1
|
Zhou DD, Xu XD, Zhang BZ, Feng JX, Zhang J. Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea. Antonie Van Leeuwenhoek 2023; 116:1337-1344. [PMID: 37833447 DOI: 10.1007/s10482-023-01890-5] [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: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
In this study, we reported a Gram-stain-negative, rod-shaped, atrichous, and aerobic bacterial strain named YMD87T, which was isolated from the intertidal zone sediment of Chinese Yellow Sea. Growth of strain YMD87T occurred at 10.0-40.0 °C (optimum, 25-30 °C), pH 4.0-12.0 (optimum, 8.0) and with 0-6.0% (w/v) NaCl (optimum, 0.0-2.0%). Phylogenetic tree analysis based on 16S rRNA gene sequence indicated that strain YMD87T belonged to the genus Tropicibacter and was closely related to Tropicibacter alexandrii LMIT003T (97.2% sequence similarity). Genomic analysis indicated that strain YMD87T contains a circular chromosome of 3,932,460 bp with G + C content of 63.8% and three circular plasmids of 116,492 bp, 49,209 bp and 49,673 bp, with G + C content of 64.3%. Genomic functional analysis revealed that strain YMD87T is potential a novel sulfur-metabolizing bacteria. The predominant respiratory quinone of YMD87T was ubiquinone-10 (Q-10). The major polar lipids of YMD87T contained phosphatidylglycerol, phosphatidylethanolamine, five unidentified lipids, five unidentified phospholipids, phosphatidylcholine, unidentified glycolipid and five unidentified aminolipids. The major fatty acids of strain YMD87T contained C12:1 3-OH, C16:0, and summed feature 8 (C18:1 ω7c or/and C18:1 ω6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD87T represents a novel species of the genus Tropicibacter, and the name Tropicibacter oceani sp. nov is proposed. The type strain is YMD87T (= MCCC 1K08473T = KCTC 92856 T).
Collapse
Affiliation(s)
- Dan-Dan Zhou
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Xiu-Dan Xu
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Bin-Zhe Zhang
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Ji-Xing Feng
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China
| | - Jian Zhang
- School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China.
| |
Collapse
|
2
|
Tiralerdpanich P, Nasaree S, Pinyakong O, Sonthiphand P. Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 289:117849. [PMID: 34325096 DOI: 10.1016/j.envpol.2021.117849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/07/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg-1), moderate (600 mg kg-1), and high (1200 mg kg-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg-1 sediment day-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg-1 sediment day-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.
Collapse
Affiliation(s)
- Parichaya Tiralerdpanich
- International Postgraduate Program in Hazardous Substance and Environmental Management, Chulalongkorn University, 9th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand
| | - Sirawit Nasaree
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Rachadhavi, Bangkok, 10400, Thailand
| | - Onruthai Pinyakong
- Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok, 10330, Thailand
| | - Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Rachadhavi, Bangkok, 10400, Thailand.
| |
Collapse
|
3
|
Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109. [PMID: 34248901 PMCID: PMC8267831 DOI: 10.3389/fmicb.2021.683109] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
Collapse
Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University Singapore, Singapore, Singapore
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
4
|
Chernikova TN, Bargiela R, Toshchakov SV, Shivaraman V, Lunev EA, Yakimov MM, Thomas DN, Golyshin PN. Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata. Front Microbiol 2020; 11:572931. [PMID: 33193176 PMCID: PMC7655873 DOI: 10.3389/fmicb.2020.572931] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.
Collapse
Affiliation(s)
- Tatyana N Chernikova
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | | | - Evgenii A Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Michail M Yakimov
- Institute for Marine Biological Resources and Biotechnology of the National Research Council, IRBIM-CNR, Messina, Italy
| | - David N Thomas
- School of Ocean Sciences, Bangor University, Menai Bridge, United Kingdom
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom.,CEB-Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| |
Collapse
|
5
|
Cao Q, Najnine F, Han H, Wu B, Cai J. BALOs Improved Gut Microbiota Health in Postlarval Shrimp ( Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment. Front Microbiol 2020; 11:1296. [PMID: 32714290 PMCID: PMC7344170 DOI: 10.3389/fmicb.2020.01296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
Abstract
White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.
