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Duan X, Li J, Li Y, Xu Y, Chai H, Chao S. Removal, accumulation, and micro-ecosystem impacts of typical POPs in bioretention systems with different media: A runoff infiltration study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174278. [PMID: 38925397 DOI: 10.1016/j.scitotenv.2024.174278] [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: 03/27/2024] [Revised: 05/31/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Bioretention systems prove effective in purifying common persistent organic pollutants (POPs) found in urban rainfall runoff. However, the response process of the microecosystem in the media becomes unclear when POPs accumulate in bioretention systems. In this study, we constructed bioretention systems and conducted simulated rainfall tests to elucidate the evolution of micro-ecosystems within the media under typical POPs pollution. The results showed all POPs in runoff were effectively removed by surface adsorption in different media, with load reduction rates of >85 % for PCBs and OCPs and > 80 % for PAHs. Bioretention soil media (BSM) + water treatment residuals (WTR) media exhibited greater stability in response to POPs contamination compared to BSM and pure soil (PS) media. POPs contamination significantly impacted the microecology of the media, reducing the number of microbial species by >52.6 % and reducing diversity by >27.6 % at the peak of their accumulation. Enzyme activities were significantly inhibited, with reductions ranging from 44.42 % to 60.33 %. Meanwhile, in terms of ecological functions, the metabolism of exogenous carbon sources significantly increased (p < 0.05), while nitrogen and sulfur cycling processes were suppressed. Microbial diversity and enzyme activities showed some recovery during the dissipation of POPs but did not reach the level observed before the experiment. Dominant bacterial species and abundance changed significantly during the experiment. Proteobacteria were suppressed, but remained the dominant phylum (all relative abundances >41 %). Bacteroidota, Firmicutes, and Actinobacteria adapted well to the contamination. Pseudomonas, a typical POPs-degrading bacterium, displayed a positive correlation between its relative abundance and POPs levels (mean > 10 %). Additionally, POPs and media properties, including TN and pH, are crucial factors that collectively shape the microbial community. This study provides new insights into the impacts of POPs contamination on the microbial community of the media, which can improve media design and operation efficiency.
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Affiliation(s)
- Xiaolong Duan
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Jiake Li
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China.
| | - Yajiao Li
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Yefeng Xu
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Senhao Chao
- State Key Laboratory of Eco-Hydraulics in the Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
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Duan X, Li J, Li Y, Xu Y, Chao S, Shi Y. Accumulation of typical persistent organic pollutants and heavy metals in bioretention facilities: Distribution, risk assessment, and microbial community impact. ENVIRONMENTAL RESEARCH 2024; 252:119107. [PMID: 38723989 DOI: 10.1016/j.envres.2024.119107] [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: 02/27/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Bioretention facilities have proven highly effective in removing pollutants from runoff. However, there is a concerning paucity of research on the contamination characteristics and associated risks posed by refractory pollutants in these facilities following long-term operation. This research focuses on the distribution, sources, microbial community impact, and human health risks of pollutants in eight bioretention facilities that have been operational for 5-11 years. The results showed that the distribution of Cu, Zn, and Cd was closely related to anti-seepage measures. PAHs, PCBs, and OCPs primarily accumulated in the surface, with concentrations ranging from 7.42 to 20.34 mg/kg, 31.8-77.3 μg/kg, and 60.5-163.6 μg/kg, respectively. Their concentrations inversely correlate with the depth of the media. Although the majority of contaminants remained below their respective risk thresholds, their concentrations typically exceeded those of background soil values, indicating an enrichment phenomenon. Source analysis revealed that PAHs primarily originate from oil combustion, PCBs were linked to their related industrial products, DDTs had their main sources in technical DDx and residues from the use of dicofol, while HCHs were traced back to historical residues from agricultural activities. Microbial α-diversity (Chao 1 and Shannon) decreased by 8.3-23.4% and 0.8-4.4%, respectively, in different facilities after long-term operation. The most dominant microbial phylum in the facilities was Proteobacteria (all relative abundances >48%). The total relative abundance of dominant genera was 6.7-34.3% higher than the control site, and Pseudomonas, a typical POPs-heavy metal degrading bacterium, had the highest relative abundance (>1.2%). Cu, Zn, and Cd present no non-carcinogenic risks and have low potential ecological risks. However, the lifetime cancer risk for PAHs is 10-6 ∼10-4 in most facilities and is of concern. The cancer risk for PCBs is acceptable, while OCPs pose a low cancer risk only for children.
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Affiliation(s)
- Xiaolong Duan
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Jiake Li
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China.
| | - Yajiao Li
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Yefeng Xu
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Senhao Chao
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Yanting Shi
- School of Architecture and Civil Engineering, Xi'an University of Science and Technology, Xi'an 710054, China
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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
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Botti A, Musmeci E, Negroni A, Capuozzo R, Fava F, Biagi E, Zanaroli G. Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165485. [PMID: 37442469 DOI: 10.1016/j.scitotenv.2023.165485] [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: 04/21/2023] [Revised: 06/23/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.
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Affiliation(s)
- Alberto Botti
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Eliana Musmeci
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Andrea Negroni
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Rosaria Capuozzo
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Fabio Fava
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Elena Biagi
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy.
| | - Giulio Zanaroli
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
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Rellegadla S, Prajapat G, Jain S, Agrawal A. Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12673-3. [PMID: 37428189 DOI: 10.1007/s00253-023-12673-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/03/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.
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Affiliation(s)
- Sandeep Rellegadla
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India
- Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Ganshyam Prajapat
- The Energy and Resources Institute (TERI), Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
| | - Shikha Jain
- Enercosm Pvt. Ltd., Jaipur, Rajasthan, 302019, India
| | - Akhil Agrawal
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Zhang Q, Gao M, Sun X, Wang Y, Yuan C, Sun H. Nationwide distribution of polycyclic aromatic hydrocarbons in soil of China and the association with bacterial community. J Environ Sci (China) 2023; 128:1-11. [PMID: 36801025 DOI: 10.1016/j.jes.2022.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 06/18/2023]
Abstract
Soil contamination by polycyclic aromatic hydrocarbons (PAHs) has raised great environmental concerns. However, the information on national wide distribution of PAHs in soil as well as their effect on soil bacterial community are limited. In this study, 16 PAHs were measured in 94 soil samples collected across China. The total concentration of 16 PAHs (∑PAHs) in soil ranged from 74.0 to 17,657 ng/g (dry weight basis), with a median value of 200 ng/g. Pyrene was the major soil PAH, with a median concentration of 71.3 ng/g. Soil samples from Northeast China had a higher median concentration of ∑PAHs (1,961 ng/g) than those from other regions. Petroleum emission and wood/grass/coal combustion were potential sources for soil PAHs based on diagnostic ratios and positive matrix factors analysis. A nonnegligible ecological risk (hazard quotients > 1) was found in over 20% of soil samples analyzed and the highest median total HQs value (8.53) was found in soils from Northeast China. The effect of PAHs on bacterial abundance, α-diversity, and β-diversity was limited in the soils surveyed. Nevertheless, the relative abundance of some members in genera Gaiella, Nocardioides, and Clostridium was significantly correlated with the concentrations of some PAHs. Especially, the bacterium Gaiella Occulta showed potential in indicating soil contamination by PAH, which is worth further exploration.
