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Liu S, Liu J, She J, Xie Z, Zhou L, Dai Q, Zhang X, Wan Y, Yin M, Dong X, Zhao M, Chen D, Wang J. Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170694. [PMID: 38325477 DOI: 10.1016/j.scitotenv.2024.170694] [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: 12/21/2022] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
The uranium (U) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium-involving anthoropogenic facilities/activities upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.
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Affiliation(s)
- Siyu Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Juan Liu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Jingye She
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Zhenyu Xie
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Lei Zhou
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Qunwei Dai
- School of Environment and Resource, Key Laboratory of Solid Waste Treatment and Resource Recycling, Ministry of Education, Southwest University of Science and Technology, Mianyang, China
| | - Xing Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Yuebing Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Meiling Yin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Xinjiao Dong
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Min Zhao
- School of Life & Environmental Science, Wenzhou University, Wenzhou, China
| | - Diyun Chen
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China
| | - Jin Wang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China; Guangdong Provincial Key Laboratory of Radionuclides Pollution Control and Resources, Guangzhou, China.
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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3
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Li A, Beek TAD, Schubert M, Yu Z, Schiedek T, Schüth C. Sedimentary archive of Polycyclic Aromatic Hydrocarbons and perylene sources in the northern part of Taihu Lake, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:198-206. [PMID: 30551038 DOI: 10.1016/j.envpol.2018.11.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
In the present work, we analyzed the concentration patterns of 20 Polycyclic Aromatic Hydrocarbons (PAHs) in 25 surface sediments and 11 sediment cores from the northern part of Taihu Lake, China. Three of the cores were dated based on 137Cs activity for the deposition age of the sediment. The spatial distributions of the PAH concentrations show that the inflow rivers into Zhushan Bay and Meiliang Bay were the main pathway for PAHs and sediment input to the northern part of the lake. This results in substantially higher PAH concentrations (up to 5000 ng/g) and sedimentation rates (higher than the average of 3-4 mm/a) in the area close to the river outlets. In addition, results also show that PAH concentrations in the sediments considerably increased from the early 1960s, but the decreasing concentrations in the upper layers of the sediment could be attributed to the introduction of measures on environmental improvement from ca. 2000. There were both anthropogenic and biogenic origins of perylene in the lake sediments, which were distinguished based on spatial distribution patterns and also the concentration proportions of perylene to the sum of the 20 PAHs. In the cores collected close to river outlets, the concentration proportions of perylene typically range from 0.02 to 0.18 and there are significant positive linear correlations between the concentration of perylene and three anthropogenic PAHs (Benzo[a]pyrene, Benzo[e]pyrene, Pyrene), suggesting that perylene was dominated by anthropogenic input. However, the cores collected further away from the river outlets show the concentration proportions between 0.13 and 0.96, and present significant negative correlations or no correlations between perylene and the three PAHs, suggesting that perylene was mainly formed by biogenic activities. Furthermore, the different perylene sources accompanied with the location distributions imply that anthropogenic activities could inhibit its biogenic formation.
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Affiliation(s)
- Aili Li
- Institute of Applied Geosciences, Technical University of Darmstadt, Schnittspahnstrasse 9, 64287, Darmstadt, Germany.
| | - Tim Aus der Beek
- IWW Water Centre, Moritzstrasse 26, 45476, Mülheim an der Ruhr, Germany.
| | - Michael Schubert
- UFZ - Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany.
| | - Zhenyang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, PR China.
| | - Thomas Schiedek
- Institute of Applied Geosciences, Technical University of Darmstadt, Schnittspahnstrasse 9, 64287, Darmstadt, Germany.
| | - Christoph Schüth
- Institute of Applied Geosciences, Technical University of Darmstadt, Schnittspahnstrasse 9, 64287, Darmstadt, Germany; IWW Water Centre, Moritzstrasse 26, 45476, Mülheim an der Ruhr, Germany.
