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Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01561-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.
Result
The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.
Conclusions
The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.
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Aalto SL, Saarenheimo J, Mikkonen A, Rissanen AJ, Tiirola M. Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents. Environ Microbiol 2018; 20:3616-3628. [PMID: 30003649 PMCID: PMC6221106 DOI: 10.1111/1462-2920.14354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 11/28/2022]
Abstract
Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia‐oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater‐influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater‐influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate‐change‐driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.
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Affiliation(s)
- Sanni L Aalto
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Jatta Saarenheimo
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Anu Mikkonen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Antti J Rissanen
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, 33101, Tampere, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014, Jyväskylä, Finland
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Uprety S, Hong PY, Sadik N, Dangol B, Adhikari R, Jutla A, Shisler JL, Degnan P, Nguyen TH. The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal. Front Microbiol 2017; 8:2380. [PMID: 29270153 PMCID: PMC5724148 DOI: 10.3389/fmicb.2017.02380] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
We conducted a study to examine the effect of seasonal variations and the disruptive effects of the 2015 Nepal earthquake on microbial communities associated with drinking water sources. We first characterized the microbial communities of water samples in two Nepali regions (Kathmandu and Jhapa) to understand the stability of microbial communities in water samples collected in 2014. We analyzed additional water samples from the same sources collected from May to August 2015, allowing the comparison of samples from dry-to-dry season and from dry-to-monsoon seasons. Emphasis was placed on microbes responsible for maintaining the geobiochemical characteristics of water (e.g., ammonia-oxidizing and nitrite-oxidizing bacteria and archaea and sulfate-reducing bacteria) and opportunistic pathogens often found in water (Acinetobacter). When examining samples from Jhapa, we identified that most geobiochemical microbe populations remained similar. When examining samples from Kathmandu, the abundance of microbial genera responsible for maintaining the geobiochemical characteristics of water increased immediately after the earthquake and decreased 8 months later (December 2015). In addition, microbial source tracking was used to monitor human fecal contamination and revealed deteriorated water quality in some specific sampling sites in Kathmandu post-earthquake. This study highlights a disruption of the environmental microbiome after an earthquake and the restoration of these microbial communities as a function of time and sanitation practices.
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Affiliation(s)
- Sital Uprety
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nora Sadik
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Bipin Dangol
- Environment and Public Health Organization, Kathmandu, Nepal
| | | | - Antarpreet Jutla
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, United States
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Patrick Degnan
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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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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