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de Paula RS, E Souza CC, Gonçalves CAX, de Holanda Moura MV, Guañabens ACP, Andrade GR, Nascimento AMA, Cardoso AV, de Paula Reis M, Jorge EC. Diversity and distribution of iron-oxidising bacteria belonging to Gallionellaceae in different sites of a hydroelectric power plant. Braz J Microbiol 2024; 55:639-646. [PMID: 38214875 PMCID: PMC10920547 DOI: 10.1007/s42770-024-01245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Iron (Fe) is the fourth most abundant element on the planet, and iron-oxidising bacteria (FeOB) play an important role in the biogeochemical cycle of this metal in nature. FeOB stands out as Fe oxidisers in microaerophilic environments, and new members of this group have been increasingly discussed in the literature, even though their isolation can still be challenging. Among these bacteria is the Gallionellaceae family, mainly composed of neutrophilic FeOB, highlighting Gallionella ferruginea, and nitrite-oxidiser genera. In the previous metagenomic study of the biofilm and sediments of the cooling system from the Irapé hydroelectric power plant (HPP-Irapé), 5% of the total bacteria sequences were related to Gallionellaceae, being 99% unclassified at genus level. Thus, in the present study, a phylogenetic tree based on this family was constructed, in order to search for shared and unique Gallionellaceae signatures in a deep phylogenetic level affiliation and correlated them with geomorphologic characteristics. The results revealed that Gallionella and Ferrigenium were ubiquitous reflecting their ability to adapt to various locations in the power plant. The cave was considered a hotspot for neutrophilic FeOB since it harboured most of the Gallionellaceae diversity. Microscopic biosignatures were detected only in the CS1 sample, which presented abundance of the stalk-forming Ferriphaselus and of the sheath-forming Crenothrix. Further studies are required to provide more detailed insights on Gallionellaceae distribution and diversity patterns in hydroelectric power plants, particularly its biotechnological potential in this industry.
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Affiliation(s)
- Rayan Silva de Paula
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Clara Carvalho E Souza
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Carlos Alberto Xavier Gonçalves
- Coordenação de Biotecnologia, Instituto SENAI de Inovação Em Biossintéticos E Fibras, Centro de Tecnologia da Indústria Química E Têxtil (SENAI CETIQT), Rio de Janeiro, RJ, Brazil
| | - Marcelo Victor de Holanda Moura
- Coordenação de Biotecnologia, Instituto SENAI de Inovação Em Biossintéticos E Fibras, Centro de Tecnologia da Indústria Química E Têxtil (SENAI CETIQT), Rio de Janeiro, RJ, Brazil
| | - Anna Carolina Paganini Guañabens
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Gabriela Rabelo Andrade
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia E Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Antonio Valadão Cardoso
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil
- Escola de Design, Universidade Do Estado de Minas Gerais (UEMG), Belo Horizonte, MG, Brazil
| | - Mariana de Paula Reis
- Centro de Bioengenharia de Espécies Invasoras de Hidrelétricas (CBEIH), Avenida José Cândido da Silveira, 2100 - Cidade Nova, Belo Horizonte, MG, 31035-536, Brazil.
| | - Erika Cristina Jorge
- Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes. Appl Environ Microbiol 2022; 88:e0013222. [PMID: 35499328 DOI: 10.1128/aem.00132-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0.67 g/L to 346 g/L). MPN results showed that the abundance of NRFeOx microorganisms significantly (P < 0.05) decreased with increasing lake salinity, from 7.55 × 103 to 8.09 cells/g dry sediment. The community composition of the NRFeOx enrichment cultures obtained from the MPNs differed distinctly among the five lakes and clustered with lake salinity. Two stable enrichment cultures, named FeN-EHL and FeN-CKL, were obtained from microcosm incubations of sediment from freshwater Lake Erhai and hypersaline Lake Chaka. The culture FeN-EHL was dominated by genus Gallionella (68.4%), while the culture FeN-CKL was dominated by genus Marinobacter (71.2%), with the former growing autotrophically and the latter requiring an additional organic substrate (acetate) and Fe(II) oxidation, caused to a large extent by chemodenitrification [reaction of nitrite with Fe(II)]. Short-range ordered Fe(III) (oxyhydr)oxides were the product of Fe(II) oxidation, and the cells were partially attached to or encrusted by the formed iron minerals in both cultures. In summary, different types of interactions between Fe(II) and nitrate-reducing bacteria may exist in freshwater and hypersaline lakes, i.e., autotrophic NRFeOx and chemodenitrification in freshwater and hypersaline environments, respectively. IMPORTANCE NRFeOx microorganisms are globally distributed in various types of environments and play a vital role in iron transformation and nitrate and heavy metal removal. However, most known NRFeOx microorganisms were isolated from freshwater and marine environments, while their identity and activity under hypersaline conditions remain unknown. Here, we demonstrated that salinity may affect the abundance, identity, and nutrition modes of NRFeOx microorganisms. Autotrophy was only detectable in a freshwater lake but not in the saline lake investigated. We enriched a mixotrophic culture capable of nitrate-reducing Fe(II) oxidation from hypersaline lake sediments. However, Fe(II) oxidation was probably caused by abiotic nitrite reduction (chemodenitrification) rather than by a biologically mediated process. Consequently, our study suggests that in hypersaline environments, Fe(II) oxidation is largely caused by chemodentrification initiated by nitrite formation by chemoheterotrophic bacteria, and additional experiments are needed to demonstrate whether or to what extent Fe(II) is enzymatically oxidized.