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Affiliation(s)
- Qiuyue Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Meng Gao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xinhui Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Chaolei Yuan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Xu Y, Teng Y, Wang X, Ren W, Zhao L, Luo Y, Christie P, Greening C. Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil. ENVIRONMENT INTERNATIONAL 2023; 176:107962. [PMID: 37196568 DOI: 10.1016/j.envint.2023.107962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of 13C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Sun H, Chen Q, Qu C, Tian Y, Song J, Liu Z, Guo J. Occurrence of OCPs & PCBs and their effects on multitrophic biological communities in riparian groundwater of the Beiluo River, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114713. [PMID: 36870171 DOI: 10.1016/j.ecoenv.2023.114713] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Persistent Organic Pollutants (POPs) may exert adverse effects on human and ecosystem health. However, as an ecologically fragile zone with strong interaction between river and groundwater, the POPs pollution in the riparian zone has received little attention. The goal of this research is to examine the concentrations, spatial distribution, potential ecological risks, and biological effects of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in the riparian groundwater of the Beiluo River, China. The results showed that the pollution level and ecological risk of OCPs in riparian groundwater of the Beiluo River were higher than PCBs. The presence of PCBs (Penta-CBs, Hexa-CBs) and CHLs, respectively, may have reduced the richness of bacteria (Firmicutes) and fungi (Ascomycota). Furthermore, the richness and Shannon's diversity index of algae (Chrysophyceae and Bacillariophyta) decreased, which could be linked to the presence of OCPs (DDTs, CHLs, DRINs), and PCBs (Penta-CBs, Hepta-CBs), while for metazoans (Arthropoda) the tendency was reversed, presumably as a result of SULPHs pollution. In the network analysis, core species belonging to bacteria (Proteobacteria), fungi (Ascomycota), and algae (Bacillariophyta) played essential roles in maintaining community function. Burkholderiaceae and Bradyrhizobium can be considered biological indicators of PCBs pollution in the Beiluo River. Note that the core species of interaction network, playing a fundamental role in community interactions, are strongly affected by POPs pollutants. This work provides insights into the functions of multitrophic biological communities in maintaining the stability of riparian ecosystems through the response of core species to riparian groundwater POPs contamination.
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Affiliation(s)
- Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Qiqi Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Chengkai Qu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Yulu Tian
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Ziteng Liu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
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10
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Hillyer KE, Raes E, Bissett A, Beale DJ. Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120857. [PMID: 36513173 DOI: 10.1016/j.envpol.2022.120857] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO2 fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.
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Affiliation(s)
- Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Eric Raes
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia; Flourishing Oceans, Minderoo Foundation, Broadway, Nedlands, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia.
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11
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Zárate A, Molina V, Valdés J, Icaza G, Vega SE, Castillo A, Ugalde JA, Dorador C. Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline. Front Microbiol 2023; 13:1020491. [PMID: 36726571 PMCID: PMC9885135 DOI: 10.3389/fmicb.2022.1020491] [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: 08/16/2022] [Accepted: 12/31/2022] [Indexed: 01/17/2023] Open
Abstract
Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Biotecnología en Ambientes Extremos, Centro de Excelencia en Medicina Traslacional, Universidad de la Frontera, Temuco, Chile,*Correspondence: Ana Zárate, ✉
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile,Verónica Molina, ✉
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Facultad de Ciencias del Mar y de Recursos Biológicos, Instituto de Ciencias Naturales A. von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | | | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados del Maule, Vicerrectoría de Investigación de Investigación y Posgrado, Universidad Católica del Maule, Campus San Miguel, Talca, Chile,J’EAI CHARISMA (IRD-France, UMNG-Colombia, UA-Chile, UCM-Chile, UCH-Chile, IGP-Peru, UPCH-Peru) and Nucleo Milenio UPWELL, Concepción, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile,Cristina Dorador, ✉
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12
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Mukherji S, Imchen M, Mondal S, Bhattacharyya A, Siddhardha B, Kumavath R, Ghosh A. Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban. CHEMOSPHERE 2022; 309:136806. [PMID: 36220439 DOI: 10.1016/j.chemosphere.2022.136806] [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: 08/27/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Sangita Mondal
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anish Bhattacharyya
- School of Biological Sciences, Division of Genomics and Evolution, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periye P.O., Kasaragod, Kerala, 671316, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014 India.
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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13
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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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14
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Fonseca A, Espinoza C, Nielsen LP, Marshall IPG, Gallardo VA. Bacterial community of sediments under the Eastern Boundary Current System shows high microdiversity and a latitudinal spatial pattern. Front Microbiol 2022; 13:1016418. [PMID: 36246233 PMCID: PMC9561620 DOI: 10.3389/fmicb.2022.1016418] [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: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The sediments under the Oxygen Minimum Zone of the Eastern Boundary Current System (EBCS) along Central-South Peru and North-Central Chile, known as Humboldt Sulfuretum (HS), is an organic-matter-rich benthic habitat, where bacteria process a variety of sulfur compounds under low dissolved-oxygen concentrations, and high sulfide and nitrate levels. This study addressed the structure, diversity and spatial distribution patterns of the HS bacterial community along Northern and South-Central Chile using 16S rRNA gene amplicon sequencing. The results show that during the field study period, the community was dominated by sulfur-associated bacteria. Indeed, the most abundant phylum was Desulfobacterota, while Sva0081 sedimentary group, of the family Desulfosarcinaceae (the most abundant family), which includes sulfate-reducer and H2 scavenger bacteria, was the most abundant genus. Furthermore, a spatial pattern was unveiled along the study area to which the family Desulfobulbaceae contributed the most to the spatial variance, which encompasses 42 uncharacterized amplicon sequence variants (ASVs), three assigned to Ca. Electrothrix and two to Desulfobulbus. Moreover, a very high microdiversity was found, since only 3.7% of the ASVs were shared among localities, reflecting a highly diverse and mature community.