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4
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Jiang T, Huang M, He H, Lu J, Zhou X, Cai M, Zhang Y. Bioprocess exploration for thermostable α-amylase production of a deep-sea thermophile Geobacillus sp. in high-temperature bioreactor. Prep Biochem Biotechnol 2016; 46:620-7. [DOI: 10.1080/10826068.2015.1128444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Tao Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Mengmeng Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jian Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Louvado A, Gomes NCM, Simões MMQ, Almeida A, Cleary DFR, Cunha A. Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe-pollutant interactions in a remote environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 526:312-328. [PMID: 25965373 DOI: 10.1016/j.scitotenv.2015.04.048] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 06/04/2023]
Abstract
Recalcitrant polycyclic aromatic hydrocarbons (PAHs) released into seawater end up in the deep sea sediments (DSSs). However, their fate here is often oversimplified by theoretical models. Biodegradation of PAHs in DSSs, is assumed to be similar to biodegradation in surface habitats, despite high hydrostatic pressures and low temperatures that should significantly limit PAH biodegradation. Bacteria residing in the DSSs (related mainly to α- and γ-Proteobacteria) have been shown to or predicted to possess distinct genes, enzymes and metabolic pathways, indicating an adaptation of these bacterial communities to the psychro-peizophilic conditions of the DSSs. This work summarizes some of the most recent research on DSS hydrocarbonoclastic populations and mechanisms of PAH degradation and discusses the challenges posed by future high CO2 and UV climate scenarios on biodegradation of PAHs in DSSs.
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Affiliation(s)
- A Louvado
- CESAM, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N C M Gomes
- CESAM, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - M M Q Simões
- QOPNA, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A Almeida
- CESAM, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - D F R Cleary
- CESAM, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A Cunha
- CESAM, Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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6
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Jiang T, Cai M, Huang M, He H, Lu J, Zhou X, Zhang Y. Characterization of a thermostable raw-starch hydrolyzing α-amylase from deep-sea thermophile Geobacillus sp. Protein Expr Purif 2015; 114:15-22. [PMID: 26073094 DOI: 10.1016/j.pep.2015.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/05/2015] [Accepted: 06/04/2015] [Indexed: 11/29/2022]
Abstract
A deep-sea thermophile, Geobacillus sp. 4j, was identified to grow on starch and produce thermostable amylase. N-terminally truncated form of Geobacillus sp. 4j α-amylase (Gs4j-amyA) was fused at its N-terminal end with the signal peptide of outer membrane protein A (OmpA) of Escherichia coli. The enzyme was over-expressed in E. coli BL21 with a maximum extracellular production of 130U/ml in shake flask. The yield of the transformant increased 22-fold as compared with that of the wild strain. The recombinant enzyme purified to apparent homogeneity by metal-affinity chromatography, exhibited a molecular mass of 62kDa. It displayed the maximal activity at 60-65°C and pH 5.5. Its half-life (t1/2) at 80°C was 4.25h with a temperature deactivation energy of 166.3kJ/mol. Compared to three commonly used commercial α-amylases, the Gs4j-amyA exhibited similar thermostable performance to BLA but better than BAA and BSA. It also showed a universally efficient raw starch hydrolysis performance superior to commercial α-amylases at an acidic pH approaching nature of starch slurry. As a new acidic-resistant thermostable α-amylase, it has the potential to bypass the industrial gelatinization step in raw starch hydrolysis.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Mengmeng Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hao He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
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7
