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Deng W, Chen S, Chen S, Xing B, Chan Z, Zhang Y, Chen B, Chen G. Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems. Front Microbiol 2024; 15:1449545. [PMID: 39206368 PMCID: PMC11350616 DOI: 10.3389/fmicb.2024.1449545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass. Methods We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China. Results Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities. Conclusion The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.
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Affiliation(s)
- Wenchao Deng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Shunyang Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
- Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China
| | - Shiquan Chen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Bingpeng Xing
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Zhuhua Chan
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bin Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
- Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
- Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China
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Qiu Z, He S, Lian CA, Qiao X, Zhang Q, Yao C, Mu R, Wang L, Cao XA, Yan Y, Yu K. Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments. NPJ Biofilms Microbiomes 2024; 10:62. [PMID: 39069527 DOI: 10.1038/s41522-024-00537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Shuhang He
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qing Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ciqin Yao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Li Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiao-Ai Cao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China.
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Wang A, He M, Liu H, Ouyang W, Liu X, Li Q, Lin C, Liu X. Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122715. [PMID: 37821043 DOI: 10.1016/j.envpol.2023.122715] [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: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.
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Affiliation(s)
- Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Huiji Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China; Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, China.
| | - Xinyi Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Qin Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Veloso S, Amouroux D, Lanceleur L, Cagnon C, Monperrus M, Deborde J, Laureau CC, Duran R. Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130858. [PMID: 36706488 DOI: 10.1016/j.jhazmat.2023.130858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ13C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.
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Affiliation(s)
- Sandrine Veloso
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Laurent Lanceleur
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Mathilde Monperrus
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Jonathan Deborde
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France; Ifremer, LITTORAL, Laboratoire Environnement Ressources des Pertuis Charentais, F-17390 La Tremblade, France
| | - Cristiana Cravo Laureau
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France.
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Hafez T, Ortiz-Zarragoitia M, Cagnon C, Cravo-Laureau C, Duran R. Cold sediment microbial community shifts in response to crude oil water-accommodated fraction with or without dispersant: a microcosm study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44640-44656. [PMID: 36694068 DOI: 10.1007/s11356-023-25264-6] [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: 08/05/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
In cold environments, the low temperature slows down microbial metabolisms, such as the biodegradation processes of hydrocarbons, which are often stimulated by the addition of dispersants in oil spill disasters. In this study, we investigated the effects of hydrocarbon water-accommodated fraction (WAF) prepared with and without dispersant on benthic microbial communities in a microcosm experiment in which hydrocarbon removal was observed. Both WAFs contained similar polycyclic aromatic hydrocarbon (PAH) content. The microcosm experiment, set up with either pristine or contaminated sediments, was conducted for 21 days at 4 °C under WAF and WAF + dispersant conditions. The behavior of bacterial communities in response to WAF and WAF + dispersant was examined at both DNA and RNA levels, revealing the effect of WAF and WAF + dispersant on the resident and active communities respectively. The contaminated sediment showed less taxa responsive to the addition of both WAF and WAF + dispersant than the pristine sediment, indicating the legacy effect by the presence hydrocarbon-degrading and dispersant-resistant taxa inhabiting the contaminated sediment.
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Affiliation(s)
- Tamer Hafez
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country, Areatza Z/G, 48620, Plentzia (Bizkaia), Basque Country, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France
| | | | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Pau, France.
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Zhang Z, Sun J, Gong X, Wang C, Wang H. Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture. WATER RESEARCH 2023; 230:119593. [PMID: 36642028 DOI: 10.1016/j.watres.2023.119593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/24/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.
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Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Moreira VA, Cravo-Laureau C, de Carvalho ACB, Baldy A, Bidone ED, Sabadini-Santos E, Duran R. Microbial indicators along a metallic contamination gradient in tropical coastal sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130244. [PMID: 36327839 DOI: 10.1016/j.jhazmat.2022.130244] [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: 07/30/2022] [Revised: 10/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.
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Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Alice Baldy
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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Châtillon E, Duran R, Rigal F, Cagnon C, Cébron A, Cravo-Laureau C. New insights into microbial community coalescence in the land-sea continuum. Microbiol Res 2022; 267:127259. [PMID: 36436444 DOI: 10.1016/j.micres.2022.127259] [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: 05/13/2022] [Revised: 10/30/2022] [Accepted: 11/13/2022] [Indexed: 11/23/2022]
Abstract
The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.