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Affiliation(s)
- Alexis Fonseca
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
- *Correspondence: Alexis Fonseca,
| | - Carola Espinoza
- Department of Oceanography, University of Concepción, Concepción, Chile
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Victor A. Gallardo
- Department of Oceanography, University of Concepción, Concepción, Chile
- Victor A. Gallardo,
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15
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Xu P, Chen X, Li K, Meng R, Pu Y. Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12039. [PMID: 36231339 PMCID: PMC9565075 DOI: 10.3390/ijerph191912039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.
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Affiliation(s)
- Pan Xu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaoxiao Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Kai Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Rong Meng
- The Husbandry Technology Promotion Center of Inner Mongolia, Hohhot 010051, China
| | - Yuewu Pu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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16
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Harilanto AF, Christelle D, Philippe C, Bettarel Y. Viral life strategies in a heavily anthropized tropical lagoon. FEMS Microbiol Lett 2022; 369:6698716. [DOI: 10.1093/femsle/fnac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ecological traits of aquatic microorganisms have been poorly investigated in tropical latitudes, especially in lagoons, which are often subjected to strong anthropogenic influence, conducive to microbial development. In this study, we examined the abundance of both viral and bacterial communities, as well as their interactions (lytic and lysogenic infections) in the water and sediment of seven main stations of the Ebrié Lagoon (Ivory Coast) with contrasting levels of eutrophication. The highest bacterial and viral concentrations in both planktonic and benthic samples were found in the most eutrophicated stations, where viral lytic infections also exhibited their highest values. Conversely, the highest fractions of inducible lysogens were measured in the most oligotrophic stations, suggesting that these two main viral life strategies are mutually exclusive in this lagoon. Our findings also revealed the importance that nutrients (especially ammonium) play as drivers of the interactions between viruses and their bacterial hosts in tropical lagoons.
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Affiliation(s)
- Andrianjakarivony Felana Harilanto
- Microbes, Evolution, Phylogeny, and Infection (MEФI) , IHU - Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille , France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO) , 163 avenue de Luminy 13009, Marseille , France
| | - Desnues Christelle
- Microbes, Evolution, Phylogeny, and Infection (MEФI) , IHU - Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille , France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO) , 163 avenue de Luminy 13009, Marseille , France
| | - Cecchi Philippe
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Univ. Montpellier , CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier , France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Univ. Montpellier , CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier , France
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17
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Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
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18
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Cai S, Zhou S, Cheng J, Wang Q, Dai Y. Heavy metals speciation and distribution of microbial communities in sediments from the abandoned Mo-Ni polymetallic mines, southwest of China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:35350-35364. [PMID: 35060049 DOI: 10.1007/s11356-022-18697-y] [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: 08/16/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Chemical fractions of heavy metals (Mo, Ni, Cu, Zn, Fe, Mn, Pb, Cd, and Cr) and compositions of bacteria and fungi in surface sediments from the Mo-Ni polymetallic mine area were analyzed. The results indicated that the mean concentrations of Mo, Ni, Cu, Zn, and Cd were higher than their background values. The mean percentage of Cr in residual fraction was much higher than that of other heavy metals. Mo, Cu, Zn, Fe, and Pb were mainly associated with oxidizable fraction. The dominant proportions of Mn and Cd were found in exchangeable fraction with mean percentages of 93.46% and 54.50%, respectively. According to RAC classification and potential ecological risk index (PERI), the Cd with high bioavailability had a very high environmental risk. The MisSeq sequencing results of bacteria and fungi revealed that microbial communities discrepantly respond to different sampling sites. The most abundant phylum of bacteria and fungi were Proteobacteria and Ascomycota, respectively. The bioavailable heavy metals including Mo-B, Pb-B, and Cd-B were recognized to have important influences on both dominant bacterial and fungal communities. The present study manifested that the bioavailability of heavy metal is very important to assess the potential environmental risk and plays a key role in shaping microbial structure.
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Affiliation(s)
- Shenwen Cai
- College of Resources and Environment, Zunyi Normal University, Zunyi, People's Republic of China.
| | - Shaoqi Zhou
- College of Resources and Environment Engineering, Guizhou University, Guiyang, People's Republic of China
| | - Junwei Cheng
- College of Resources and Environment, Zunyi Normal University, Zunyi, People's Republic of China
| | - Qinghe Wang
- College of Resources and Environment, Zunyi Normal University, Zunyi, People's Republic of China
| | - Ying Dai
- College of Resources and Environment, Zunyi Normal University, Zunyi, People's Republic of China
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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20
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Gas Hydrate-Based Heavy Metal Ion Removal from Industrial Wastewater: A Review. WATER 2022. [DOI: 10.3390/w14071171] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Innovating methods for treating industrial wastewater containing heavy metals frequently incorporate toxicity-reduction technologies to keep up with regulatory requirements. This article reviews the latest advances, benefits, opportunities and drawbacks of several heavy metal removal treatment systems for industrial wastewater in detail. The conventional physicochemical techniques used in heavy metal removal processes with their advantages and limitations are evaluated. A particular focus is given to innovative gas hydrate-based separation of heavy metals from industrial effluent with their comparison, advantages and limitations in the direction of commercialization as well as prospective remedies. Clathrate hydrate-based removal is a potential technology for the treatment of metal-contaminated wastewater. In this work, a complete assessment of the literature is addressed based on removal efficiency, enrichment factor and water recovery, utilizing the gas hydrate approach. It is shown that gas hydrate-based treatment technology may be the way of the future for water management purposes, as the industrial treated water may be utilized for process industries, watering, irrigation and be safe to drink.
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21
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Liu J, Liu Y, Dong W, Li J, Yu S, Wang J, Zuo R. Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics. CHEMOSPHERE 2022; 293:133509. [PMID: 34995620 DOI: 10.1016/j.chemosphere.2021.133509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.
