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Kiledal EA, Moxley I, Shevchenko O, Goff JL, Maresca JA. Genome sequence of Methylobacterium fujisawaense strain C14, isolated from concrete. Microbiol Resour Announc 2024:e0053124. [PMID: 38953339 DOI: 10.1128/mra.00531-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024] Open
Abstract
Methylobacterium fujisawaense strain C14 was isolated from a weathered concrete cylinder. Using PacBio sequencing, we generated a complete genome for strain C14, which includes one circular chromosome (6,656,731 bp) and six putative plasmids (35,452 to 85,428 bp).
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Affiliation(s)
- E Anders Kiledal
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Iz Moxley
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Olga Shevchenko
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
| | - Jennifer L Goff
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Julia A Maresca
- Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
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Kiledal EA, Shaw M, Polson SW, Maresca JA. Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea. Microbiol Spectr 2023; 11:e0511222. [PMID: 37404173 PMCID: PMC10434110 DOI: 10.1128/spectrum.05112-22] [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: 12/13/2022] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.
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Affiliation(s)
- E. Anders Kiledal
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Mark Shaw
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Julia A. Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
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Tadley P, Bennett A, Hansen K, Hanson T, Colosi J, Goudsouzian LK. Identification of Bacterial Taxa Present in a Concrete Pennsylvania Bridge. Microbiol Resour Announc 2023:e0021123. [PMID: 37154767 DOI: 10.1128/mra.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Concrete contains low microbial biomass, but some bacteria can grow in this highly alkaline environment. We used silica-based DNA extraction and 16S rRNA sequence analysis to identify the bacteria in a corroded concrete bridge sample from Bethlehem, Pennsylvania. Staphylococcus, Streptococcus, Corynebacterium, Leifsonia, Vicinamibacterales, and Actinophytocola were the most abundant genera.
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Affiliation(s)
- Patricia Tadley
- Department of Biology, DeSales University, Center Valley, Pennsylvania, USA
| | - Alexa Bennett
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Kirstin Hansen
- Department of Biology, DeSales University, Center Valley, Pennsylvania, USA
| | - Thomas Hanson
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Joseph Colosi
- Department of Biology, DeSales University, Center Valley, Pennsylvania, USA
| | - Lara K Goudsouzian
- Department of Biology, DeSales University, Center Valley, Pennsylvania, USA
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Impact of a biorepair treatment on the diversity of calcifying bacterial communities at the surface of cracked concrete walls. Appl Microbiol Biotechnol 2022; 107:187-200. [DOI: 10.1007/s00253-022-12313-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
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Beattie RE, Su B, Thill R, Hristova KR. Recycled concrete aggregates are an economic form of urban riparian erosion management with limited impacts on freshwater chemistry and microbial diversity. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128934. [PMID: 35461000 DOI: 10.1016/j.jhazmat.2022.128934] [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: 01/28/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Urban streams are at high risk of riparian erosion which impacts adjacent infrastructure stability. Methods to prevent stream erosion have been proposed including using recycled concrete (RC) materials to help stabilize the streambed; however, little is known about the environmental and biological impacts of using RC in urban streams. RC, new concrete (NC), and river rock controls were evaluated for their impact on water chemistry, water quality, and microbial community composition over 6.5 months in controlled laboratory mesocosms. Concentrations of 19 metals, nutrients, and pH of mesocosms containing RC were not significantly different from the river rock mesocosm throughout the experiment; however, NC mesocosms contained significantly higher (p < 0.05) concentrations of Co, As, Al, and V in mesocosm water samples compared to both RC and the river rock control. Microbial community diversity was not significantly impacted by mesocosm treatment. Microbial sequences mapping to taxa including Rhodoferax, Acidovorax, Nitrosomonas, and Novosphingobium were significantly more abundant (p < 0.01) in RC and NC mesocosm samples; however, the overall microbial community structure was similar across treatment types. Results from this study suggest that RC does not significantly alter the stream environment including microbial community diversity and is a viable option for use in stream restoration projects.
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Affiliation(s)
- Rachelle E Beattie
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Bixia Su
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Rebecca Thill
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
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Tong X, Leung MHY, Shen Z, Lee JYY, Mason CE, Lee PKH. Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. MICROBIOME 2021; 9:213. [PMID: 34724986 PMCID: PMC8562002 DOI: 10.1186/s40168-021-01166-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different physical attributes and environmental factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail. RESULTS Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely correlated with taxonomy, rather than surface attributes and geography. CONCLUSIONS Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures. Video Abstract.
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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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