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Affiliation(s)
- Elise Châtillon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - François Rigal
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
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Moreira VA, Cravo-Laureau C, Borges de Carvalho AC, Baldy A, Bidone ED, Sabadini-Santos E, Duran R. Microbial community metabolic alterations and resistance to metals and antibiotics driven by chronic exposition to multiple pollutants in a highly impacted tropical coastal bay. CHEMOSPHERE 2022; 307:135928. [PMID: 35944693 DOI: 10.1016/j.chemosphere.2022.135928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/23/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities from Sepetiba Bay (SB, Rio de Janeiro, Brazil), characterized by 16S rRNA gene (V4-V5 region) sequencing analysis, were found to be correlated with the metallic contamination factor and the Quality Ratio (QR) index. Consistently, the predicted function of microbial communities, obtained with Tax4Fun2, showed that the functional patterns in SB internal sector under the highest anthropogenic pressure were different from that observed in the external sector with the lowest contamination level. Signal transduction, cellular community, membrane transport, and energy metabolism were among the KEGG pathways favored by metallic contamination in the SB internal sector, while lipid metabolism, transcription, and translation were among the pathways favored in the SB external sector. Noteworthy, the relative proportions of KEGG pathways and genes associated with metallic homeostasis showed significant differences according to the SB sectors, consistently with the ecological risk classification (QR index) of sediments. The functional prediction approach is an economically viable alternative and presents an overview of the main pathways/genes favored in the SB microbiota exposed to long-term pollution. In contrast, the microgAMBI, ecological status index based on bacterial community composition, was not consistent with the metallic contamination of SB, suggesting that this index requires improvements to be applied in tropical areas. Our study also revealed a strong correlation between metal resistance genes (MRG) and antibiotic resistance genes (ARG), indicating that MRG and ARG are co-selected by the metallic contamination prevailing in SB.
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Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil; Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Alice Baldy
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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10
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Lyu L, He Y, Dong C, Li G, Wei G, Shao Z, Zhang S. Characterization of chlorinated paraffin-degrading bacteria from marine estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129699. [PMID: 35963094 DOI: 10.1016/j.jhazmat.2022.129699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
This study explored chlorinated paraffin (CP)-degrading bacteria from the marine environment. Aequorivita, Denitromonas, Parvibaculum, Pseudomonas and Ignavibacterium were selected as the dominant genera after enrichment with chlorinated paraffin 52 (CP52) as the sole carbon source. Eight strains were identified as CP degraders, including Pseudomonas sp. NG6 and NF2, Erythrobacter sp. NG3, Castellaniella sp. NF6, Kordiimonas sp. NE3, Zunongwangia sp. NF12, Zunongwangia sp. NH1 and Chryseoglobus sp. NF13, and their degradation efficiencies ranged from 6.4% to 19.0%. In addition to Pseudomonas, the other six genera of bacteria were first reported to have the degradation ability of CPs. Bacterial categories, carbon-chain lengths and chlorination degrees were three crucial factors affecting the degradation efficiencies of CPs, with their influential ability of chlorinated degrees > bacterial categories > carbon-chain lengths. CP degradation can be performed by producing chlorinated alcohols, chlorinated olefins, dechlorinated alcohols and lower chlorinated CPs. This study will provide valuable information on CP biotransformation and targeted bacterial resources for studying the transformation processes of specific CPs in marine environments.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yufei He
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chunming Dong
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guizhen Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Guangshan Wei
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361005, China; Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Xiamen 361005, China; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China.
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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11
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Jaouani R, Mouneyrac C, Châtel A, Amiard F, Dellali M, Beyrem H, Michelet A, Lagarde F. Seasonal and spatial distribution of microplastics in sediments by FTIR imaging throughout a continuum lake - lagoon- beach from the Tunisian coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156519. [PMID: 35690197 DOI: 10.1016/j.scitotenv.2022.156519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Plastics pollution in marine environment has become an issue of increasing scientific concern. This work aims to study the temporal and spatial distribution of plastics in sediments from three different Tunisian ecosystems; Rimel Beach, Bizerta lagoon and Ichkeul lake. Sediment sampling was conducted in surface (2 cm) and depth (15 cm) during spring, summer and winter. Plastics debris were separated by size fractions: macro (>5 mm), meso (1-5 mm) and microplastics (<1 mm) to optimize the time necessary for their characterisation. Macroplastics and mesoplastics were identified using an IR Attenuated total reflectance (ATR) and microplastics with Imaging Fourier transform infrared spectroscopy (FTIR) spectroscopy after an optimized extraction protocol. Results indicate that, the lowest contamination degree with macroplastics was recorded in Ichkeul lake, 2 macro debris/m2 (marine protected area, national parc of Ichkeul). Mesoparticles were only detected in lagoon of Bizerte in large quantities (4900 item/kg of sediment in surface and 680 item/kg of sediment in depth) and were identified principally as paint products. For microplastics, the repartition was quite homogeneous between the three sites with an average abundance was 130.55 ± 65.61 items/kg for all seasons. The variations of microplastics abundances on the three sites could not be clearly related to the seasons. Whereas the polymer characterisation in the surface and depth sediments of the three studied areas were principally due to eight types of polymers (PVC, PET, PP, PE PS, Polyamide (PA) and polymeric methyl methacrylate (PMMA)) as reported in many other studies, surprisingly all MPs recovered in the study were smaller than 300 μm, >70 % being fragments. This study brings new results as regards to the state of plastic contamination in Tunisian coast and shows the importance of investigating different ecosystems in such studies.