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Effect of copper exposure on bacterial community structure and function in the sediments of Jiaozhou Bay, China. World J Microbiol Biotechnol 2014; 30:2033-43. [DOI: 10.1007/s11274-014-1628-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/24/2014] [Indexed: 11/26/2022]
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8
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Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum "Nitrospinae". Syst Appl Microbiol 2014; 37:170-6. [PMID: 24581679 DOI: 10.1016/j.syapm.2013.12.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/06/2013] [Accepted: 12/23/2013] [Indexed: 11/22/2022]
Abstract
Nitrite oxidizing bacteria are an integral part of the nitrogen cycle in marine waters, but the knowledge about their diversity is limited. Recently, a high abundance of Nitrospina-like 16S rRNA gene sequences has been detected in oceanic habitats with low oxygen content by molecular methods. Here, we describe a new strain of Nitrospina, which was sampled in 100m depth from the Black Sea. It coexisted with a not-yet cultivated chemoorganotrophic gammaproteobacterium and could be purified by classical isolation methods including Percoll density gradient centrifugation. The new Nitrospina-like bacterium grew lithoautotrophically at 28°C in diluted seawater supplemented with inorganic salts and nitrite. Gram-negative rods were characterized morphologically, physiologically and partly biochemically. The 16S rRNA gene of the new strain of Nitrospina is 97.9% similar to the described species N. gracilis and DNA/DNA hybridization experiments revealed a relatedness of 30.0%. The data from both Nitrospina species and environmental clones were used for an extensive 16S rRNA based phylogenetic study applying high quality filtering. Treeing analyses confirm the newly defined phylum status for "Nitrospinae" [18]. The results of phylogenetic and genotypic analyses support the proposal of a novel species Nitrospina watsonii sp. nov. (type strain 347(T), LMG 27401(T), NCIMB 14887(T)).
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9
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Expression and characterization of a thermostable penicillin G acylase from an environmental metagenomic library. Biotechnol Lett 2013; 36:617-25. [PMID: 24338159 DOI: 10.1007/s10529-013-1403-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/31/2013] [Indexed: 10/25/2022]
Abstract
One clone (ACPGA001) exhibiting penicillin G acylase (PGA) activity was screened from a metagenomic library by using a medium containing penicillin G. A novel PGA gene from the inserted fragment of ACPGA001 was obtained by sequencing. The amino acid sequence of ACPGA001 PGA exhibited <33 % similarity to PGAs retrieved from GenBank. This gene was expressed in Escherichia coli M15 and the recombinant protein was purified and characterized. The ACPGA001 PGA exhibited a maximum activity at 60 °C and showed high activity at pH 4-10 with an optimum pH of 8.0. This enzyme was stable at 40 °C for 70 min with a half-life of 60 min at 55 °C. These beneficial characteristics of ACPGA001 PGA provide some advantages for the potential application of ACPGA001 PGA in industry.
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Gutierrez T, Nichols PD, Whitman WB, Aitken MD. Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton. Appl Environ Microbiol 2012; 78:628-37. [PMID: 22139001 PMCID: PMC3264135 DOI: 10.1128/aem.06398-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 11/11/2011] [Indexed: 11/20/2022] Open
Abstract
A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate Lingulodinium polyedrum CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to Porticoccus litoralis IMCC2115(T) (96.5%) and to members of the genera Microbulbifer (91.4 to 93.7%) and Marinimicrobium (90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class Gammaproteobacteria for which P. litoralis is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C(16:1ω7c), C(18:1ω7c), and C(16:0). DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of Porticoccus, for which the name Porticoccus hydrocarbonoclasticus sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean.
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Affiliation(s)
- Tony Gutierrez
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.
