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Lu H, Chen L, Huang L. Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 38629951 DOI: 10.1099/ijsem.0.006345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.
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Affiliation(s)
- Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Linpei Huang
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
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Pitt A, Lienbacher S, Schmidt J, Neumann-Schaal M, Wolf J, Hahn MW. Description of a new freshwater bacterium Aquirufa regiilacus sp. nov., classification of the genera Aquirufa, Arundinibacter, Sandaracinomonas, and Tellurirhabdus to the family Spirosomataceae, classification of the genus Chryseotalea to the family Fulvivirgaceae and Litoribacter to the family Cyclobacteriaceae, as well as classification of Litoribacter alkaliphilus as a later heterotypic synonym of Litoribacter ruber. Arch Microbiol 2024; 206:79. [PMID: 38280955 PMCID: PMC10821818 DOI: 10.1007/s00203-023-03801-8] [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: 11/01/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/29/2024]
Abstract
Strains LEOWEIH-7CT and LEPPI-3A were isolated from the Leopoldskroner Weiher, a lake located in the city of Salzburg, Austria. 16S rRNA gene similarities and phylogenetic reconstructions with 16S rRNA gene sequences as well as based on genome sequences revealed that the new strains belong to the A. antheringensis branch of the genus Aquirufa. Calculated whole-genome average nucleotide identity (gANI) and digital DNA-DNA hybridization (dDDH) values with the closely related type strains showed that the two strains represent a single new species. The strains grew aerobically and chemoorganotrophically, and the cells were rod shaped, on average 0.8 µm long and 0.3 µm wide, red pigmented and motile by gliding. The genome size of both strains was 2.6 Mbp and the G+C value was 41.9%. The genomes comprised genes predicted for the complete light-harvesting rhodopsin system and various carotenoids. We proposed to establish the name Aquirufa regiilacus sp. nov. for strain LEOWEIH-7CT (=DSM 116390T = JCM 36347T) as the type strain. Strain LEPPI-3A (=DSM 116391 = JCM 36348) also belongs to this new species. The calculated genome-based phylogenetic tree revealed that Aquirufa and some other genera currently allocated in the family Cytophagaceae need a reclassification. Aquirufa, Arundinibacter, Sandaracinomonas, and Tellurirhabdus should be designated to the family Spirosomataceae, the genus Chryseotalea to the family Fulvivirgaceae, and the genus Litoribacter to the family Cyclobacteriaceae. Furthermore, based on calculated gANI and dDDH values, Litoribacter alkaliphilus should be reclassified as a later heterotypic synonym of Litoribacter ruber.
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria.
| | - Stefan Lienbacher
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Meina Neumann-Schaal
- Chemical Analytics and Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Chemical Analytics and Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Martin W Hahn
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
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Plaimart J, Acharya K, Blackburn A, Mrozik W, Davenport RJ, Werner D. Effective removal of iron, nutrients, micropollutants, and faecal bacteria in constructed wetlands cotreating mine water and sewage treatment plant effluent. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:116-131. [PMID: 38214989 PMCID: wst_2024_001 DOI: 10.2166/wst.2024.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Regulators in England and Wales have set new targets under the Environment Act 2021 for freshwater quality by 2038 that include halving the length of rivers polluted by harmful metals from abandoned mines and reducing phosphorus loadings from treated wastewater by 80%. In this context, an intriguing win-win opportunity exists in the removal of iron from abandoned mines and phosphate from small sewage treatment plants by coprecipitation in constructed wetlands (CWs). We investigated such a CW located at Lamesley, Northeast England, which cotreats abandoned coal mine and secondary-treated sewage treatment plant effluents. We assessed the removal of nutrients, heavy metals, organic micropollutants, and faecal coliforms by the CW, and characterized changes in the water bacteriology comprehensively using environmental DNA. The CW effectively removed ammonium-nitrogen, phosphorus, iron, and faecal coliforms by an average of 86, 74, 98, and 75%, respectively, to levels below or insignificantly different from those in the receiving river. The CW also effectively removed micropollutants such as acetaminophen, caffeine, and sulpiride by 70-100%. Molecular microbiology methods showed successful conversion of sewage and mine water microbiomes into a freshwater microbiome. Overall, the CW significantly reduced impacts on the rural water environment with minimal operational requirements.
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Affiliation(s)
- Jidapa Plaimart
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK E-mail:
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wojciech Mrozik
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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4
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Zhang X, Feng GD, Liu Y, Yang F, Li Y, Deng X, Zhu H, Yao Q. Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales. Arch Microbiol 2023; 205:345. [PMID: 37768397 DOI: 10.1007/s00203-023-03685-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.