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Affiliation(s)
- Jiayou Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yun Liu
- South China Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, Guangzhou, 510655, China
| | - Weihong Dong
- Key Laboratory of Groundwater Resources and Environments, Ministry of Education, Jilin University, Changchun, Jilin, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, Jilin, 130021, China
| | - Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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22
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Huang Z, Liu Y, Dai H, Gui D, Hu BX, Zhang J. Spatial distribution and source apportionment of polycyclic aromatic hydrocarbons in typical oasis soil of north-western China and the bacterial community response. ENVIRONMENTAL RESEARCH 2022; 204:112401. [PMID: 34801544 DOI: 10.1016/j.envres.2021.112401] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/01/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Oases environments in oases to be sensitive to anthropogenic activity because of ecological fragility. Polycyclic aromatic hydrocarbon (PAH) pollution resulting from anthropogenic activity leads to ecological degradation in oases. To examine the impact of anthropogenic activity on the oasis ecological environment, the present study focused on the spatial distribution and source apportionment of soil PAHs and bacterial community responses in typical oases in Xinjiang, China. The results showed that the soil PAH level were higher in the city centres of Urumqi (9-6340 μg kg-1), Aksu (8-957 μg kg-1) and Korla (8-1103 μg kg-1) and lower in the centres of Hotan city (11-268 μg kg-1) and Qira county (7-163 μg kg-1). Source apportionment suggested that gasoline emissions, diesel emissions, vehicle emissions, coal combustion, coke processing and biomass burning were the sources of soil PAHs. The integrated lifetime cancer risks of soil PAH exceeding the guideline safety values (10-6) recommended by United States Environmental Protection Agency. The ingestion and dermal exposure pathways caused the greatest health risk (contribution ≤82%). Additionally, in the soil with low PAH concentrations, the richness and evenness of the soil bacterial community were great, and the molecular ecological network (MEN) structure was complex. Among populations, Proteobacteria and Actinobacteria (relative abundance ≥17%) are the main dominant species in the bacterial communities and the keystone species in the MEN.
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Affiliation(s)
- Zhenyu Huang
- Department of Ecology and Institute of Hydrobiology, College of Life Science and Technology, Jinan University, 510632, Guangzhou, China
| | - Yi Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, China
| | - Heng Dai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, 430078, Wuhan, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, NO. 68 Jincheng Street, East Lake High-Tech Development Zone, 430078, Wuhan, China.
| | - Dongwei Gui
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, China
| | - Bill X Hu
- School of Water Conservancy and Environment, University of Jinan, 250022, Jinan, Shandong, China.
| | - Jin Zhang
- Department of Ecology and Institute of Hydrobiology, College of Life Science and Technology, Jinan University, 510632, Guangzhou, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011, Urumqi, China
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23
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Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [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: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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24
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Orel N, Fadeev E, Klun K, Ličer M, Tinta T, Turk V. Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem. Front Microbiol 2022; 12:765091. [PMID: 35111137 PMCID: PMC8801744 DOI: 10.3389/fmicb.2021.765091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 01/18/2023] Open
Abstract
Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- *Correspondence: Neža Orel,
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Matjaž Ličer
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Office for Meteorology, Hydrology and Oceanography, Slovenian Environment Agency, Ljubljana, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
- Tinkara Tinta,
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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25
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Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality. Sci Rep 2022; 12:80. [PMID: 34997015 PMCID: PMC8742047 DOI: 10.1038/s41598-021-03949-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/07/2021] [Indexed: 01/22/2023] Open
Abstract
The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.
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26
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Tong T, Li R, Chai M, Wang Q, Yang Y, Xie S. Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148486. [PMID: 34465064 DOI: 10.1016/j.scitotenv.2021.148486] [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: 04/05/2021] [Revised: 05/31/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.
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Affiliation(s)
- Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ruili Li
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
| | - Minwei Chai
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Qian Wang
- School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environmental and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
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27
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Birrer SC, Wemheuer F, Dafforn KA, Gribben PE, Steinberg PD, Simpson SL, Potts J, Scanes P, Doblin MA, Johnston EL. Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities. Front Microbiol 2021; 12:661177. [PMID: 34690940 PMCID: PMC8531495 DOI: 10.3389/fmicb.2021.661177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour, Australia, using 16S rRNA gene sequencing. Sediment samples were collected monthly during the Austral summer-autumn 2014 at increasing distance from a large storm drain in each channel and embayment. Bacterial communities differed significantly between sites that varied in proximity to storm drains, with a gradient of change apparent for sites within embayments. We explored this pattern for embayment sites with analysis of RNA-Seq gene expression patterns and found higher expression of multiple genes involved in bacterial stress response far from storm drains, suggesting that bacterial communities close to storm drains may be more tolerant of localised anthropogenic stressors. Several bacterial groups also differed close to and far from storm drains, suggesting their potential utility as bioindicators to monitor contaminants in estuarine sediments. Overall, our study provides useful insights into changes in the composition and functioning of benthic bacterial communities as a result of multiple anthropogenic stressors in differing hydrological conditions.
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Affiliation(s)
- Simone C. Birrer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Franziska Wemheuer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Katherine A. Dafforn
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Paul E. Gribben
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Peter D. Steinberg
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Stuart L. Simpson
- CSIRO Land and Water, Centre for Environmental Contaminants Research, Canberra, ACT, Australia
| | - Jaimie Potts
- Coastal Waters Unit, Science Division, NSW Department of Planning, Industry and Environment, Sydney, NSW, Australia
| | - Peter Scanes
- Coastal Waters Unit, Science Division, NSW Department of Planning, Industry and Environment, Sydney, NSW, Australia
| | - Martina A. Doblin
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Climate Change Cluster, University of Technology, Sydney, NSW, Australia
| | - Emma L. Johnston
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
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Zárate A, Dorador C, Valdés J, Molina V, Icaza G, Pacheco AS, Castillo A. Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117281. [PMID: 33992902 DOI: 10.1016/j.envpol.2021.117281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas Mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Humedales Del Caribe Colombiano, Universidad Del Atlántico, Barranquilla, Colombia.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias Del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Instituto de Ciencias Naturales A. von Humboldt, Facultad de Ciencias Del Mar y de Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile; HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Aldo S Pacheco
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados Del Maule. Vicerrectoría de Investigación de Investigación y Posgrado. Universidad Católica Del Maule, Campus San Miguel. Talca, Chile
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Basili M, Campanelli A, Frapiccini E, Luna GM, Quero GM. Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117672. [PMID: 34380232 DOI: 10.1016/j.envpol.2021.117672] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The transport of a variety of pollutants from agricultural, industrial and urbanised areas makes rivers major contributors to the contamination of coastal marine environments. Too little is known of their role in carrying pathogens to the coast. We used DNA-based metabarcoding data to describe the microbial community composition in seawater and sediment collected in front of the estuary of the Tronto, the Chienti and the Esino, three Italian rivers with different pollution levels that empty into the north-central Adriatic Sea, and to detect and measure within these communities the relative abundance of microbial pollutants, including traditional faecal indicators and alternative faecal and sewage-associated pollutants. We then applied the FORENSIC algorithm to distinguish human from non-human sources of microbial pollution and FAPROTAX to map prokaryotic clades to established metabolic or other ecologically relevant functions. Finally, we searched the dataset for other common pathogenic taxa. Seawater and sediment contained numerous potentially pathogenic bacteria, mainly faecal and sewage-associated. The samples collected in front of the Tronto estuary showed the highest level of contamination, likely sewage-associated. The pathogenic signature showed a weak but positive correlation with some nutrients and strong correlations with some polycyclic aromatic hydrocarbons. This study confirms that rivers transport pathogenic bacteria to the coastal sea and highlights the value of expanding the use of HTS data, source tracking and functional identification tools to detect microbial pollutants and identify their sources with a view to gaining a better understanding of the pathways of sewage-associated discharges to the sea.