Collapse
Affiliation(s)
- Qingqing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Farhana Najnine
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hongcao Han
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Bing Wu
- Modern Analysis Centre, South China University of Technology, Guangzhou, China
| | - Junpeng Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
6
|
Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
Collapse
Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| |
Collapse
|
7
|
Wang X, Zhu J, Feng J, Sardar A, Hu Z, Wang H. Tropicibacter alexandrii sp. nov., a novel marine bacterium isolated from the phycosphere of a dinoflagellate, Alexandrium minutum. Antonie van Leeuwenhoek 2019; 113:311-320. [PMID: 31595364 DOI: 10.1007/s10482-019-01339-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 01/31/2023]
Abstract
An aerobic, Gram-negative, rod-shaped, non-motile bacterium was isolated from a liquid culture of the dinoflagellate Alexandrium minutum and designated as strain LMIT003T. Analyses of 16S rRNA gene sequences revealed that this strain is affiliated with the genus Tropicibacter in the family Rhodobacteraceae of the class Alphaproteobacteria and shows high similarity (97.3%) with the type species Tropicibacter naphthalenivorans C02T. Phylogenetic analysis based on core genes showed that the isolate groups with members of the genus Tropicibacter. The G + C content of strain LMIT003T was determined to be 61.9 mol%. The major fatty acids identified included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C18:0, C12:1 3-OH and C16:0. The sole respiratory lipoquinone was found to be ubiquinone-10. The major polar lipids were found to be phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. The draft genome size of strain LMIT003T was determined to be 4.8 Mbp. The average nucleotide identity values between strain LMIT003T and reference Tropicibacter species were determined to be 78.7% (T. naphthalenivorans) and 74.2% (Tropicibacter phthalicicus). Based on physiological, chemotaxonomic and phylogenetic analysis, strain LMIT003T is concluded to represent a novel species in the genus Tropicibacter, for which the name Tropicibacter alexandrii sp. nov., is proposed. The type strain is LMIT003T (= CICC 24660T = KCTC 62895T).
Collapse
Affiliation(s)
- Xiaoli Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jianming Zhu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jiarong Feng
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Ali Sardar
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China.
| |
Collapse
|
8
|
Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393-2411. [DOI: 10.1099/ijsem.0.002833] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joseph S. Wirth
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
9
|
Cho S, Kim J, Kim S, Lee SS. Nitrogen and phosphorus treatment of marine wastewater by a laboratory-scale sequencing batch reactor with eco-friendly marine high-efficiency sediment. ENVIRONMENTAL TECHNOLOGY 2018; 39:1721-1732. [PMID: 28590161 DOI: 10.1080/09593330.2017.1337234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED We screened and identified a NH3-N-removing bacterial strain, Bacillus sp. KGN1, and a [Formula: see text] removing strain, Vibrio sp. KGP1, from 960 indigenous marine isolates from seawater and marine sediment from Tongyeong, South Korea. We developed eco-friendly high-efficiency marine sludge (eco-HEMS), and inoculated these marine bacterial strains into the marine sediment. A laboratory-scale sequencing batch reactor (SBR) system using the eco-HEMS for marine wastewater from land-based fish farms improved the treatment performance as indicated by 88.2% removal efficiency (RE) of total nitrogen (initial: 5.6 mg/L) and 90.6% RE of total phosphorus (initial: 1.2 mg/L) under the optimal operation conditions (food and microorganism (F/M) ratio, 0.35 g SCODCr/g mixed liquor volatile suspended solids (MLVSS)·d; dissolved oxygen (DO) 1.0 ± 0.2 mg/L; hydraulic retention time (HRT), 6.6 h; solids retention time (SRT), 12 d). The following kinetic parameters were obtained: cell yield (Y), 0.29 g MLVSS/g SCODCr; specific growth rate (µ), 0.06 d-1; specific nitrification rate (SNR), 0.49 mg NH3-N/g MLVSS·h; specific denitrification rate (SDNR), 0.005 mg [Formula: see text]/g MLVSS·h; specific phosphorus uptake rate (SPUR), 0.12 mg [Formula: see text]/g MLVSS·h. The nitrogen- and phosphorus-removing bacterial strains comprised 18.4% of distribution rate in the microbial community of eco-HEMS under the optimal operation conditions. Therefore, eco-HEMS effectively removed nitrogen and phosphorus from highly saline marine wastewater from land-based fish farms with improving SNR, SDNR, and SPUR values in more diverse microbial communities. ABBREVIATIONS DO: dissolved oxygen; Eco-HEMS: eco-friendly high efficiency marine sludge; F/M: food and microorganism ratio; HRT: hydraulic retention time; ML(V)SS: mixed liquor (volatile) suspended solids; NCBI: National Center for Biotechnology Information; ND: not determined; qPCR: quantitative real-time polymerase chain reaction; RE: removal efficiency; SBR: sequencing batch reactor; SD: standard deviation; SDNR: specific denitrification rate; SNR: specific nitrification rate; SPUR: specific phosphate uptake rate; SRT: solids retention time; T-N: total nitrogen; T-P: total phosphorus; (V)SS: (volatile) suspended solids; w.w.: wet weight.