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Liu C, Huang G, Song P, An C, Zhang P, Shen J, Ren S, Zhao K, Huang W, Xu Y, Zheng R. Treatment of decentralized low-strength livestock wastewater using microcurrent-assisted multi-soil-layering systems: performance assessment and microbial analysis. CHEMOSPHERE 2022; 294:133536. [PMID: 34999101 DOI: 10.1016/j.chemosphere.2022.133536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Discharge of decentralized livestock wastewater without effective treatment has become a common problem in rural areas, threatening the regional water environment. A new microcurrent-assisted multi-soil-layering (MSL) system was developed for treating rural decentralized livestock wastewater. The results showed the highest removal rates of chemical oxygen demand (COD) and total phosphorus (TP) in MSL systems reached 95.45% and 92.0%, respectively. The removal rate of total nitrogen (TN) in MSL systems ranged from 60 to 75%. The bacterial diversity changes among MSL systems showed that high-level height of bottom submergence had a positive effect on the abundance of denitrifying bacteria, while low-level height of bottom submergence had a positive impact on the abundance of nitrifying bacteria. The effect of low-level external voltage on bacterial abundance was better than that of high-level external voltage. Both high- and low-level influent C/N ratios had no significant effect on bacterial abundance. The metabolism and activity of microorganisms were promoted with microcurrent stimulation from the perspective of increased bacterial abundance in MSL systems with improved treatment performance.
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Affiliation(s)
- Chao Liu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Guohe Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, China-Canada Center for Energy, Environment and Ecology Research, UR-BNU, School of Environment, Beijing Normal University, Beijing, 100875, China; Environmental Systems Engineering Program, University of Regina, Regina, S4S 0A2, Canada.
| | - Pei Song
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Chunjiang An
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, H3G 1M8, Canada
| | - Peng Zhang
- Environmental Systems Engineering Program, University of Regina, Regina, S4S 0A2, Canada
| | - Jian Shen
- Environmental Systems Engineering Program, University of Regina, Regina, S4S 0A2, Canada
| | - Shaojie Ren
- China-Canada Center of Energy, Environment and Sustainability Research, UR-SDU, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Kai Zhao
- Environmental Systems Engineering Program, University of Regina, Regina, S4S 0A2, Canada
| | - Wendy Huang
- Department of Civil Engineering, Schulich School of Engineering, University of Calgary, Calgary, T2N 1N4, Canada
| | - Ye Xu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Rubing Zheng
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
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Regina ALA, Medeiros JD, Teixeira FM, Côrrea RP, Santos FAM, Brantes CPR, Pereira IA, Stapelfeldt DMA, Diniz CG, da Silva VL. A watershed impacted by anthropogenic activities: Microbial community alterations and reservoir of antimicrobial resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148552. [PMID: 34328962 DOI: 10.1016/j.scitotenv.2021.148552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Water is the main resource for maintaining life. Anthropic activities influence the microbial epidemiological chain in watersheds, which can act as ways of disseminating microorganisms resistant to antimicrobial drugs, with impacts on human, animal, and environmental health. Here, we characterized aquatic microbial communities and their resistomes in samples collected along Rio das Ostras watershed during two seasons. Surface water samples were collected at eleven sites from the Jundiá, Iriry, and Rio das Ostras rivers in two seasons (dry and wet season). Microbial DNA was extracted, high-throughput sequenced and screened for antimicrobial resistance genetic (ARG) markers. The physicochemical characteristics and the microbiota data confirmed that Rio das Ostras watershed can be divided into three well defined portions: rural, urban, and marine. Rural areas were enriched by bacteria typically found in limnic environments and Patescibacteria phyla. The urban portion was characterized by sites with low pH and groups associated with iron oxidation. Some genera of clinical relevance were also identified, though in relatively low abundance. The marine site was enriched mainly by Cyanobacteria and bacteria that showed strong correlation with conductivity, salinity, and chloride. Twenty-six ARG markers were identified on the resistome, being found most frequently in the urban area, despite being present in rural sites. Among them were some related to classes of great clinical concern, such as genes coding for extended-spectrum beta-lactamase (blaCTX-M and blaTEM), resistance to carbapenems (blaKPC) and to methicillin by Staphylococcus aureus (mecA). These results broaden our understanding of the microbial community of a watershed impacted by anthropogenic actions. The large number of ARGs detected along the Rio das Ostras watershed contrasts with the small number of microorganisms of clinical relevance observed, suggesting that antimicrobial resistance has arisen from non-clinical environments and microbes. Our results corroborate that freshwater acts as a reservoir of antimicrobial resistance genes.