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Affiliation(s)
- Rihab Jaouani
- Institut des Molécules et Matériaux du Mans (IMMM, UMR CNRS 6283), Le Mans Université, Avenue Olivier Messiaen, F-72085 Le Mans, France; Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BIOSSE), Université Catholique de l'Ouest, F-49000 Angers, France; Laboratoire de biosurveillance de l'environnement, Faculté des Sciences de Bizerte, Zarzouna 7021, Tunisie.
| | - Catherine Mouneyrac
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BIOSSE), Université Catholique de l'Ouest, F-49000 Angers, France
| | - Amélie Châtel
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BIOSSE), Université Catholique de l'Ouest, F-49000 Angers, France
| | - Frédéric Amiard
- Institut des Molécules et Matériaux du Mans (IMMM, UMR CNRS 6283), Le Mans Université, Avenue Olivier Messiaen, F-72085 Le Mans, France
| | - Mohamed Dellali
- Laboratoire de biosurveillance de l'environnement, Faculté des Sciences de Bizerte, Zarzouna 7021, Tunisie
| | - Hamouda Beyrem
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BIOSSE), Université Catholique de l'Ouest, F-49000 Angers, France
| | - Alexandre Michelet
- Perkin Elmer, ZA Courtaboeuf, 12, 14 Avenue de la Baltique, 91140 Villebon sur Yvette, France
| | - Fabienne Lagarde
- Institut des Molécules et Matériaux du Mans (IMMM, UMR CNRS 6283), Le Mans Université, Avenue Olivier Messiaen, F-72085 Le Mans, France
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12
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Hafez T, Ortiz-Zarragoitia M, Cagnon C, Cravo-Laureau C, Duran R. Legacy and dispersant influence microbial community dynamics in cold seawater contaminated by crude oil water accommodated fractions. ENVIRONMENTAL RESEARCH 2022; 212:113467. [PMID: 35588780 DOI: 10.1016/j.envres.2022.113467] [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: 02/21/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Dispersants, used for combating oil spills, increase hydrocarbon bioavailability promoting their biodegradation. Oil weathering process introduces harmful soluble hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), into the water column, resulting in water-accommodated fraction (WAF). The presence of dispersants can influence the weathering process by increasing PAHs solubility, toxicity and biodegradability. However, little is known on how dispersants affect microbial communities and their degradation capacities, especially in cold environment where low temperature decreases microbial activity and thus hydrocarbon degradation. Here, we investigated the microbial community dynamics in cold water contaminated by WAF prepared from crude oil with or without a commercial dispersant (Finasol OSR52). The WAFs, prepared with Naphthenic North Atlantic crude oil, were used to contaminate seawater from Norwegian cold sites, one oil-contaminated and the other pristine. The WAF-contaminated seawaters were maintained in microcosms at 4 °C for 21 days. The content of PAHs and microbial compositions (16S rRNA gene sequencing) were determined at days 0, 7, 14 and 21. In addition, the 96 h toxicity assay with adult Acartia tonsa revealed WAFs toxicity at days 0 and 21. The toxicity of WAF mixtures, with and without dispersant, against Acartia tonsa was reduced during the experiment, but PAHs removal was not increased. The water from the oil-contaminated site showed the highest PAHs removal revealing legacy effect (presence of microorganisms adapted to PAHs). Additionally, our results reveal: i) microbial community plasticity allowing the adaptation to the presence of PAHs and dispersant, ii) specific bacteria taxa probably involved in PAHs degradation, and iii) dispersants shape the microbial communities dynamics by stimulating potential dispersant-degrading taxa, such as Fusibacter. Thus, our results provide valuable insights on the role of microbial community in determining the fate of water-solubilized hydrocarbon in cold environment while questioning the role of dispersant used for fighting oil spill.