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Affiliation(s)
- Marco Basili
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Alessandra Campanelli
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Emanuela Frapiccini
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Gian Marco Luna
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Grazia Marina Quero
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
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Rajeev M, Sushmitha TJ, Aravindraja C, Toleti SR, Pandian SK. Thermal discharge-induced seawater warming alters richness, community composition and interactions of bacterioplankton assemblages in a coastal ecosystem. Sci Rep 2021; 11:17341. [PMID: 34462511 PMCID: PMC8405676 DOI: 10.1038/s41598-021-96969-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/10/2021] [Indexed: 02/01/2023] Open
Abstract
Despite accumulating evidence on the impact of global climate warming on marine microbes, how increasing seawater temperature influences the marine bacterioplankton communities is elusive. As temperature gradient created by thermal discharges provides a suitable in situ model to study the influence of warming on marine microorganisms, surface seawater were sampled consecutively for one year (September-2016 to August-2017) from the control (unimpacted) and thermal discharge-impacted areas of a coastal power plant, located in India. The bacterioplankton community differences between control (n = 16) and thermal discharge-impacted (n = 26) areas, as investigated using 16S rRNA gene tag sequencing revealed reduced richness and varied community composition at thermal discharge-impacted areas. The relative proportion of Proteobacteria was found to be higher (average ~ 15%) while, Bacteroidetes was lower (average ~ 10%) at thermal discharge-impacted areas. Intriguingly, thermal discharge-impacted areas were overrepresented by several potential pathogenic bacterial genera (e.g. Pseudomonas, Acinetobacter, Sulfitobacter, Vibrio) and other native marine genera (e.g. Marinobacter, Pseudoalteromonas, Alteromonas, Pseudidiomarina, Halomonas). Further, co-occurrence networks demonstrated that complexity and connectivity of networks were altered in warming condition. Altogether, results indicated that increasing temperature has a profound impact on marine bacterioplankton richness, community composition, and inter-species interactions. Our findings are immensely important in forecasting the consequences of future climate changes especially, ocean warming on marine microbiota.
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Affiliation(s)
- Meora Rajeev
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, 630 003, Tamil Nadu, India
| | - T J Sushmitha
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, 630 003, Tamil Nadu, India
| | | | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, 603 102, Tamil Nadu, India
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, 630 003, Tamil Nadu, India.
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Bergsveinson J, Lawrence J, Schebel A, Wasserscheid J, Roy J, Conly FM, Sanschagrin S, Korber DR, Tremblay J, Greer CW, Droppo IG. Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River. Can J Microbiol 2021; 67:813-826. [PMID: 34171204 DOI: 10.1139/cjm-2021-0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilm, suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the level of phyla, different niche communities were highly similar to one another and across locations. However, there were significant differences in the abundance of specific genera amongst different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though "suspended load" communities collected by any means remained stably diverse across locations. Though there was influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.
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Affiliation(s)
- Jordyn Bergsveinson
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - John Lawrence
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Alixandra Schebel
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Jessica Wasserscheid
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Julie Roy
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - F Malcom Conly
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Sylvie Sanschagrin
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Darren R Korber
- University of Saskatchewan, Department of Food and Bioproduct Science, Saskatoon, Saskatchewan, Canada;
| | - Julien Tremblay
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Charles W Greer
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Ian G Droppo
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, Ontario, Canada;
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Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
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Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy). Microorganisms 2021; 9:microorganisms9040859. [PMID: 33923677 PMCID: PMC8072921 DOI: 10.3390/microorganisms9040859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022] Open
Abstract
Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.
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Metals Alter Membership but Not Diversity of a Headwater Stream Microbiome. Appl Environ Microbiol 2021; 87:AEM.02635-20. [PMID: 33452033 DOI: 10.1128/aem.02635-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 11/20/2022] Open
Abstract
Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a two-by-two factorial design: (i) location (upstream or downstream of contaminating tributary), and (ii) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.IMPORTANCE Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study, in combination with previously published work on this same ecosystem, are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health, which currently does not include assessments of the microbiome.
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Dell'Anno F, Rastelli E, Tangherlini M, Corinaldesi C, Sansone C, Brunet C, Balzano S, Ianora A, Musco L, Montereali MR, Dell'Anno A. Highly Contaminated Marine Sediments Can Host Rare Bacterial Taxa Potentially Useful for Bioremediation. Front Microbiol 2021; 12:584850. [PMID: 33732217 PMCID: PMC7956957 DOI: 10.3389/fmicb.2021.584850] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/02/2021] [Indexed: 01/04/2023] Open
Abstract
Coastal areas impacted by high anthropogenic pressures typically display sediment contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). Microbial-based bioremediation represents a promising strategy for sediment reclamation, yet it frequently fails due to poor knowledge of the diversity and dynamics of the autochthonous microbial assemblages and to the inhibition of the target microbes in the contaminated matrix. In the present study, we used an integrated approach including a detailed environmental characterization, high-throughput sequencing and culturing to identify autochthonous bacteria with bioremediation potential in the sediments of Bagnoli-Coroglio (Gulf of Naples, Mediterranean Sea), a coastal area highly contaminated by PAHs, aliphatic hydrocarbons and HMs. The analysis of the benthic prokaryotic diversity showed that the distribution of the dominant taxon (Gammaproteobacteria) was mainly influenced by PAHs, As, and Cd concentrations. The other abundant taxa (including Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, NB1-j, Desulfobacterota, and Myxococcota) were mainly driven by sediment grain size and by Cu and Cr concentrations, while the rare taxa (i.e., each contributing <1%) by As and aliphatic hydrocarbons concentrations and by sediment redox potential. These results suggest a differential response of bacterial taxa to environmental features and chemical contamination and those different bacterial groups may be inhibited or promoted by different contaminants. This hypothesis was confirmed by culturing and isolating 80 bacterial strains using media highly enriched in PAHs, only nine of which were contextually resistant to high HM concentrations. Such resistant isolates represented novel Gammaproteobacteria strains affiliated to Vibrio, Pseudoalteromonas, and Agarivorans, which were only scarcely represented in their original assemblages. These findings suggest that rare but culturable bacterial strains resistant/tolerant to high levels of mixed contaminants can be promising candidates useful for the reclamation by bioaugmentation strategies of marine sediments that are highly contaminated with PAHs and HMs.
