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Yin X, Chen H, Jiang K, Zhang B, Li R, Zhu X, Sun L, Ng ZL, Su M. Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea. Microorganisms 2024; 12:1901. [PMID: 39338575 PMCID: PMC11434414 DOI: 10.3390/microorganisms12091901] [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: 08/19/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.
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Affiliation(s)
- Xingjia Yin
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Hui Chen
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Kaixi Jiang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Office of Laboratory Safety and Equipment Management, Beijing Normal University, Zhuhai 519087, China
| | - Boda Zhang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Center for Environmental Monitoring of Geology, Shenzhen 518034, China
| | - Ruohong Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Xinzhe Zhu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Zhi Lin Ng
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
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2
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Kokate PP, Bales E, Joyner D, Hazen TC, Techtmann SM. Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates. FEMS Microbiol Lett 2023; 370:fnad081. [PMID: 37573136 DOI: 10.1093/femsle/fnad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.
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Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Erika Bales
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Terry C Hazen
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
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Alhajjar RK, Ghannam RB, Chen See JR, Wright OG, Campa MF, Hazen TC, Lamendella R, Techtmann SM. Comparative study of the effects of biocides and metal oxide nanoparticles on microbial community structure in a stream impacted by hydraulic fracturing. CHEMOSPHERE 2021; 284:131255. [PMID: 34214929 DOI: 10.1016/j.chemosphere.2021.131255] [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: 01/27/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Our study goal was to investigate the impact of biocides and nanoparticles (NPs) on the microbial diversity in a hydraulic fracturing impacted stream. Biocides and NPs are known for their antimicrobial properties and controlling microbial growth. Previous work has shown that biocides can alter the microbial community composition of stream water and may select for biocide-resistant bacteria. Additional studies have shown that nanoparticles can also alter microbial community composition. However, previous work has often focused on the response to a single compound. Here we provide a more thorough analysis of the microbial community response to three different biocides and three different nanoparticles. A microcosm-based study was undertaken that exposed stream microbial communities to either biocides or NPs. Our results showed a decrease in bacterial abundance with different types of nanoparticles, but an increase in microbial abundance in biocide-amended treatments. The microbial community composition (MCC) was distinct from the controls in all biocide and NP treatments, which resulted in differentially enriched taxa in the treatments compared to the controls. Our results indicate that NPs slightly altered the MCC compared to the biocide-treated microcosms. After 14 days, the MCC in the nanoparticle-treated conditions was similar to the MCC in the control. Conversely, the MCC in the biocide-treated microcosms was distinct from the controls at day 14 and distinct from all conditions at day 0. This finding may point to the use of NPs as an alternative to biocides in some settings.
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Affiliation(s)
- Rehab K Alhajjar
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Ryan B Ghannam
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | | | | | - Maria Fernanda Campa
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, USA
| | | | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA.
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Miller JI, Techtmann S, Fortney J, Mahmoudi N, Joyner D, Liu J, Olesen S, Alm E, Fernandez A, Gardinali P, GaraJayeva N, Askerov FS, Hazen TC. Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities. Front Microbiol 2019; 10:995. [PMID: 31143165 PMCID: PMC6521576 DOI: 10.3389/fmicb.2019.00995] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/18/2019] [Indexed: 12/03/2022] Open
Abstract
The Caspian Sea, which is the largest landlocked body of water on the planet, receives substantial annual hydrocarbon input from anthropogenic sources (e.g., industry, agriculture, oil exploration, and extraction) and natural sources (e.g., mud volcanoes and oil seeps). The Caspian Sea also receives substantial amounts of runoff from agricultural and municipal sources, containing nutrients that have caused eutrophication and subsequent hypoxia in the deep, cold waters. The effect of decreasing oxygen saturation and cold temperatures on oil hydrocarbon biodegradation by a microbial community is not well characterized. The purpose of this study was to investigate the effect of oxic and anoxic conditions on oil hydrocarbon biodegradation at cold temperatures by microbial communities derived from the Caspian Sea. Water samples were collected from the Caspian Sea for study in experimental microcosms. Major taxonomic orders observed in the ambient water samples included Flavobacteriales, Actinomycetales, and Oceanospirillales. Microcosms were inoculated with microbial communities from the deepest waters and amended with oil hydrocarbons for 17 days. Hydrocarbon degradation and shifts in microbial community structure were measured. Surprisingly, oil hydrocarbon biodegradation under anoxic conditions exceeded that under oxic conditions; this was particularly evident in the degradation of aromatic hydrocarbons. Important microbial taxa associated with the anoxic microcosms included known oil degraders such as Oceanospirillaceae. This study provides knowledge about the ambient community structure of the Caspian Sea, which serves as an important reference point for future studies. Furthermore, this may be the first report in which anaerobic biodegradation of oil hydrocarbons exceeds aerobic biodegradation.
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Affiliation(s)
- John I Miller
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Stephen Techtmann
- Biosciences Division, Michigan Technological University, Houghton, MI, United States
| | - Julian Fortney
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montreal, QC, Canada
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jiang Liu
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Scott Olesen
- Harvard School of Public Health, Cambridge, MA, United States
| | - Eric Alm
- Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Adolfo Fernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Piero Gardinali
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | | | | | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Oak Ridge National Laboratory, Oak Ridge, TN, United States
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5
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Butler TM, Wilhelm AC, Dwyer AC, Webb PN, Baldwin AL, Techtmann SM. Microbial Community Dynamics During Lake Ice Freezing. Sci Rep 2019; 9:6231. [PMID: 30996247 PMCID: PMC6470161 DOI: 10.1038/s41598-019-42609-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/27/2019] [Indexed: 01/22/2023] Open
Abstract
Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity.
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Affiliation(s)
- Timothy M Butler
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | | | - Amber C Dwyer
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Paige N Webb
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Andrew L Baldwin
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technology University, Houghton, MI, USA.
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Marietou A, Chastain R, Beulig F, Scoma A, Hazen TC, Bartlett DH. The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill. Front Microbiol 2018; 9:808. [PMID: 29755436 PMCID: PMC5932198 DOI: 10.3389/fmicb.2018.00808] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/10/2018] [Indexed: 01/13/2023] Open
Abstract
The Deepwater Horizon oil spill was one of the largest and deepest oil spills recorded. The wellhead was located at approximately 1500 m below the sea where low temperature and high pressure are key environmental characteristics. Using cells collected 4 months following the Deepwater Horizon oil spill at the Gulf of Mexico, we set up Macondo crude oil enrichments at wellhead temperature and different pressures to determine the effect of increasing depth/pressure to the in situ microbial community and their ability to degrade oil. We observed oil degradation under all pressure conditions tested [0.1, 15, and 30 megapascals (MPa)], although oil degradation profiles, cell numbers, and hydrocarbon degradation gene abundances indicated greatest activity at atmospheric pressure. Under all incubations the growth of psychrophilic bacteria was promoted. Bacteria closely related to Oleispira antarctica RB-8 dominated the communities at all pressures. At 30 MPa we observed a shift toward Photobacterium, a genus that includes piezophiles. Alphaproteobacterial members of the Sulfitobacter, previously associated with oil-degradation, were also highly abundant at 0.1 MPa. Our results suggest that pressure acts synergistically with low temperature to slow microbial growth and thus oil degradation in deep-sea environments.
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Affiliation(s)
- Angeliki Marietou
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Roger Chastain
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Felix Beulig
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Douglas H Bartlett
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
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