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Affiliation(s)
- Ana Luísa Almeida Regina
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora - UFJF, José Lourenço Kelmer, Martelos, CEP 36036-900 Juiz de Fora, MG, Brazil
| | - Julliane Dutra Medeiros
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora - UFJF, José Lourenço Kelmer, Martelos, CEP 36036-900 Juiz de Fora, MG, Brazil; Faculty of Biological and Agricultural Sciences, Mato Grosso State University - UNEMAT, Perimetral Rogério Silva - Norte 2, CEP 78580-000 Alta Floresta, MT, Brazil
| | - Francisco Martins Teixeira
- Laboratory of Microbiology and Parasitology, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560 Macaé, RJ, Brazil
| | - Raíssa Pereira Côrrea
- Laboratory of Microbiology and Parasitology, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560 Macaé, RJ, Brazil
| | - Fernanda Almeida Maciel Santos
- Laboratory of Microbiology and Parasitology, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560 Macaé, RJ, Brazil
| | - Caique Pinheiro Rosa Brantes
- Laboratory of Microbiology and Parasitology, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560 Macaé, RJ, Brazil
| | - Ingrid Annes Pereira
- Laboratory of Food Microbiology, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560, Macaé, RJ, Brazil
| | - Danielle Marques Araújo Stapelfeldt
- Laboratory of Chemistry, Federal University of Rio de Janeiro - UFRJ, Macaé Campus, Aloísio da Silva Gomes, Granja dos Cavaleiros, CEP 27930-560 Macaé, RJ, Brazil
| | - Cláudio Galuppo Diniz
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora - UFJF, José Lourenço Kelmer, Martelos, CEP 36036-900 Juiz de Fora, MG, Brazil
| | - Vânia Lúcia da Silva
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora - UFJF, José Lourenço Kelmer, Martelos, CEP 36036-900 Juiz de Fora, MG, Brazil.
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5
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Reis MP, Suhadolnik MLS, Dias MF, Ávila MP, Motta AM, Barbosa FAR, Nascimento AMA. Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami. CHEMOSPHERE 2020; 253:126584. [PMID: 32278186 DOI: 10.1016/j.chemosphere.2020.126584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/18/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.
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Affiliation(s)
- Mariana P Reis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Maria Luíza S Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcela F Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcelo P Ávila
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Amanda M Motta
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Francisco A R Barbosa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
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Song P, Huang G, Hong Y, An C, Xin X, Zhang P. A biophysiological perspective on enhanced nitrate removal from decentralized domestic sewage using gravitational-flow multi-soil-layering systems. CHEMOSPHERE 2020; 240:124868. [PMID: 31542583 DOI: 10.1016/j.chemosphere.2019.124868] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Multi-soil-layering (MSL) system with brick-wall pattern structure and gravitational flow can be used for decentralized rural domestic sewage treatment. The capability of soil for contaminant removal is maximized within soil mixture blocks (SMBs). However, the performance of removing nitrate was still not ideal during operation. To improve its performance in MSL system, the relationship between biophysiological characteristics of denitrifying species and operating conditions was studied. Microbial species diversity of activated sludge and soil samples were analyzed. The significant effects of independent factors and their interactions on microbial species diversity and denitrifying species abundance were revealed on the basis of factorial analysis. The results indicated activated sludge in SMBs played a key role in increasing the richness of denitrifying species in MSL system. Slow-release poly (butylene succinate) (PBS) had the most dominant positive effect on increasing denitrifying species abundance. Submersion had significantly positive effect on species richness in SMBs. These three factors, including activated sludge, PBS in SMBs, and submersion condition had different significant effects on microbial responses. They were favorable for denitrification and ensuring a better removal efficiency of nitrate and total nitrogen. The porous zeolites were served as the habitats for most of aerobic bacteria to form biofilms, which could promote the oxygen consumption in both sewage and system to improve denitrification in SMBs. The results could help on the enhancement of denitrification in MSL system from biophysiological insights. It can provide a sound strategy for using MSL system with great performance on contaminant removal.