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Affiliation(s)
- Xianjiao Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Guang-Da Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Fan Yang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yanxuan Li
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Xiaoqin Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
| | - Qing Yao
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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5
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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6
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Klair D, Dobhal S, Ahmad A, Hassan ZU, Uyeda J, Silva J, Wang KH, Kim S, Alvarez AM, Arif M. Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms. Front Microbiol 2023; 14:1039292. [PMID: 36876060 PMCID: PMC9981659 DOI: 10.3389/fmicb.2023.1039292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/16/2023] [Indexed: 02/19/2023] Open
Abstract
Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.
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Affiliation(s)
- Diksha Klair
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Amjad Ahmad
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Zohaib Ul Hassan
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Bio-Medical Measurement, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jensen Uyeda
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Joshua Silva
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Koon-Hui Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Seil Kim
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Bio-Medical Measurement, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
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Hahn MW, Pitt A, Schmidt J, Koll U, Wolf J, Whitman WB, Bodelier PLE, Neumann-Schaal M. Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65T (=CCUG 56422T=DSM 107630T) and MWH-P2sevCIIIbT (=CCUG 56420T=DSM 107629T), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family
Alcaligenaceae
and revealed
Orrella amnicola
and
Orrella marina
(=
Algicoccus marinus
) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus
Orrella
represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65T and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIbT. Furthermore, we propose the reclassification of the species
Orrella amnicola
in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.
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Affiliation(s)
- Martin W. Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Rau J, Werner D, Beer M, Höper D, Kampen H. The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany. Parasitol Res 2022; 121:2587-2599. [PMID: 35857094 PMCID: PMC9378336 DOI: 10.1007/s00436-022-07576-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022]
Abstract
Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.
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Affiliation(s)
- Janine Rau
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research, Muencheberg, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
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9
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Pitt A, Koll U, Schmidt J, Neumann-Schaal M, Wolf J, Krausz S, Hahn MW. Aquirufa lenticrescens sp. nov. and Aquirufa aurantiipilula sp. nov.: two new species of a lineage of widespread freshwater bacteria. Arch Microbiol 2022; 204:356. [PMID: 35654990 PMCID: PMC9163014 DOI: 10.1007/s00203-022-02950-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
Abstract
Two bacterial strains, 9H-EGSET and 15D-MOBT, were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa (Bacteroidota). Genome-based phylogenetic reconstructions with 119 amino acid sequences assigned the new taxa to the two distinct branches of the genus Aquirufa. Whole-genome average nucleotide identities were calculated with all possible pairs belonging to the genus. Values between 75.4% and 88.6% revealed that the two new strains represent each a new species. Like all, so far described members of the genus, they grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented, and motile by gliding, and showed genome sizes of about 3 Mbp and G + C values of about 40%. They could be distinguished by some phenotypic and chemotaxonomic features from their nearest related species. Until now, strain 9H-EGSET is the only one among the Aquirufa strains which contained traces of MK8 as respiratory quinone, and strain 15D-MOBT is the only one that formed tiny orange globules in liquid medium. The genome of strain 9H-EGSET comprised genes for the complete light-harvesting rhodopsin / retinal system, in the case of 15D-MOBT genes predicted for a nitrous oxide reductase were present. For the two new species of the genus Aquirufa, we propose to establish the names Aquirufa lenticrescens for strain 9H-EGSET (= JCM 34077 T = CIP 111926 T) and Aquirufa aurantiipilula for strain 15D-MOBT (= JCM 34078 T = CIP 111925 T).
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Contribution of single-cell omics to microbial ecology. Trends Ecol Evol 2021; 37:67-78. [PMID: 34602304 DOI: 10.1016/j.tree.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022]
Abstract
Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.