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Affiliation(s)
| | | | | | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
| | | | | | | | | | - Luigi Musco
- Stazione Zoologica Anton Dohrn, Naples, Italy.,Laboratory of Marine Biology and Zoology, DiSTeBA, University of Salento, Lecce, Italy
| | - Maria Rita Montereali
- ENEA - Agenzia per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile, Rome, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Coclet C, Garnier C, D’Onofrio S, Durrieu G, Pasero E, Le Poupon C, Omanović D, Mullot JU, Misson B, Briand JF. Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area. Front Microbiol 2021; 12:589948. [PMID: 33679628 PMCID: PMC7933014 DOI: 10.3389/fmicb.2021.589948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/29/2021] [Indexed: 12/25/2022] Open
Abstract
Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.
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Affiliation(s)
- Clément Coclet
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Sébastien D’Onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Gaël Durrieu
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Emilie Pasero
- Microbia Environnement Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Dario Omanović
- Division for Marine and Environmental Research, Ruðer Bošković Institute, Zagreb, Croatia
| | | | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
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Jokanović S, Kajan K, Perović S, Ivanić M, Mačić V, Orlić S. Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116383. [PMID: 33387780 DOI: 10.1016/j.envpol.2020.116383] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.
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Affiliation(s)
- Sandra Jokanović
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Katarina Kajan
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia
| | - Svetlana Perović
- Faculty of Science and Mathematics, University of Montenegro, 81 000, Podgorica, Montenegro
| | - Maja Ivanić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10 000, Zagreb, Croatia
| | - Vesna Mačić
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia.
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Rajeev M, Sushmitha TJ, Aravindraja C, Toleti SR, Pandian SK. Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111808. [PMID: 33360289 DOI: 10.1016/j.ecoenv.2020.111808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/12/2023]
Abstract
One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.
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Affiliation(s)
- Meora Rajeev
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - T J Sushmitha
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | | | - Subba Rao Toleti
- Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam 603 102, Tamil Nadu, India
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Sibanda T, Ramganesh S. Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations. Arch Microbiol 2021; 203:1753-1766. [PMID: 33474608 PMCID: PMC7816837 DOI: 10.1007/s00203-020-02165-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/25/2020] [Accepted: 12/27/2020] [Indexed: 11/21/2022]
Abstract
Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.
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Affiliation(s)
- Timothy Sibanda
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia.
| | - Selvarajan Ramganesh
- Department of Environmental Sciences, UNISA Florida Campus, Johannesburg, RSA, South Africa
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Nazina TN, Bidzhieva SK, Grouzdev DS, Sokolova DS, Tourova TP, Parshina SN, Avtukh AN, Poltaraus AB, Talybly AK. Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia. Microorganisms 2020; 8:E1967. [PMID: 33322329 PMCID: PMC7763609 DOI: 10.3390/microorganisms8121967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 02/05/2023] Open
Abstract
A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13-55 °C (optimum 35 °C), with 0-3.0% (w/v) NaCl (optimum 0-2.0%) and in the pH range of 6.7-8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Sofiya N. Parshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Azhdar K. Talybly
- Institute of Microbiology of the National Academy of Sciences of Azerbaijan, Baku AZ1073, Azerbaijan;
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Suárez-Moo P, Lamelas A, Garcia-Bautista I, Barahona-Pérez LF, Sandoval-Flores G, Valdes-Lozano D, Toledano-Thompson T, Polanco-Lugo E, Valdez-Ojeda R. Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico. PeerJ 2020; 8:e10339. [PMID: 33354414 PMCID: PMC7731659 DOI: 10.7717/peerj.10339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
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Affiliation(s)
- Pablo Suárez-Moo
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Itza Garcia-Bautista
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | | | - Gloria Sandoval-Flores
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autonoma de Tamaulipas, Merida, Yucatan, Mexico
| | - David Valdes-Lozano
- Centro de Investigación y de Estudios Avanzados, Insituto Politecnico Nacional, Merida, Yucatan, Mexico
| | - Tanit Toledano-Thompson
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | - Erik Polanco-Lugo
- Campus de Ciencias Biológicas y Agropecuarias,, Universidad Autonoma de Yucatan, Merida, Yucatan, Mexico
| | - Ruby Valdez-Ojeda
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
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Hong H, Li J, Wang Q, Lu H, Liu J, Dong YW, Zhang J, Li J, Williams MA, Huang B, Yan C. The legacy of trace metal deposition from historical anthropogenic river management: A regional driver of offshore sedimentary microbial diversity. JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123164. [PMID: 32563906 DOI: 10.1016/j.jhazmat.2020.123164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/30/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
River management, both modern and historical, have dramatically modified offshore environments. While numerous studies have described the modern impacts, very few have evaluated the legacies remaining from hundreds of years ago. Herein, we show trace metal enrichment in the surface sediment of the abandoned Yellow River Delta, hypothesized to be associated with ancient river management. Essentially, anthropogenic modification caused the river to shift, creating a 12.4×103 km2 area with elevated trace metals; characterized by clear metal deposition gradients. Geographical factors related to the ancient river mouth had the most significant influences on Zn (explained by distance to the river mouth, DTM) and Cd (DTM and sediment salinity), while the sediment absorptive capacity was associated with the reallocation of Cu (clay, silt, and iron), Ni (clay and iron), and Pb (silt and iron). Trace metal legacies showed stronger influences on prokaryotic diversity than on micro-eukaryotic diversity, with the former best described by changes in rare, rather than dominant families and classes, and explainable by an "overlapping micro-niche" model. The ancient river's legacies provide evidence of longer-term human disturbance over hundreds of years; as its impacts on associated benthic microbiomes have led to lessons for modern-day waterway management of benthic ecosystems.