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Affiliation(s)
- Tamer Hafez
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU) University of the Basque Country, Areatza z/g, 48620, Plentzia, Bizkaia, Basque Country, Spain; Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France
| | - Maren Ortiz-Zarragoitia
- CBET Research Group, Department of Zoology and Cell Biology, Faculty of Science and Technology and Research Center for Marine Biology and Biotechnology (PiE-UPV/EHU) University of the Basque Country, Areatza z/g, 48620, Plentzia, Bizkaia, Basque Country, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France
| | | | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S/UPPA, IPREM5254, 64000, Pau, France.
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13
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Chen Y, Zheng M, Qiu Y, Wang H, Zhang H, Tao Q, Luo H, Zhang Z. Organic Matter and Total Nitrogen Lead to Different Microbial Community Structure in Sediments Between Lagoon and Surrounding Areas by Regulating Xenococcus Abundance. Front Microbiol 2022; 13:859921. [PMID: 35531298 PMCID: PMC9069056 DOI: 10.3389/fmicb.2022.859921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Coastal lagoon is an important productive ecosystem on the Earth. In this study, we compared microbial community in the sediments between lagoon and surrounding areas, and explored mechanism for the variation of microbial community. As a result, the sediment of surrounding area showed significantly higher organic matter and total nitrogen than that of the lagoon. The linear regression analysis revealed that organic matter and total nitrogen are positively correlated with Xenococcus. Bacterial and fungal PCoA1 showed significantly positive relationships with the relative abundance of Xenococcus, indicating that Xenococcus affects the bacterial and fungal community in the sediments of both the lagoon and surrounding area. ANOSIM analysis demonstrated that there were significant differences in bacterial and fungal community structure in the sediments between the lagoon and surrounding areas. Therefore, organic matter and total nitrogen affect the microbial community structure in the sediments of lagoon and surrounding areas by regulating the abundance of Xenococcus.
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Affiliation(s)
- Yonggan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, China
| | - Minjing Zheng
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, China
| | - Yue Qiu
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Hong Wang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Haonan Zhang
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Qiongren Tao
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Hongwei Luo
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Zhenhua Zhang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, China
- *Correspondence: Zhenhua Zhang,
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14
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Xu M, Xu RZ, Shen XX, Gao P, Xue ZX, Huang DC, Jin GQ, Li C, Cao JS. The response of sediment microbial communities to temporal and site-specific variations of pollution in interconnected aquaculture pond and ditch systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150498. [PMID: 34563908 DOI: 10.1016/j.scitotenv.2021.150498] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Sediment microbial communities play critical roles in the health of fish and the biogeochemical cycling of elements in aquaculture ecosystems. However, the response of microbial communities to temporal and spatial variations in interconnected aquaculture pond and ditch systems remains unclear. In this study, 61 sediment bacterial samples were collected over one year from 11 sites (including five ponds and six ditches) in a 30-year-old fish aquaculture farm. The 16S rRNA approach was used to determine the relative abundances of microbial communities in the sediment samples. The relationships among nutrients, heavy metals, and abundant microorganisms were analyzed. Our results showed that Proteobacteria, Bacteroides and Chloroflexi were the predominant phyla in the sediments of aquaculture pond, with average abundances of 36.33%, 18.60%, and 14.58%, respectively. The microbial diversity in aquaculture sediments was negatively correlated (P < 0.05) with the concentrations of total nitrogen and total phosphorus in sediments, indicating that the microbial diversity is highly associated with the remediation of nutrients in sediments. The sediment samples with high similarities were discovered by the t-distributed stochastic neighbor embedding (t-SNE) method. The site-specific correlations between specific microorganisms and heavy metals were explored. The network analysis revealed that the microbial diversities in aquaculture ponds were more stable than that in aquaculture ditches. The network analysis also illustrated that the microbial genera with low relative abundances may become key groups of microbial communities in sediment ecosystems. Our work deepens the understanding of the relationships between microbial communities and the spatiotemporal characteristics of surface water and sediments in aquaculture farms.