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Zeng Y, Zou Y, Chen B, Grebmeier JM, Li H, Yu Y, Zheng T. Phylogenetic diversity of sediment bacteria in the northern Bering Sea. Polar Biol 2011. [DOI: 10.1007/s00300-010-0947-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Forget NL, Murdock SA, Juniper SK. Bacterial diversity in Fe-rich hydrothermal sediments at two South Tonga Arc submarine volcanoes. GEOBIOLOGY 2010; 8:417-432. [PMID: 20533949 DOI: 10.1111/j.1472-4669.2010.00247.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Seafloor iron oxide deposits are a common feature of submarine hydrothermal systems. Morphological study of these deposits has led investigators to suggest a microbiological role in their formation, through the oxidation of reduced Fe in hydrothermal fluids. Fe-oxidizing bacteria, including the recently described Zetaproteobacteria, have been isolated from a few of these deposits but generally little is known about the microbial diversity associated with this habitat. In this study, we characterized bacterial diversity in two Fe oxide samples collected on the seafloor of Volcanoes 1 and 19 on the South Tonga Arc. We were particularly interested in confirming the presence of Zetaproteobacteria at these two sites and in documenting the diversity of groups other than Fe oxidizers. Our results (small subunit rRNA gene sequence data) showed a surprisingly high bacterial diversity, with 150 operational taxonomic units belonging to 19 distinct taxonomic groups. Both samples were dominated by Zetaproteobacteria Fe oxidizers. This group was most abundant at Volcano 1, where sediments were richer in Fe and contained more crystalline forms of Fe oxides. Other groups of bacteria found at these two sites include known S- and a few N-metabolizing bacteria, all ubiquitous in marine environments. The low similarity of our clones with the GenBank database suggests that new species and perhaps new families were recovered. The results of this study suggest that Fe-rich hydrothermal sediments, while dominated by Fe oxidizers, can be exploited by a variety of autotrophic and heterotrophic micro-organisms.
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Affiliation(s)
- N L Forget
- Department of Biology, University of Victoria, Petch Building 116, 3800 Finnerty Rd, Victoria, BC, Canada.
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Zhang Y, Zhao J, Zeng R. Expression and characterization of a novel mesophilic protease from metagenomic library derived from Antarctic coastal sediment. Extremophiles 2010; 15:23-9. [PMID: 21069403 DOI: 10.1007/s00792-010-0332-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 10/22/2010] [Indexed: 10/18/2022]
Abstract
A metagenomic cosmid library was constructed, in which the insert DNA was derived from the coastal sediment near Antarctic China Zhongshan Station. One clone (ACPRO001) expressing protease activity was isolated from the library using milk agar plates. Sequencing of the clone revealed a novel protease gene. The amino acid sequence comparison and phylogenetic analysis indicated that it could be classified as a subtilisin-like serine protease, though the highly conserved residue Asp was replaced by Ala. The ACPRO001 protease gene was expressed in pET-His and purified for characterization. The optimal temperature and pH for the activity of the ACPRO001 protease were 60°C and pH 9.0, respectively. The enzyme retained about 73% of residual activity after 2 h incubation at 50°C in the presence of Ca(2+). The presence of Ca(2+) increased the thermostability of ACPRO001 protease obviously. The enzymatic activity was inhibited by 1 mM phenylmethyl sulfonylfluoride (PMSF) and hydrochloride 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), indicating that it was a serine protease.
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Affiliation(s)
- Yingjing Zhang
- Key Lab of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, Daxue Road 178#, Xiamen 361005, China
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Oh HM, Kim H, Kim KM, Min GS, Cho JC. Porticoccus litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from the Yellow Sea. Int J Syst Evol Microbiol 2010; 60:727-732. [DOI: 10.1099/ijs.0.013938-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A marine bacterium, designated IMCC2115T, was isolated from coastal seawater (Yellow Sea, Korea) using a high throughput cultivation method based on dilution-to-extinction, and taxonomically investigated. Cells of the strain formed tiny, beige to off-white colonies and were Gram-stain-negative, obligately aerobic, chemoheterotrophic, non-motile cocci. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to the genera Marinimicrobium (92.0–92.4 %) and Microbulbifer (91.6–92.8 %), but phylogenetic trees showed that the strain formed a distinct phyletic line in the class Gammaproteobacteria adjacent to the OM60 and SAR92 clades. The DNA G+C content of the strain was 47.8 mol% and the predominant cellular fatty acids were anteiso-C15 : 0 (67.6 %), anteiso-C17 : 0 (14.4 %) and C16 : 0 (6.9 %). The 16S rRNA gene sequence analyses and phenotypic and chemotaxonomic tests allowed the differentiation of IMCC2115T from other related genera in the class Gammaproteobacteria. Therefore, strain IMCC2115T (=KCCM 42369T =NBRC 102686T) is proposed as the representative of a new genus and species, for which the name Porticoccus litoralis gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Hyun-Myung Oh
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Hana Kim
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Kyung-Mi Kim
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Gi-Sik Min
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
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Li H, Yu Y, Luo W, Zeng Y, Chen B. Bacterial diversity in surface sediments from the Pacific Arctic Ocean. Extremophiles 2009; 13:233-46. [PMID: 19153801 DOI: 10.1007/s00792-009-0225-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 10/20/2008] [Indexed: 11/30/2022]
Abstract
In order to assess bacterial diversity within four surface sediment samples (0-5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (alpha, beta, gamma, delta and epsilon-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). alpha, gamma, and delta-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The gamma-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of gamma-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.