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Affiliation(s)
- Pei Song
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Guohe Huang
- Center for Energy, Environment and Ecology Research, UR-BNU, Beijing Normal University, Beijing, 100875, China.
| | - Yongyuan Hong
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Chunjiang An
- Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, Quebec, H3G 1M8, Canada
| | - Xiaying Xin
- Institute for Energy, Environment and Sustainable Communities, University of Regina, Regina, S4S 0A2, Canada
| | - Peng Zhang
- Institute for Energy, Environment and Sustainable Communities, University of Regina, Regina, S4S 0A2, Canada
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Reis MP, Dias MF, Costa PS, Ávila MP, Leite LR, de Araújo FMG, Salim ACM, Bucciarelli-Rodriguez M, Oliveira G, Chartone-Souza E, Nascimento AMA. Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks. CHEMOSPHERE 2016; 161:266-273. [PMID: 27441985 DOI: 10.1016/j.chemosphere.2016.06.097] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
Bacteria from aquatic ecosystems significantly contribute to biogeochemical cycles, but details of their community structure in tropical mining-impacted environments remain unexplored. In this study, we analyzed a bacterial community from circumneutral-pH tropical stream sediment by 16S rRNA and shotgun deep sequencing. Carrapatos stream sediment, which has been exposed to metal stress due to gold and iron mining (21 [g Fe]/kg), revealed a diverse community, with predominance of Proteobacteria (39.4%), Bacteroidetes (12.2%), and Parcubacteria (11.4%). Among Proteobacteria, the most abundant reads were assigned to neutrophilic iron-oxidizing taxa, such as Gallionella, Sideroxydans, and Mariprofundus, which are involved in Fe cycling and harbor several metal resistance genes. Functional analysis revealed a large number of genes participating in nitrogen and methane metabolic pathways despite the low concentrations of inorganic nitrogen in the Carrapatos stream. Our findings provide important insights into bacterial community interactions in a mining-impacted environment.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcela F Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Laura R Leite
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Flávio M G de Araújo
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Anna C M Salim
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil
| | - Mônica Bucciarelli-Rodriguez
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Guilherme Oliveira
- Centro de Pesquisas René Rachou Fundação Oswaldo Cruz, Av. Augusto de Lima 1715, Belo Horizonte, Minas Gerais 30190-002, Brazil; Instituto Tecnológico Vale, Rua Boaventura da Silva 955, Belém, Pará 66055-090, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil.