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Affiliation(s)
- Ming Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Run-Ze Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Xiao-Xiao Shen
- College of Agricultural science and Engineering, Hohai University, Nanjing 210098, China
| | - Peng Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Zhao-Xia Xue
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - De-Chun Huang
- Collaborative Innovation Center of World Water Valley and Water Ecological Civilization, Jiangning, Nanjing, PR China
| | - Guang-Qiu Jin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China.
| | - Chao Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jia-Shun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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15
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Bourhane Z, Lanzén A, Cagnon C, Ben Said O, Mahmoudi E, Coulon F, Atai E, Borja A, Cravo-Laureau C, Duran R. Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126789. [PMID: 34365235 DOI: 10.1016/j.jhazmat.2021.126789] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/21/2023]
Abstract
Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.
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Affiliation(s)
- Zeina Bourhane
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, E-48011 Bilbao, Spain
| | - Christine Cagnon
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France
| | - Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, LBE, Tunisia
| | - Ezzeddine Mahmoudi
- Laboratoire de Biosurveillance de l'Environnement, Faculté des Sciences de Bizerte, LBE, Tunisia
| | - Frederic Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield MK430AL, UK
| | - Emmanuel Atai
- Cranfield University, School of Water, Energy and Environment, Cranfield MK430AL, UK
| | - Angel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain; King Abdulaziz University, Faculty of Marine Sciences, Jeddah, Saudi Arabia
| | | | - Robert Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS 5254, Pau, France.
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16
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Liu S, Wang P, Wang C, Chen J, Wang X, Hu B, Yuan Q. Ecological insights into the disturbances in bacterioplankton communities due to emerging organic pollutants from different anthropogenic activities along an urban river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148973. [PMID: 34274679 DOI: 10.1016/j.scitotenv.2021.148973] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Emerging organic pollutants (EOPs) in urban rivers have raised concerns regarding their eco-toxicological effects. However, the bacterioplankton community disturbances caused by EOPs in urban rivers and the associated ecological mechanisms remain unclear. This study provided profiles of the spatial distribution of a bacterioplankton community disturbed by human activity along an urban river. The results showed that EOP concentration and composition were differently distributed in residential and industrial areas, which significantly influenced bacterioplankton community structure. Based on redundancy analysis, parabens (methylparaben and propylparaben) were the major factors driving bacterioplankton community changes. Parabens inhibited gram-positive bacteria and promoted oxidative stress-tolerant bacteria in the river ecosystem. Parabens also disturbed ecological processes of bacterioplankton community assembly, shifting from a homogeneous selection (consistent selection pressure under similar environmental condition) to stochastic processes (random changes due to birth, death, immigration, and emigration) with changing in paraben concentrations. Heterogeneous selection was predicted to dominate microbial community assembly with paraben concentration changes exceeding 61.6 ng/L, which could deteriorate the river ecosystem. Furthermore, specific bacterial genera were identified as potential bioindicators to assess the condition of EOP contaminants in the river. Overall, this study highlights significant disturbances in bacterioplankton communities by EOPs at environmental concentrations, and our results could facilitate generation of appropriate management strategies aimed at EOPs in urban rivers.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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17
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Mazière C, Agogué H, Cravo-Laureau C, Cagnon C, Lanneluc I, Sablé S, Fruitier-Arnaudin I, Dupuy C, Duran R. New insights in bacterial and eukaryotic diversity of microbial mats inhabiting exploited and abandoned salterns at the Ré Island (France). Microbiol Res 2021; 252:126854. [PMID: 34454310 DOI: 10.1016/j.micres.2021.126854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/09/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023]
Abstract
In order to understand the effect of human practices on microbial mats organisation, the study aimed to investigate the biodiversity within microbial mats from exploited and abandoned salterns. Despite several attempts, archaeal 16S rRNA gene fragment sequences were not obtained, indicating that microbial mats were probably dominated by Bacteria with very low abundance of Archaea (< 1%). Thus, the study compared the bacterial and meiofaunal diversity of microbial mats from abandoned and exploited salterns. The higher salinity (101 ± 3.7 psu vs. 51.1 ± 0.7 psu; Welch t-test p < 0.05) of the exploited site maintained lower bacterial diversity in comparison to the abandoned site where the salinity gradient was no longer maintained. However, the microbial mats exhibited similar bacterial class composition while the eukaryotic diversity was significantly higher in the exploited saltern. The abandoned saltern was dominated by sulfate-reducing bacteria and Nematoda, while the exploited saltern was characterized by the presence of halophilic bacteria belonging to Marinobacter, Salinivibrio and Rhodohalobacter genera, and the larger abundance of Hypotrichia (ciliates). Such bacterial and eukaryotic diversity difference might be explained by human actions for salt recovery in exploited salterns such as scraping the surface of microbial mat and increasing salinity renewing the microbial mat each year. Such action decreases the bacterial diversity changing the food web structure that favour the presence of a larger diversity of eukaryotic organisms. Our study provides new insights on microbial mat communities inhabiting salterns, especially the consequences of abandoning saltern exploitation.