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Affiliation(s)
- Huirong Li
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 200136 Shanghai, China.
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Dang H, Li J, Chen M, Li T, Zeng Z, Yin X. Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9877-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhao J, Yang N, Zeng R. Phylogenetic analysis of type I polyketide synthase and nonribosomal peptide synthetase genes in Antarctic sediment. Extremophiles 2007; 12:97-105. [PMID: 17726573 DOI: 10.1007/s00792-007-0107-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 08/01/2007] [Indexed: 11/26/2022]
Abstract
The modular polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) have been found to be involved in natural product synthesis in many microorganisms. Study on their diversities in natural environment may provide important ecological insights, in addition to opportunities for antibacterial drugs development. In this study, the PKS and NRPS gene diversities in two coast sediments near China Zhongshan Station were studied. The phylogenetic analysis of amino acid (AA) sequences indicated that the identified ketosynthase (KS) domains were clustered with those from diverse bacterial groups, including Proteobacteria, Firmicutes, Planctomycetes, Cyanobacteria, Actinobacteria, and some uncultured symbiotic bacteria. One new branch belonging to hybrid PKS/NRPS enzyme complexes and five independent clades were found on the phylogenetic tree. The obtained adenylation (A) domains were mainly clustered within the Cyanobacteria and Proteobacteria group. Most of the identified KS and A domains showed below 80 and 60% identities at the AA level to their closest matches in GenBank, respectively. The diversities of both KS and A domains in natural environmental sample were different from those in sewage-contaminated sample. These results revealed the great diversity and novelty of both PKS and NRPS genes in Antarctic sediment.
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Affiliation(s)
- Jing Zhao
- School of Life Sciences, Xiamen University, Xiamen 361005, China
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18
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Zhang JW, Zeng RY. Psychrotrophic amylolytic bacteria from deep sea sediment of Prydz Bay, Antarctic: diversity and characterization of amylases. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9400-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Alekhina IA, Marie D, Petit JR, Lukin VV, Zubkov VM, Bulat SA. Molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at Vostok, East Antarctica. FEMS Microbiol Ecol 2007; 59:289-99. [PMID: 17313578 DOI: 10.1111/j.1574-6941.2006.00271.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. At the Vostok drill site, a total of 3650 m of ice core have now been obtained from the East Antarctic ice sheet. The ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. In the present study we used 16S rRNA gene sequencing to analyze the bacterial content of the Vostok drilling fluid sampled from four depths in the borehole. Six phylotypes were identified in three of four samples studied. The two dominant phylotypes recovered from the deepest (3400 and 3600 m) and comparatively warm (-10 degrees C and -6 degrees C, respectively) borehole horizons were from within the genus Sphingomonas, a well-known degrader of polyaromatic hydrocarbons. The remaining phylotypes encountered in all samples proved to be human- or soil-associated bacteria and were presumed to be drilling fluid contaminants of rare occurrence. The results obtained indicate the persistence of bacteria in extremely cold, hydrocarbon-rich environments. They show the potential for contamination of ice and subglacial water samples during lake exploration, and the need to develop a microbiological database of drilling fluid findings.