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Hahn MW, Pitt A, Koll U, Schmidt J, Maresca JA, Neumann-Schaal M. Aurantimicrobium photophilum sp. nov., a non-photosynthetic bacterium adjusting its metabolism to the diurnal light cycle and reclassification of Cryobacterium mesophilum as Terrimesophilobacter mesophilus gen. nov., comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34431766 DOI: 10.1099/ijsem.0.004975] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aerobic primarily chemoorganotrophic actinobacterial strain MWH-Mo1T was isolated from a freshwater lake and is characterized by small cell lengths of less than 1 µm, small cell volumes of 0.05-0.06 µm3 (ultramicrobacterium), a small genome size of 1.75 Mbp and, at least for an actinobacterium, a low DNA G+C content of 54.6 mol%. Phylogenetic analyses based on concatenated amino acid sequences of 116 housekeeping genes suggested the type strain of Aurantimicrobium minutum affiliated with the family Microbacteriaceae as its closest described relative. Strain MWH-Mo1T shares with the type strain of that species a 16S rRNA gene sequence similarity of 99.6 % but the genomes of the two strains share an average nucleotide identity of only 79.3 %. Strain MWH-Mo1T is in many genomic, phenotypic and chemotaxonomic characteristics quite similar to the type strain of A. minutum. Previous intensive investigations revealed two unusual traits of strain MWH-Mo1T. Although the strain is not known to be phototrophic, the metabolism is adjusted to the diurnal light cycle by up- and down-regulation of genes in light and darkness. This results in faster growth in the presence of light. Additionally, a cell size-independent protection against predation by bacterivorous flagellates, most likely mediated by a proteinaceous cell surface structure, was demonstrated. For the previously intensively investigated aerobic chemoorganotrophic actinobacterial strain MWH-Mo1T (=CCUG 56426T=DSM 107758T), the establishment of the new species Aurantimicrobium photophilum sp. nov. is proposed.
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Julia A Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Pitt A, Schmidt J, Koll U, Hahn MW. Aquiluna borgnonia gen. nov., sp. nov., a member of a Microbacteriaceae lineage of freshwater bacteria with small genome sizes. Int J Syst Evol Microbiol 2021; 71. [PMID: 33999796 DOI: 10.1099/ijsem.0.004825] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The actinobacterial strain 15G-AUS-rotT was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rotT to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rotT were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C16 : 0, antiso-C15 : 0 and iso-C14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rotT (=DSM 107803T=JCM 32974T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Rapid Changes in Microbial Community Structures along a Meandering River. Microorganisms 2020; 8:microorganisms8111631. [PMID: 33105630 PMCID: PMC7690413 DOI: 10.3390/microorganisms8111631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/02/2022] Open
Abstract
Streams and rivers convey freshwater from lands to the oceans, transporting various organic particles, minerals, and living organisms. Microbial communities are key components of freshwater food webs and take up, utilize, and transform this material. However, there are still important gaps in our understanding of the dynamic of these organisms along the river channels. Using high-throughput 16S and 18S rRNA gene sequencing and quantitative PCR on a 11-km long transect of the Saint-Charles River (Quebec, CA), starting from its main source, the Saint-Charles Lake, we show that bacterial and protist community structures in the river drifted quickly but progressively downstream of its source. The dominant Operational Taxonomic Units (OTUs) of the lake, notably related to Cyanobacteria, decreased in proportions, whereas relative proportions of other OTUs, such as a Pseudarcicella OTU, increased along the river course, becoming quickly predominant in the river system. Both prokaryotic and protist communities changed along the river transect, suggesting a strong impact of the shift from a stratified lake ecosystem to a continuously mixed river environment. This might reflect the cumulative effects of the increasing water turbulence, fluctuations of physicochemical conditions, differential predation pressure in the river, especially in the lake outlet by benthic filter feeders, or the relocation of microorganisms, through flocculation, sedimentation, resuspension, or inoculation from the watershed. Our study reveals that the transit of water in a river system can greatly impact both bacterial and micro-eukaryotic community composition, even over a short distance, and, potentially, the transformation of materials in the water column.
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Szuróczki S, Szabó A, Korponai K, Felföldi T, Somogyi B, Márialigeti K, Tóth E. Prokaryotic community composition in a great shallow soda lake covered by large reed stands (Neusiedler See/Lake Fertő) as revealed by cultivation- and DNA-based analyses. FEMS Microbiol Ecol 2020; 96:5895321. [PMID: 32821929 DOI: 10.1093/femsec/fiaa159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/11/2020] [Indexed: 11/15/2022] Open
Abstract
Little is known about the detailed community composition of heterotrophic bacterioplankton in macrophyte-dominated littoral systems, where a considerable amount of dissolved organic carbon originates from aquatic macrophytes instead of phytoplankton. The aim of the present study was to reveal the effect of macrophytes on the microbial community and to elucidate their role in a macrophyte-dominated shallow soda lake, which can be characterised by a mosaic of open waters and reed marsh. Therefore, 16S rRNA gene amplicon sequencing, the most probable number method, cultivation of bacterial strains, EcoPlate and cultivation-based substrate utilisation techniques were applied. Differences in the structures of microbial communities were detected between the water and the sediment samples and between vegetated and unvegetated water samples. Planktonic bacterial communities of an inner pond and a reed-covered area showed significant similarities to each other. Woesearchaeia was the dominant archaeal taxon in the water samples, while Bathyarchaeia, 'Marine Benthic Group D' and 'DHVEG-1' were abundant in the sediment samples. The most probable number of heterotrophic bacteria was lower in the open water than in the reed-associated areas. The vast majority (83%) of the isolated bacterial strains from the water samples of the reed-covered area were able to grow on a medium containing reed extract as the sole source of carbon.