Collapse
Affiliation(s)
- Seonghyeon Cho
- a Department of Biological Engineering , Kyonggi University , Suwon-si , Republic of Korea
| | - Jinsoo Kim
- b Department of Life Science , Kyonggi University , Suwon-si , Republic of Korea
| | - Sungchul Kim
- c Department of Environmental Energy Engineering , Kyonggi University , Suwon-si , Republic of Korea
| | - Sang-Seob Lee
- a Department of Biological Engineering , Kyonggi University , Suwon-si , Republic of Korea
- b Department of Life Science , Kyonggi University , Suwon-si , Republic of Korea
| |
Collapse
|
10
|
Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int J Syst Evol Microbiol 2018; 68:736-744. [DOI: 10.1099/ijsem.0.002573] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
11
|
Feng T, Kim KH, Jeong SE, Kim W, Jeon CO. Aquicoccus porphyridii gen. nov., sp. nov., isolated from a small marine red alga, Porphyridium marinum. Int J Syst Evol Microbiol 2018; 68:283-288. [DOI: 10.1099/ijsem.0.002498] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tingye Feng
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
12
|
Loredana S, Graziano P, Antonio M, Carlotta NM, Caterina L, Maria AA, Carlo Z, Giuseppe C, Pietro A. Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon perlevis. Mar Drugs 2017; 15:md15040108. [PMID: 28383507 PMCID: PMC5408254 DOI: 10.3390/md15040108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
Lindane is an organochlorine pesticide belonging to persistent organic pollutants (POPs) that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we assessed the role of bacteria associated with the sponge Hymeniacidon perlevis in lindane degradation. Seven bacteria isolates were characterized and identified. These isolates showed a remarkable capacity to utilize lindane as a sole carbon source leading to a percentage of residual lindane ranging from 3% to 13% after 12 days of incubation with the pesticide. The lindane metabolite, 1,3–6-pentachloro-cyclohexene, was identified as result of lindane degradation and determined by gas chromatography–mass spectrometry (GC–MS). The bacteria capable of lindane degradation were identified on the basis of the phenotypic characterization by morphological, biochemical and cultural tests, completed with 16S rDNA sequence analysis, and assigned to Mameliella phaeodactyli, Pseudovibrioascidiaceicola, Oceanicaulis stylophorae, Ruegeria atlantica and to three new uncharacterized species. The results obtained are a prelude to the development of future strategies for the in situ bioremediation of lindane.
Collapse
Affiliation(s)
- Stabili Loredana
- Istituto per l'Ambiente Marino Costiero, Unità Operativa di Supporto di Taranto, CNR, Via Roma 3, 74123 Taranto, Italy.
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Pizzolante Graziano
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Morgante Antonio
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Nonnis Marzano Carlotta
- Dipartimento di Biologia, Università di Bari Aldo Moro, 70125 Bari, Italy.
- CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy.
| | - Longo Caterina
- Dipartimento di Biologia, Università di Bari Aldo Moro, 70125 Bari, Italy.
- CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy.
| | | | - Zambonin Carlo
- Dipartimento di Chimica, Università di Bari Aldo Moro, 70125 Bari, Italy.
| | - Corriero Giuseppe
- Dipartimento di Biologia, Università di Bari Aldo Moro, 70125 Bari, Italy.
- CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy.
| | - Alifano Pietro
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| |
Collapse
|
13
|
Thelusmond JR, Strathmann TJ, Cupples AM. The identification of carbamazepine biodegrading phylotypes and phylotypes sensitive to carbamazepine exposure in two soil microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:1241-1252. [PMID: 27481454 DOI: 10.1016/j.scitotenv.2016.07.154] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Carbamazepine (CBZ), an antiepileptic drug, has been introduced into agricultural soils via irrigation with treated wastewater and biosolids application. Such contamination is problematic because CBZ is persistent and the risks to ecosystems or human health are unknown. The current study examined CBZ biodegradation in two agricultural soils (soil 1 and 2) and the effects on the soil microbial communities during CBZ exposure. The experimental design involved three CBZ concentrations (50, 500, 5000ng/g), under aerobic as well as anaerobic conditions. CBZ concentrations were determined using solid phase extraction and LC MS/MS. The effect of CBZ on the soil microbial community was investigated using high throughput sequencing and a computational approach to predict functional composition of the metagenomes (phylogenetic investigation of communities by reconstruction of unobserved states, PICRUSt). The most significant CBZ biodegradation occurred in soil 1 under aerobic conditions. In contrast, CBZ biodegradation was limited under anaerobic conditions in soil 1 and under both conditions in soil 2. For soil 1, several phylotypes were enriched following CBZ degradation compared to the controls, including unclassified Sphingomonadaceae, Xanthomonadaceae and Rhodobacteraceae, as well as Sphingomonas, Aquicella and Microvirga. These phylotypes are considered putative CBZ degraders as they appear to be benefiting from CBZ biodegradation. PICRUSt revealed that soil 1 contained a greater abundance of xenobiotic degrading genes compared to soil 2, and thus, this analysis method offers a potential valuable approach for predicting CBZ attenuation in soils. PICRUSt analysis also implicated Sphingomonadaceae and Xanthomonadaceae in drug metabolism. Interestingly, numerous phylotypes decreased in abundance following CBZ exposure and these varied with soil type, concentration, duration of exposure, and the availability of oxygen. For three phylotypes (Flavobacterium, 3 genus incertae sedis and unclassified Bacteroidetes), the relative abundance was reduced in both soils, indicating a notable sensitivity to CBZ for these microorganisms.
Collapse
Affiliation(s)
- Jean-Rene Thelusmond
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy J Strathmann
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
14
|
Hameed A, Shahina M, Lin SY, Nakayan P, Liu YC, Lai WA, Hsu YH. Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007. Int J Syst Evol Microbiol 2014; 64:2729-2737. [DOI: 10.1099/ijs.0.060962-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-ET, was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-ET shared 95.7 and 93.9 % 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera
Donghicola
(
Donghicola eburneus
SW-277T) and
Roseovarius
(
Roseovarius tolerans
EL-172T). The predominant (>75 % of the total) fatty acid was summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-ET represents a novel genus and species of the family
Rhodobacteraceae
, for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-ET ( = JCM 18819T = BCRC 80549T). In addition, an emended description of the genus
Donghicola
Yoon et al. 2007 and the reclassification of
Donghicola xiamenensis
Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2T = MCCC 1A00107T = LMG 24574T = CGMCC 1.7081T) are proposed.
Collapse
Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Phanit Nakayan
- Faculty of Agricultural Production, Maejo University, Sansai, Chiang Mai 50290, Thailand
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| | - Yi-Han Hsu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan ROC
| |
Collapse
|
15
|
Lamendella R, Strutt S, Borglin S, Chakraborty R, Tas N, Mason OU, Hultman J, Prestat E, Hazen TC, Jansson JK. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. Front Microbiol 2014; 5:130. [PMID: 24772107 PMCID: PMC3982105 DOI: 10.3389/fmicb.2014.00130] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/13/2014] [Indexed: 02/01/2023] Open
Abstract
One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.