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Affiliation(s)
- Camille Mazière
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France; UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Hélène Agogué
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | | | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Isabelle Lanneluc
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Sophie Sablé
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Ingrid Fruitier-Arnaudin
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Christine Dupuy
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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Moreira VA, Carvalho ACBD, Fontana LF, Bidone ED, Sabadini-Santos E. Applying enzymatic biomarkers of the in situ microbial community to assess the sediment risk from Sepetiba Bay (Brazil). MARINE POLLUTION BULLETIN 2021; 169:112547. [PMID: 34118576 DOI: 10.1016/j.marpolbul.2021.112547] [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: 12/12/2020] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
The Quality Ratio (QR) index was applied in Sepetiba Bay to integrate geochemical and microbiological parameters of the in situ microbial community in order to classify the ecological risk of sediments. Total concentrations (C) of Hg, Cd, As, Pb, Cr, Cu and Zn (indicators of the mixture of contaminants) were determined at 26 stations and at a background area (C0) to calculate the contamination factor (CF = C/C0) and the degree of contamination (ΣCF). Enzymatic biomarkers of energy production into cell (dehydrogenase - DHA) and hydrolase of organic matter outside the cell (esterases - EST) were determined. The QR, a function of the microbial term (DHA/EST) and the geochemical term (TOC × ΣCF/fine-grained content), was able to segregate stations into the internal sector (east of the bay with the largest continental contributions) and the external sector (west of the bay), proving its accessibility (low-cost and fast) and efficiency for assessing ecological risk.
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Affiliation(s)
- Vanessa Almeida Moreira
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil.
| | - Angelo Cezar Borges de Carvalho
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Luiz Francisco Fontana
- Universidade Federal do Estado do Rio de Janeiro - UNIRIO, Laboratório de Micropaleontologia - LABMICRO, Av. Pasteur 458, s. 500, Urca, Rio de Janeiro CEP 22290-240, RJ, Brazil
| | - Edison Dausacker Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24020-150, Brazil
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Becarelli S, Chicca I, La China S, Siracusa G, Bardi A, Gullo M, Petroni G, Levin DB, Di Gregorio S. A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons. Front Microbiol 2021; 12:647373. [PMID: 34177829 PMCID: PMC8221241 DOI: 10.3389/fmicb.2021.647373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.
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Affiliation(s)
- Simone Becarelli
- Department of Biology, University of Pisa, Pisa, Italy.,BD Biodigressioni, Pisa, Italy
| | - Ilaria Chicca
- Department of Biology, University of Pisa, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - Alessandra Bardi
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | - Maria Gullo
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - David Bernard Levin
- BD Biodigressioni, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
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Liu TT, Yang H. Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu. FEMS Microbiol Ecol 2020; 96:5815072. [PMID: 32239216 DOI: 10.1093/femsec/fiaa059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/29/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities play crucial roles in the biogeochemical cycle of the surface sediments of freshwater lakes, but previous studies on bacterial community changes in this habitat have mostly been based on the total bacterial community (DNA level), while an exploration of the active microbiota at the RNA level has been lacking. Herein, we analysed the bacterial communities in the surface sediments of Lake Taihu at the DNA and RNA levels. Using MiSeq sequencing and real-time quantification, we found that the sequencing and quantitative results obtained at the RNA level compared with the DNA level were more accurate in responding to the spatiotemporal dynamic changes of the bacterial community. Although both sequencing methods indicated that Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Bacteroidetes and Actinobacteria were the dominant phyla, the co-occurrence network at the RNA level could better reflect the close relationship between microorganisms in the surface sediment. Additionally, further analysis showed that Prochlorococcus and Microcystis were the most relevant and dominant genera of Cyanobacteria in the total and active bacterial communities, respectively; our results also demonstrated that the analysis of Cyanobacteria-related groups at the RNA level was more 'informative'.
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Affiliation(s)
- Tong-Tong Liu
- State Key Laboratory of Microbial metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Hong Yang
- State Key Laboratory of Microbial metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
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