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Affiliation(s)
- Hualong Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061, Virginia, USA.
| | - Junwei Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; Key Laboratory of the Ministry of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Qiang Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Haoliang Lu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Jingchun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Jie Zhang
- Key Laboratory of Urban Environment Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian, China.
| | - Jian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Mark A Williams
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061, Virginia, USA.
| | - Bangqin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Chongling Yan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
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Beattie RE, Skwor T, Hristova KR. Survivor microbial populations in post-chlorinated wastewater are strongly associated with untreated hospital sewage and include ceftazidime and meropenem resistant populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140186. [PMID: 32569917 DOI: 10.1016/j.scitotenv.2020.140186] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 05/21/2023]
Abstract
Wastewater treatment plant (WWTP) effluent has been implicated in the spread of antibiotic resistant bacteria (ARB), including pathogens, as the WWTP environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In WWTPs receiving hospital sewage, this selective effect may be more pronounced due to increased concentrations of antibiotics, ARB, and clinical pathogens from hospital sewage. To determine the extent to which hospital sewage contributes to the microbial community of disinfected wastewater which is released into the environment, we used 16S rRNA sequencing of hospital sewage, WWTP influent, primary effluent, Post-Chlorinated Effluent, and receiving sediments in a combined sewage system to track changes in microbial community composition. We also sequenced the culturable survivor community resistant to β-lactam antibiotics within disinfected effluent. Using molecular source tracking, we found that the hospital sewage microbiome contributes an average of 11.49% of the microbial community in Post-Chlorinated Effluents, suggesting microorganisms identified within hospital sewage can survive or are enriched by the chlorination disinfection process. Additionally, we identified 28 potential pathogens to the species level, seven of which remained detectable in Post-Chlorinated Effluent and environmental sediments. When Post-Chlorinated Effluents were cultured on media containing β-lactam antibiotics ceftazidime and meropenem, a diverse antibiotic resistant survivor community was identified including potential human pathogens Bacillus cereus, Bacillus pumilus, and Chryseobacterium indologenes. Together, these results indicate that although wastewater treatment does significantly reduce pathogenic loads and ARBs, their continual presence in disinfected wastewater and receiving sediments suggests additional treatment and microbial tracking systems are needed to reduce human and animal health risks.
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Affiliation(s)
- Rachelle E Beattie
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee 53233, WI, USA.
| | - Troy Skwor
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee 53211, WI, USA.
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee 53233, WI, USA.
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Lavrentyeva EV, Banzaraktsaeva TG, Radnagurueva AA, Buryukhaev SP, Dambaev VB, Baturina OA, Kozyreva LP, Barkhutova DD. Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425519060088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Di Cesare A, Pjevac P, Eckert E, Curkov N, Miko Šparica M, Corno G, Orlić S. The role of metal contamination in shaping microbial communities in heavily polluted marine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114823. [PMID: 32512474 DOI: 10.1016/j.envpol.2020.114823] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/25/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.
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Affiliation(s)
- Andrea Di Cesare
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Petra Pjevac
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090, Vienna, Austria
| | - Ester Eckert
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Neven Curkov
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
| | | | - Gianluca Corno
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Material Chemistry, Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, Zagreb, Croatia.
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Cai Y, Chen H, Yuan R, Wang F, Chen Z, Zhou B. Metagenomic analysis of soil microbial community under PFOA and PFOS stress. ENVIRONMENTAL RESEARCH 2020; 188:109838. [PMID: 32798955 DOI: 10.1016/j.envres.2020.109838] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.
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Affiliation(s)
- Yanping Cai
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Huilun Chen
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Rongfang Yuan
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Fei Wang
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhongbing Chen
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500, Prague, Czech Republic
| | - Beihai Zhou
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Tangherlini M, Corinaldesi C, Rastelli E, Musco L, Armiento G, Danovaro R, Dell'Anno A. Chemical contamination can promote turnover diversity of benthic prokaryotic assemblages: The case study of the Bagnoli-Coroglio bay (southern Tyrrhenian Sea). MARINE ENVIRONMENTAL RESEARCH 2020; 160:105040. [PMID: 32907739 DOI: 10.1016/j.marenvres.2020.105040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Chemical contamination of marine ecosystems represents a major concern for the detrimental consequences at different levels of biological organization. However, the impact of chronic contamination on the diversity and assemblage composition of benthic prokaryotes is still largely unknown, and this limits our understanding of the potential implications on ecosystem functioning. The Bagnoli-Coroglio bay (Gulf of Naples, Tyrrhenian Sea) is a typical example of coastal area heavily contaminated by metals and hydrocarbons, released for decades by industrial activities, which ceased at the beginning of nineties. In the present study we analyzed the abundance, diversity and assemblage composition of benthic prokaryotic assemblages at increasing distance from the historical source of contamination in relation to the heavy hydrocarbons (C > 12), polycyclic aromatic hydrocarbons (PAHs) and heavy metal concentrations in the sediments. Prokaryotic abundance in the sediments differed among sites, and was mostly driven by environmental factors rather than by contamination levels. Conversely, the richness of prokaryotic taxa was relatively high in all samples, was driven by contamination levels and decreased significantly with increasing contamination (15-38%). Moreover, our results indicate large variations in the composition of the benthic prokaryotic assemblages among sites, mostly explained by the different levels and types of chemical contaminants found in the sediments. Overall, our findings suggest that chemical contaminants, even after decades from the end of their release, can profoundly influence the richness and turnover diversity of the benthic prokaryotic assemblages, in turn promoting a high diversification of the benthic bacterial and archaeal assemblages by selecting those lineages more adapted to specific mixtures of different contaminants. Our results open new perspectives for understanding of the long-term effects of chemical contamination on the benthic prokaryotic assemblages and the ecological processes they mediate.
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Affiliation(s)
- M Tangherlini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - C Corinaldesi
- Dipartimento di Scienze e Ingegneria Della Materia, Dell'Ambiente Ed Urbanistica, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - E Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - L Musco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - G Armiento
- ENEA - Agenzia per le Nuove Tecnologie, L'Energia e Lo Sviluppo Economico Sostenibile, Via Anguillarese 301, 00123, Roma, Italy
| | - R Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Dell'Anno
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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Faheem M, Shabbir S, Zhao J, G. Kerr P, Ali S, Sultana N, Jia Z. Multifunctional Periphytic Biofilms: Polyethylene Degradation and Cd 2+ and Pb 2+ Bioremediation under High Methane Scenario. Int J Mol Sci 2020; 21:ijms21155331. [PMID: 32727088 PMCID: PMC7432609 DOI: 10.3390/ijms21155331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/26/2022] Open
Abstract
Priority pollutants such as polyethylene (PE) microplastic, lead (Pb2+), and cadmium (Cd2+) have attracted the interest of environmentalists due to their ubiquitous nature and toxicity to all forms of life. In this study, periphytic biofilms (epiphyton and epixylon) were used to bioremediate heavy metals (HMs) and to biodegrade PE under high (120,000 ppm) methane (CH4) doses. Both periphytic biofilms were actively involved in methane oxidation, HMs accumulation and PE degradation. Epiphyton and epixylon both completely removed Pb2+ and Cd2+ at concentrations of 2 mg L−1 and 50 mg L−1, respectively, but only partially removed these HMs at a relatively higher concentration (100 mg L−1). Treatment containing 12% 13CH4 proved to be most effective for biodegradation of PE. A synergistic effect of HMs and PE drastically changed microbial biota and methanotrophic communities. High-throughput 16S rRNA gene sequencing revealed that Cyanobacteria was the most abundant class, followed by Gammaproteobacteria and Alphaproteobacteria in all high-methane-dose treatments. DNA stable-isotope probing was used to label 13C in a methanotrophic community. A biomarker for methane-oxidizing bacteria, pmoA gene sequence of a 13C-labeled fraction, revealed that Methylobacter was most abundant in all high-methane-dose treatments compared to near atmospheric methane (NAM) treatment, followed by Methylococcus. Methylomonas, Methylocystis, Methylosinus, and Methylocella were also found to be increased by high doses of methane compared to NAM treatment. Overall, Cd+2 had a more determinantal effect on methanotrophic activity than Pb2+. Epiphyton proved to be more effective than epixylon in HMs removal and PE biodegradation. The findings proved that both epiphyton and epixylon can be used to bioremediate HMs and biodegrade PE as an efficient ecofriendly technique under high methane concentrations.