Collapse
Affiliation(s)
- Regina Lamendella
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Biology Department, Juniata College Huntingdon, PA, USA
| | - Steven Strutt
- Biology Department, Juniata College Huntingdon, PA, USA
| | - Sharon Borglin
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Neslihan Tas
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Olivia U Mason
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Earth, Ocean and Atmospheric Science, Florida State University Tallahassee, FL, USA
| | - Jenni Hultman
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Food Hygiene and Environmental Health, University of Helsinki Helsinki, Finland
| | - Emmanuel Prestat
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA
| | - Terry C Hazen
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Civil and Environmental Engineering, University of Tennessee Knoxville, TN, USA ; Oak Ridge National Laboratory, Biosciences Division Oak Ridge, TN, USA
| | - Janet K Jansson
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department Berkeley, CA, USA ; Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| |
Collapse
|
16
|
Lee DH, Cho SJ, Kim SM, Lee SB. Sagittula marina sp. nov., isolated from seawater and emended description of the genus
Sagittula. Int J Syst Evol Microbiol 2013; 63:2101-2107. [DOI: 10.1099/ijs.0.040766-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain F028-2T, was isolated from seawater at Damupo beach in Pohang, Korea, and investigated in a taxonomic study using a polyphasic approach. This novel strain was strictly aerobic, non-motile, Gram-stain-negative and rod-shaped, and occasionally formed aggregates. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 6.5–9.0 and 1–7 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F028-2T formed a lineage within the family
Rhodobacteraceae
of the class
Alphaproteobacteria
, and was closely related to members of the genera
Sagittula
and
Antarctobacter
with 96.3–96.4 % sequence similarities. The polar lipid profile of strain F028-2T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and six unidentified lipids. The predominant cellular fatty acids were C18 : 1ω7c and C12 : 1 3-OH. The genomic DNA G+C content of strain F028-2T was 61.6 mol% and the major respiratory quinone was Q-10. Based on phenotypic, phylogenetic and genotypic data, strain F028-2T is considered to represent a novel species in the genus
Sagittula
, for which the name Sagittula marina sp. nov. is proposed. The type strain is F028-2T ( = KCTC 23543T = JCM 17627T). An emended description of the genus Sagittula is also proposed.
Collapse
Affiliation(s)
- Dong-Heon Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Sun Ja Cho
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Suk Min Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Sun Bok Lee
- Gyeongbuk Sea Grant Institute, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| |
Collapse
|
17
|
Yoon JH, Park S, Jung YT. Aestuariihabitans beolgyonensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. Antonie van Leeuwenhoek 2013; 104:217-24. [DOI: 10.1007/s10482-013-9940-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 05/24/2013] [Indexed: 11/28/2022]
|
18
|
Lucena T, Ruvira MA, Macián MC, Pujalte MJ, Arahal DR. Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov. Syst Appl Microbiol 2013; 36:325-9. [PMID: 23706913 DOI: 10.1016/j.syapm.2013.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/28/2013] [Accepted: 04/02/2013] [Indexed: 11/28/2022]
Abstract
Four strains (M15∅_3, M17(T), M49 and R37(T)) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF) data proved: (i) non clonality among the strains, and (ii) the existence of two genospecies, one consisting of strains M15∅_3, M17(T), M49 and 2OM6 and another one consisting of strain R37(T). Phenotypic traits determined allow differentiating both genospecies from each other and from closely related taxa. In view of all data collected we propose to accommodate these isolates in two species as members of the genus Tropicibacter, Tropicibacter mediterraneus sp. nov. (type strain M17(T)=CECT 7615(T)=KCTC 23058(T)) and Tropicibacter litoreus sp. nov. (type strain R37(T)=CECT 7639(T)=KCTC 23353(T)).
Collapse
Affiliation(s)
- Teresa Lucena
- Colección Española de Cultivos Tipo CECT and Departamento de Microbiología y Ecología, Universidad de Valencia, Spain
| | | | | | | | | |
Collapse
|
19
|
Starting Up Microbial Enhanced Oil Recovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:1-94. [DOI: 10.1007/10_2013_256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
20
|
Iwaki H, Nishimura A, Hasegawa Y. Tropicibacter phthalicus sp. nov., a phthalate-degrading bacterium from seawater. Curr Microbiol 2012; 64:392-6. [PMID: 22278761 DOI: 10.1007/s00284-012-0085-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/28/2011] [Indexed: 12/01/2022]
Abstract
An aerobic, Gram-negative bacterial strain, designated KU27E1(T), which degrades phthalate and dimethylphthalate, was isolated from seawater obtained from the coastal region of Ishigaki Island, Japan. Cells are motile rods with polar flagella. Strain KU27E1(T) grew at 15-30°C, pH 6.0-8.0, in the presence of 1.0-2.0% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that this strain was affiliated with the family Rhodobacteraceae in the class Alphaproteobacteria, and was most closely related to Tropicibacter naphthalenivorans (96.8%). The predominant respiratory lipoquinone was ubiquinone-10, and the major cellular fatty acid was C(18:1)ω7c (88.5%). The G+C content of genomic DNA was 58.7 mol%. Based on the physiological, chemotaxonomic, and phylogenetic data, strain KU27E1(T) is suggested to represent a novel species of the genus Tropicibacter, for which the name Tropicibacter phthalicus sp. nov. is proposed. The type strain of Tropicibacter phthalicus is designated as KU27E1(T) (=JCM 17793(T) = KCTC 23703(T)).
