase, protease, and urease production by bacterial isolates. Molecular identification based on 16S rDNA region of a potential strain, Vibrio alginolyticus Jme3-20 is then reported as a newly proteolytic agent. The strain also showed a stable growth under salinity (NaCl) stress with considerable phosphate solubilization activities. Protease activity was enhanced by optimizing the 0.5 % (w/v) sucrose and soy peptone in the fermentation medium. SDS-PAGE and zymogram analysis showed the presence of a 35-kDa MW protease. Hence, our study revealed important insights into the bacterial diversity and activity in mangrove ecosystems, evidencing the importance of microbial exploration in this ecosystem.
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Affiliation(s)
- Jendri Mamangkey
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Dwi Suryanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Erman Munir
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Biotechnology, Indonesian Institute of Science, Jl. Raya Bogor Km. 46, Cibinong, West Java, 16911, Indonesia
| | - Mada Triandala Sibero
- Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Jl. Prof. Soedarto S.H., Tembalang, Semarang, 50275, Central Java, Indonesia
- Natural Product Laboratory, Integrated Laboratory for Research and Services, Universitas Diponegoro, Jl. Prof. Soedarto S.H., Tembalang, Semarang, 50275, Central Java, Indonesia
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Adrian Hartanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Steven Taniwan
- Department of Agricultural Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Maria Julissa Ek-Ramos
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, Mexico
| | - Arman Harahap
- Faculty of Teacher Training and Education, Universitas Labuhanbatu, Rantauprapat, Indonesia
| | - Amit Verma
- Department of Biochemistry, College of Basic Science and Humanities, SD Agricultural University, Gujarat, 385506, India
| | - Edy Trihatmoko
- Department of Geography, Universitas Negeri Semarang, Semarang, 50229, Indonesia
| | | | - Lukas Pardosi
- Biology Study Program, Faculty of Agriculture, Universitas Timor, Kefamenanu, 85613, Indonesia
| | - La Ode Adi Parman Rudia
- Faculty of Mathematics and Natural Sciences, Halu Oleo University, Jalan H.E.A. Mokodompit, Kampus Baru, Kampus Hijau Bumi Tridharma Anduonohu, Kendari, 93232, Indonesia
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15
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16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya. PLoS One 2021; 16:e0248485. [PMID: 33755699 PMCID: PMC7987175 DOI: 10.1371/journal.pone.0248485] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/28/2021] [Indexed: 12/30/2022] Open
Abstract
Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.
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Erazo NG, Bowman JS. Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent. iScience 2021; 24:102204. [PMID: 33786421 PMCID: PMC7994199 DOI: 10.1016/j.isci.2021.102204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/25/2020] [Accepted: 02/15/2021] [Indexed: 02/05/2023] Open
Abstract
Mangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem health. In this study, we used 16S rRNA gene analysis, metabolic inference, nutrient concentrations, and δ13C and δ15N isotopes to evaluate the impact of land use change on near-shore biogeochemical cycles and microbial community structures within mangrove-dominated estuaries. Samples in close proximity to active shrimp aquaculture were high in NH4+, NO3− NO2−, and PO43−; lower in microbial community and metabolic diversity; and dominated by putative nitrifiers, denitrifies, and sulfur-oxidizing bacteria. Near intact mangrove forests we observed the presence of potential nitrogen fixers of the genus Calothrix and order Rhizobiales. We identified possible indicators of aquaculture effluents such as Pseudomonas balearica, Ponitmonas salivibrio, family Chromatiaceae, and genus Arcobacter. These results highlight the sensitivity of the estuarine-mangrove microbial community, and their ecosystem functions, to land use changes. In near-intact mangrove forests, we observed the presence of nitrogen fixers Calothrix could play a role in increasing nitrogen inventories via nitrogen fixation Disturbed sites were correlated with increased nitrogen and reduction in diversity Disturbed sites were dominated by nitrifiers, denitrifies, and sulfur-oxidizing bacteria
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Affiliation(s)
- Natalia G Erazo
- Scripps Institution of Oceanography, UC San Diego, 8622 Kennel Way, La Jolla, CA 92037, USA.,Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, USA
| | - Jeff S Bowman
- Scripps Institution of Oceanography, UC San Diego, 8622 Kennel Way, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, UC San Diego, La Jolla, CA, USA.,Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, USA
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17
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Ramakodi MP. Effect of Amplicon Sequencing Depth in Environmental Microbiome Research. Curr Microbiol 2021; 78:1026-1033. [PMID: 33537885 DOI: 10.1007/s00284-021-02345-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
Abstract
Amplicon sequencing approach is commonly employed in microbiome studies and sequencing depth is considered as a major factor influencing the outcome of data analyses. As of now, the effect of amplicon sequencing depth in environmental microbiome analyses is not explicitly illustrated. In this study, microbiome data of nine aquatic samples from Sundarbans mangrove region, obtained from SRA, were analyzed to explain the influence of sequencing depth variation in environmental microbiome data analyses. Briefly, four groups based on number of reads (NOR) were created comprising of, total NOR, 75 k, 50 k and 25 k, followed by data analyses. The results showed that the observed ASVs among four groups were significantly different (P value 1.094e-06). The Bray-Curtis dissimilarity analysis showed differences in microbiome composition and also, each group exhibited slightly different core-microbiome structure. Importantly, the variation in sequencing depth was found to affect the predictions of environmental drivers associated with microbiome composition. Thus, this study emphasizes that the microbiome data are compositional and the NOR in the data could affect the microbial composition. In summary, this study demonstrates the consequences of sequencing depth variation on microbiome data analyses and suggests the researchers to take proper cautions to avoid misleading results due to sequencing depth variation.
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Affiliation(s)
- Meganathan P Ramakodi
- Hyderabad Zonal Centre, CSIR-National Environmental Engineering Research Institute (NEERI), IICT Campus, Tarnaka, Hyderabad, Telangana, 500007, India.
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Kopprio GA, Neogi SB, Rashid H, Alonso C, Yamasaki S, Koch BP, Gärdes A, Lara RJ. Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers. Front Microbiol 2020; 11:594. [PMID: 32351470 PMCID: PMC7174592 DOI: 10.3389/fmicb.2020.00594] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 01/23/2023] Open
Abstract
The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.
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Affiliation(s)
- Germán A Kopprio
- Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Tropical Marine Microbiology, Leibniz Centre for Tropical Marine Research, Bremen, Germany.,Marine Biogeochemistry, Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Sucharit B Neogi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Harunur Rashid
- Department of Fisheries Management, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Systems, Centro Universitario Región Este, Universidad de la República, Rocha, Uruguay
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Boris P Koch
- Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Rubén J Lara
- Marine Biogeochemistry, Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Sur, Bahía Blanca, Argentina
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