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Affiliation(s)
- Sára Szuróczki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Boglárka Somogyi
- Centre for Ecological Research, Balaton Limnological Institute, Hungarian Academy of Sciences, Klebelsberg Kuno u. 3., 8237 Tihany, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
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Oren A. Prokaryotic names: the bold and the beautiful. FEMS Microbiol Lett 2020; 367:5854537. [PMID: 32510563 DOI: 10.1093/femsle/fnaa096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/05/2020] [Indexed: 11/14/2022] Open
Abstract
In recent years, names of ∼170 new genera and ∼1020 new species were added annually to the list of prokaryotic names with standing in the nomenclature. These names were formed in accordance with the Rules of the International Code of Nomenclature of Prokaryotes. Most of these names are not very interesting as specific epithets and word elements from existing names are repeatedly recycled. The rules of the Code provide many opportunities to create names in far more original ways. A survey of the lists of names of genera and species of prokaryotes shows that there is no lack of interesting names. The annotated selection presented here proves that at least some authors have exploited the possibilities allowed by the rules of the Code to name novel organisms in ways that are more attractive. I here call upon all colleagues who describe new taxa to devote more thought to the naming of new genera and species. It takes some effort, and it requires proper use of the lexicon of Classical Greek and Latin as well as an understanding of the Code and the guidelines of its orthography appendix. Creation of attractive names will boost the general interest in prokaryotic nomenclature.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
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Pitt A, Koll U, Schmidt J, Hahn MW. Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae. Int J Syst Evol Microbiol 2020; 70:4602-4609. [PMID: 32658638 DOI: 10.1099/ijsem.0.004319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus Aquirufa. Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigated. Like strains of other Aquirufa species, 50A-KIRBAT and 50C-KIRBAT grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented and motile, most likely by gliding. They could be distinguished by slight differences in the chemotaxonomic features. We propose to establish for strain 50A-KIRBAT (=CIP 111735T=LMG 31080T) as type strain the name Aquirufa ecclesiirivi and for strain 50C-KIRBAT (=CIP 111736T=LMG 31501T) as type strain the name Aquirufa beregesia. Furthermore, the relationship between the type strains of Aquirufa nivalisilvae (59G-WUEMPELT) and Allopseudarcicella aquatilis (HME7025T) was investigated. Results of polyphasic analyses, especially a gANI value of 97.6 %, as well as the genome-based phylogenetic reconstruction, suggested that Allopseudarcicella aquatilis is a heterotypic synonym of Aquirufa nivalisilvae. According to rule 24b of the International Code of Nomenclature of Prokaryotes we propose to classify strain HME7025 as Aquirufa nivalisilvae and provide an emended description for the latter.
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Pitt A, Koll U, Schmidt J, Hahn MW. Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats. Int J Syst Evol Microbiol 2020; 70:1630-1638. [PMID: 31904321 PMCID: PMC7386786 DOI: 10.1099/ijsem.0.003947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 33A1-SZDPT was isolated from a small creek located in Puch, Austria. Strain SP-Ram-0.45-NSY-1T was obtained from a small pond located in Schönramer Moor, Germany. 16S rRNA gene sequence similarities between the type strain of Silvanigrella aquatica, currently the only member of the family Silvanigrellaceae, and strains 33A1-SZDPT and SP-Ram-0.45-NSY-1T of 94.1 and 99.1 %, respectively, suggested affiliation of the two strains with this family. Phylogenetic reconstructions with 16S rRNA gene sequences and phylogenomic analyses with amino acid sequences obtained from 103 single-copy genes suggested that the strains represent a new genus and a new species in the case of strain 33A1-SZDPT (=JCM 32978T=DSM 107810T), and a new species within the genus Silvanigrella in the case of strain SP-Ram-0.45-NSY-1T (=JCM 32975T=DSM 107809T). Cells of strain 33A1-SZDPT were motile, pleomorphic, purple-pigmented on agar plates, putatively due to violacein, and showed variable pigmentation in liquid media. They grew chemoorganotrophically and aerobically and tolerated salt concentrations up to 1.2 % NaCl (v/w). The genome size of strain 33A1-SZDPT was 3.4 Mbp and the G+C content was 32.2 mol%. For this new genus and new species, we propose the name Fluviispira multicolorata gen. nov., sp. nov. Cells of strain SP-Ram-0.45-NSY-1T were motile, pleomorphic, red-pigmented and grew chemoorganotrophically and aerobically. They tolerated salt concentrations up to 1.1 % NaCl (v/w). The genome size of strain SP-Ram-0.45-NSY-1T was 3.9 Mbp and the G+C content 29.3 mol%. For the new species within the genus Silvanigrella we propose the name Silvanigrella paludirubra sp. nov.