Collapse
Affiliation(s)
- Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, Suita, Osaka, Japan.
| | | | | |
Collapse
|
21
|
Na H, Kim OS, Yoon SH, Kim Y, Chun J. Comparative approach to capture bacterial diversity of coastal waters. J Microbiol 2011; 49:729-40. [PMID: 22068488 DOI: 10.1007/s12275-011-1205-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 05/27/2011] [Indexed: 01/28/2023]
Abstract
Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.
Collapse
Affiliation(s)
- Hyunsoo Na
- Center for Geomicrobiology, University of Aarhus, Ny Munkegade, Bld. 1535, 8000, Århus C, Denmark
| | | | | | | | | |
Collapse
|
22
|
Lucena T, Pujalte MJ, Ruvira MA, Garay E, Macián MC, Arahal DR. Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater. Int J Syst Evol Microbiol 2011; 62:844-848. [PMID: 21602360 DOI: 10.1099/ijs.0.030973-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MD5T, an aerobic marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized in a polyphasic study and was placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD5T is related to Tropicibacter naphthalenivorans C02T, Phaeobacter inhibens T5T, P. gallaeciensis BS107T and P. daeponensis TF-218T, with 96.9, 96.2, 96.1 and 96.1 % sequence similarity, respectively. Phylogenetic analyses also showed that strain MD5T forms a stable clade only with T. naphthalenivorans C02T. Strain MD5T requires Na+ plus a divalent cation (either Mg2+ or Ca2+) to grow, does not reduce nitrate to nitrite and uses a large number of carbohydrates as sole carbon sources. It is positive for β-galactosidase and urease activities and aesculin hydrolysis. Enzyme activities displayed in the API ZYM strip were alkaline phosphatase, leucine arylamidase, acid phosphatase and α-glucosidase. Major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c; 70.9 %) and C16:0 (8.2 %). The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from the only described species of the genus Tropicibacter. It is evident from the genotypic and phenotypic data obtained that the strain should be classified in a novel species in the genus Tropicibacter. The name Tropicibacter multivorans sp. nov. is proposed, with the type strain MD5T (=CECT 7557T=KCTC 23350T).
Collapse
Affiliation(s)
- Teresa Lucena
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| | - Esperanza Garay
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología, Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain
| |
Collapse
|
23
|
Zheng Q, Chen C, Yan XJ, Wang YN, Zeng YH, Hao LK, He WH, Jiao NZ. Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 2010; 60:953-957. [DOI: 10.1099/ijs.0.011437-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, rod-shaped bacterial strain, JLT354-WT, that accumulates poly-β-hydroxybutyrate granules was isolated from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was related to members of the genera Antarctobacter, Sagittula, Oceanicola and Loktanella; levels of similarity between strain JLT354-WT and members of the above genera were less than 92.0 %. The predominant fatty acid of strain JLT354-WT was C18 : 1
ω7c (83.1 %); significant amounts of C18 : 0 (7.9 %) and C12 : 1 3-OH (3.7 %) were also present. The predominant respiratory ubiquinone was Q-10. The DNA G+C content of strain JLT354-WT was 63.7 mol%. The isolate was distinguishable from members of the order Rhodobacterales based on phenotypic and biochemical characteristics. On the basis of the taxonomic data presented, strain JLT354-WT is considered to represent a novel species of a new genus, for which the name Mameliella alba gen. nov., sp. nov. is proposed. The type strain of Mameliella alba is JLT354-WT (=LMG 24665T=CGMCC 1.7290T).
Collapse
Affiliation(s)
- Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Chuang Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Xiao-Jun Yan
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, PR China
| | - Ya-Nan Wang
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou 450008, PR China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Yong-Hui Zeng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Li-Kai Hao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| | - Wei-Hong He
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Nian-Zhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China
| |
Collapse
|