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8
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Fabisch M, Freyer G, Johnson CA, Büchel G, Akob DM, Neu TR, Küsel K. Dominance of 'Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge. GEOBIOLOGY 2016; 14:68-90. [PMID: 26407813 DOI: 10.1111/gbi.12162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
Heavy metal-contaminated, pH 6 mine water discharge created new streams and iron-rich terraces at a creek bank in a former uranium-mining area near Ronneburg, Germany. The transition from microoxic groundwater with ~5 mm Fe(II) to oxic surface water may provide a suitable habitat for microaerobic iron-oxidizing bacteria (FeOB). In this study, we investigated the potential contribution of these FeOB to iron oxidation and metal retention in this high-metal environment. We (i) identified and quantified FeOB in water and sediment at the outflow, terraces, and creek, (ii) studied the composition of biogenic iron oxides (Gallionella-like twisted stalks) with scanning and transmission electron microscopy (SEM, TEM) as well as confocal laser scanning microscopy (CLSM), and (iii) examined the metal distribution in sediments. Using quantitative PCR, a very high abundance of FeOB was demonstrated at all sites over a 6-month study period. Gallionella spp. clearly dominated the communities, accounting for up to 88% of Bacteria, with a minor contribution of other FeOB such as Sideroxydans spp. and 'Ferrovum myxofaciens'. Classical 16S rRNA gene cloning showed that 96% of the Gallionella-related sequences had ≥ 97% identity to the putatively metal-tolerant 'Gallionella capsiferriformans ES-2', in addition to known stalk formers such as Gallionella ferruginea and Gallionellaceae strain R-1. Twisted stalks from glass slides incubated in water and sediment were composed of the Fe(III) oxyhydroxide ferrihydrite, as well as polysaccharides. SEM and scanning TEM-energy-dispersive X-ray spectroscopy revealed that stalk material contained Cu and Sn, demonstrating the association of heavy metals with biogenic iron oxides and the potential for metal retention by these stalks. Sequential extraction of sediments suggested that Cu (52-61% of total sediment Cu) and other heavy metals were primarily bound to the iron oxide fractions. These results show the importance of 'G. capsiferriformans' and biogenic iron oxides in slightly acidic but highly metal-contaminated freshwater environments.
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MESH Headings
- Aerobiosis
- Biota
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ferric Compounds/analysis
- Gallionellaceae/chemistry
- Gallionellaceae/classification
- Gallionellaceae/genetics
- Gallionellaceae/isolation & purification
- Germany
- Hydrogen-Ion Concentration
- Iron/metabolism
- Metals, Heavy/analysis
- Microscopy, Confocal
- Microscopy, Electrochemical, Scanning
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Oxidation-Reduction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Water/chemistry
- Water Microbiology
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Affiliation(s)
- M Fabisch
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - G Freyer
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - C A Johnson
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - G Büchel
- Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
| | - D M Akob
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- U.S. Geological Survey, Reston, VA, USA
| | - T R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle - UFZ, Magdeburg, Germany
| | - K Küsel
- Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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9
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Ben Maamar S, Aquilina L, Quaiser A, Pauwels H, Michon-Coudouel S, Vergnaud-Ayraud V, Labasque T, Roques C, Abbott BW, Dufresne A. Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths. Front Microbiol 2015; 6:1457. [PMID: 26733990 PMCID: PMC4686674 DOI: 10.3389/fmicb.2015.01457] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities.
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Affiliation(s)
- Sarah Ben Maamar
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche ScientifiqueRennes, France; OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche ScientifiqueRennes, France; BRGM, Laboratory DepartmentOrléans, France
| | - Luc Aquilina
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Achim Quaiser
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | | | - Sophie Michon-Coudouel
- OSUR-UMS 3343, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Virginie Vergnaud-Ayraud
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Thierry Labasque
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Clément Roques
- OSUR-UMR 6118 Géosciences, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Benjamin W Abbott
- OSUR-UMS 3343, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
| | - Alexis Dufresne
- OSUR-UMR 6553 ECOBIO, Université de Rennes 1 and Centre National de la Recherche Scientifique Rennes, France
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10
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Reis MP, Ávila MP, Keijzer RM, Barbosa FAR, Chartone-Souza E, Nascimento AMA, Laanbroek HJ. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Front Microbiol 2015; 6:898. [PMID: 26379659 PMCID: PMC4553384 DOI: 10.3389/fmicb.2015.00898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
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Affiliation(s)
- Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil ; Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais Belo Horizonte, Brazil
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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11
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Febria CM, Hosen JD, Crump BC, Palmer MA, Williams DD. Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison. Front Microbiol 2015; 6:522. [PMID: 26089816 PMCID: PMC4454877 DOI: 10.3389/fmicb.2015.00522] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 05/11/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence.
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Affiliation(s)
- Catherine M Febria
- Department of Entomology, University of Maryland College Park, MD, USA ; Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science Solomons, MD, USA ; School of Biological Sciences, University of Canterbury Christchurch, New Zealand
| | - Jacob D Hosen
- Department of Entomology, University of Maryland College Park, MD, USA ; Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science Solomons, MD, USA
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University Corvallis, OR, USA
| | - Margaret A Palmer
- Department of Entomology, University of Maryland College Park, MD, USA ; Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science Solomons, MD, USA ; National Socio-Environmental Synthesis Center, University of Maryland College Park, MD, USA
| | - D Dudley Williams
- Department of Biological Sciences, University of Toronto Scarborough Scarborough, ON, Canada
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