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Affiliation(s)
- Muhammad Faheem
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sadaf Shabbir
- College of Environment, Hohai University, 1 Xikang Road, Nanjing 210008, China;
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
| | - Philip G. Kerr
- School of biomedical Science, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad 38000, Pakistan;
- Department of Biological Sciences and Technology, China Medical University, Taichung 40402, Taiwan
| | - Nasrin Sultana
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Agroforestry and Environmental Science, Sher-e-Bangla Agricultural University (SAU), Sher-e-Bangla nagar, Dhaka 1207, Bangladesh
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- Correspondence:
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49
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Tsiola A, Michoud G, Fodelianakis S, Karakassis I, Kotoulas G, Pavlidou A, Pavloudi C, Pitta P, Simboura N, Daffonchio D, Tsapakis M. Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone. Viruses 2020; 12:v12080806. [PMID: 32722579 PMCID: PMC7472104 DOI: 10.3390/v12080806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 01/21/2023] Open
Abstract
Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.
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Affiliation(s)
- Anastasia Tsiola
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
- Department of Biology, University of Crete, 70013 Heraklion Crete, Greece;
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
- Correspondence: ; Tel.: +30-2810-337713; Fax: +30-2810-337822
| | - Grégoire Michoud
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Stilianos Fodelianakis
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Ioannis Karakassis
- Department of Biology, University of Crete, 70013 Heraklion Crete, Greece;
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
| | - Alexandra Pavlidou
- Institute of Oceanography, Hellenic Centre for Marine Research, 19013 Anavyssos Attiki, Greece; (A.P.); (N.S.)
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology & Aquaculture, 71003 Heraklion Crete, Greece; (G.K.); (C.P.)
| | - Paraskevi Pitta
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
| | - Nomiki Simboura
- Institute of Oceanography, Hellenic Centre for Marine Research, 19013 Anavyssos Attiki, Greece; (A.P.); (N.S.)
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Saudi Arabia; (G.M.); (S.F.); (D.D.)
| | - Manolis Tsapakis
- Institute of Oceanography, Hellenic Centre for Marine Research, 71003 Heraklion Crete, Greece; (P.P.); (M.T.)
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Zampieri BDB, da Costa Andrade V, Chinellato RM, Garcia CAB, de Oliveira MA, Brucha G, de Oliveira AJFC. Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:512. [PMID: 32661589 DOI: 10.1007/s10661-020-08413-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
The objectives of this study were to analyze the difference in ways in which metals polluting Brazilian port areas influence bacterial communities and the selection of resistant strains. The hypothesis tested was that port areas would have microbial communities significantly different from a pristine area, mainly due to a greater load of metals found in these areas. Sediment samples were collected in two port areas (Santos and São Sebastião) and one pristine area (Ubatuba). Total DNA was extracted and MiSeq sequencing was performed. A hundred strains were isolated from the same samples and were tested for metal resistance. The community composition was similar in the two port regions, but differed from the pristine area. Microbial diversity was significantly lower in the port areas. The phyla Proteobacteria, Cyanobacteria, and Thermodesulfobacteria exhibited positive correlations with copper and zinc concentrations. Chloroflex, Nitrospirae, Planctomycetes, and Chlorobi exhibited negative correlations with copper, chromium, and zinc. Cr and Zn had higher concentrations at port areas and were responsible to select more metal-resistant strains. Some genera were found to be able to easily develop metal resistance. The most isolated genera were Bacillus, Vibrio, and Pseudomonas. This type of study can illustrate, even in very complex natural environments, the influence of pollution on the community as a whole and the consequences of these changes.
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Affiliation(s)
- Bruna Del Busso Zampieri
- Department of Biochemistry and Microbiology, School of Biology, São Paulo State University - Rio Claro Campus (UNESP Rio Claro), Av. 24 A, 1515 - Jardim Vila Bela, Rio Claro, São Paulo, 13506-900, Brazil.
| | - Vanessa da Costa Andrade
- Department of Biochemistry and Microbiology, School of Biology, São Paulo State University - Rio Claro Campus (UNESP Rio Claro), Av. 24 A, 1515 - Jardim Vila Bela, Rio Claro, São Paulo, 13506-900, Brazil
| | - Roberta Merguizo Chinellato
- School of Biosciences, São Paulo State University - São Vicente Campus (UNESP São Vicente), Praça Infante Dom Henrique, s/n, Parque Bitaru, São Paulo, 11330-900, Brazil
| | - Carlos Alexandre Borges Garcia
- Department of Chemistry, Center for Exact Sciences and Technology, Federal University of Sergipe - São Cristóvão Campus (UFS São Cristóvão), Cidade Universitária Prof. José Aloísio de Campos Rosa Elze, São Cristóvão, Sergipe, 49100000, Brazil
| | - Marcos Antônio de Oliveira
- School of Biosciences, São Paulo State University - São Vicente Campus (UNESP São Vicente), Praça Infante Dom Henrique, s/n, Parque Bitaru, São Paulo, 11330-900, Brazil
| | - Gunther Brucha
- School of Technological Sciences, Federal University of Alfenas (UNIFAL-MG), Rodovia Aurélio Vilela, n 11.999 Cidade Universitária, Poços de Caldas, Minas Gerais, 37715400, Brazil
| | - Ana Julia Fernandes Cardoso de Oliveira
- School of Biosciences, São Paulo State University - São Vicente Campus (UNESP São Vicente), Praça Infante Dom Henrique, s/n, Parque Bitaru, São Paulo, 11330-900, Brazil
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