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Affiliation(s)
- Irina A Alekhina
- Petersburg Nuclear Physics Institute RAS, St Petesrburg-Gatchina, Russia.
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20
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Lian M, Lin S, Zeng R. Chitinase gene diversity at a deep sea station of the east Pacific nodule province. Extremophiles 2007; 11:463-7. [PMID: 17225927 DOI: 10.1007/s00792-006-0057-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 12/06/2006] [Indexed: 11/30/2022]
Abstract
The Pacific nodule province covered about 4.5 million km(2) in the east tropical Pacific with an abundance of polymetallic nodules at the seafloor. In view of the environmental protection and resource preservation, the survey of biodiversity was important during the reconnaissance and exploitation in this area. As one of the important component of the deep sea ecosystem, the microbial community in the Pacific nodule province was still largely unknown. The chitinolytic bacteria diversity in deep-sea sediment of a station within the Pacific nodule province was examined by molecular technology. A total of 18 chitinase genes were detected by a set of degenerate PCR primer specific for chiA gene fragment of family 18 chitinase. Most of them belonged to the Serratia-like chitinase. Eight genes had different amino acid sequences in the conserved motif, encompassing the catalytic site among the ChiA protein of family 18 glycosyl hydrolases, and clustered in an independent clade on the phylygenetic tree.
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Affiliation(s)
- Mingzhu Lian
- Key Lab of Marine Biogenetic Resources, Third Institute of Oceanography, SOA, Daxue road, No. 178, Xiamen, 361005, China
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21
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Abstract
The eubacterial communities adherent to sediment particles were studied in heavy metal contaminated coastal sediments. Six sampling sites on the Belgian continental plate and presenting various metal loads, granulometries, and organic matter content, were compared. The results indicated that the total microbial biomass (attached + free-living bacteria) was negatively correlated to HCl-extractable metal levels (p<0.05) and that the percentage of cells adherent to sediment particles was close to 100% in every site even in highly contaminated sediments. Consequently, it seems that heavy metal contamination does affect total bacterial biomass in marine sediments but that the ratio between attached and free living microorganisms is not affected. The composition of the eubacterial communities adherent to the fine fraction of the sediments (<150 microm) was determined using fluorescent in situ hybridisation (FISH). The FISH results indicated that the proportion of gamma- and delta-Proteobacteria, and Cytophaga-Flexibacter-Bacteroides (CFB) bacteria, was not related to the HCl extractable metal levels. Most of the 79 complete 16S rRNA sequences obtained from the attached microbial communities were classified in the gamma- and delta-Proteobacteria and in the CFB bacteria. A large proportion of the attached gamma-Proteobacterial sequences found in this study (56%) was included in the uncultivated GMS clades that are indigenous to marine sediments.
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Affiliation(s)
- David C Gillan
- Marine Biology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.
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22
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Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial community composition in deep-sea sediments of the South China Sea. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9181-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Keinänen-Toivola MM, Revetta RP, Santo Domingo JW. Identification of active bacterial communities in a model drinking water biofilm system using 16S rRNA-based clone libraries. FEMS Microbiol Lett 2006; 257:182-8. [PMID: 16553851 DOI: 10.1111/j.1574-6968.2006.00167.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recent phylogenetic studies have used DNA as the target molecule for the development of environmental 16S rRNA gene clone libraries. As DNA may persist in the environment, DNA-based libraries cannot be used to identify metabolically active bacteria in water systems. In this study, an annular reactor was used to generate model drinking water biofilms grown on polycarbonate slides. High-quality RNA was extracted from 2-month-old biofilms and used to generate 16S rRNA-based clones. Sequencing analyses of 16S rRNA-based clones suggested that the active bacterial fraction consisted of a few dominant bacterial groups related to Nevskia ramosa and to uncultured bacteria. Several of these bacterial groups were closely related to clones characterized in a DNA-based clone library also generated in this study. Altogether, these results suggest that some of the predominant drinking water bacteria identified using DNA-based techniques are indeed active.
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