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Sheu SY, Chen TY, Chen WM. Aquirufa rosea sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:3145-3153. [PMID: 32267219 DOI: 10.1099/ijsem.0.004147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated CAR-16T was isolated from a freshwater lake in Taiwan and characterized using the polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed rose-colored colonies. Optimal growth occurred at 30 °C, pH 7 and with 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that CAR-16T represented a member of the family Cytophagaceae and formed a phylogenetic lineage in the genus Aquirufa. CAR-16T was most closely related to Aquirufa nivalisilvae 59G-WUEMPELT with a 99.7 % 16S rRNA gene sequence similarity. CAR-16T showed 71.2-79.5 % average nucleotide identity and 17.8-21.7 % digital DNA-DNA hybridization identity with the strains of other species of the genus Aquirufa. The major fatty acids of strain CAR-16T were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c and/or iso-C15 : 0 2-OH). The polar lipid profile consisted of a mixture of phosphatidylethanolamine and several uncharacterized aminophospholipids, phospholipids and lipids. The major isoprenoid quinone was MK-7. The genomic DNA G+C content of CAR-16T was 38.8 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, CAR-16T should be classified as representing a novel species of the genus Aquirufa, for which the name Aquirufa rosea sp. nov. is proposed. The type strain is CAR-16T (=BCRC 81153T=LMG 30923T=KCTC 62869T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan, ROC
| | - Tzu-Ying Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC
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Pitt A, Schmidt J, Koll U, Hahn MW. Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat. Int J Syst Evol Microbiol 2020; 70:1830-1836. [PMID: 31958053 DOI: 10.1099/ijsem.0.003980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain 53C-WASEF was isolated from a small freshwater ditch located in Eugendorf, Austria. Phylogenetic reconstructions with 16S rRNA gene sequences and genome based, with amino acid sequences obtained from 105 single copy genes, suggested that the strain represents a new genus and a new species within the family Opitutaceae, which belongs to the class Opitutae of the phylum Verrucomicrobia. Comparisons of the 16S rRNA gene sequence of strain 53C-WASEF with those of related type strains revealed a highest sequence similarity of 93.5 % to Nibricoccus aquaticus and of 92.9 % to Geminisphaera colitermitum. Interestingly, phylogentic trees indicated the latter as being the closest known relative of the new strain. Phenotypic, chemotaxonomic and genomic traits were investigated. Cells were observed to be small, spherical, motile and unpigmented, and grew chemoorganotrophically and aerobically. The respiratory quinone was MK-7, the predominant fatty acids were anteiso-C15 : 0, C16 : 1ω5c and C16 : 0. The identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genome sequencing revealed genes putatively encoding for flagella synthesis and cellulose degradation. The genome size was 4.1 Mbp and the G+C content 60.6 mol%. For the new genus and the new species, we propose the name Rariglobus hedericola gen. nov., sp. nov. (=CIP 111665T=DSM 109123T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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Sheu SY, Chen TY, Kwon SW, Chen WM. Lacibacter luteus sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2019; 70:1404-1411. [PMID: 31851601 DOI: 10.1099/ijsem.0.003926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An isolate, designated TTM-7T, recovered from a freshwater river in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-7T is affiliated with species in the genus Lacibacter. Strain TTM-7T was most closely related to Lacibacter cauensis NJ-8T with a 98.2 % 16S rRNA gene sequence similarity, followed by Lacibacter daechungensis H32-4T (97.4 %) and Lacibacter nakdongensis SS2-56T (96.3 %). Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed orange colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. The major fatty acids of strain TTM-7T were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c and/or iso-C15 : 0 2-OH) and iso-C15 : 1 G. The predominant hydroxy fatty acid was iso-C17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminoglycolipids, five unidentified aminophospholipids and one unidentified lipid. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TTM-7T was 40.6 mol%. Strain TTM-7T showed 83.6 % average nucleotide identity and 16.0 % digital DNA-DNA hybridization identity with Lacibacter cauensis NJ-8T. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TTM-7T should be classified in a novel species of the genus Lacibacter, for which the name Lacibacter luteus sp. nov. is proposed. The type strain is TTM-7T (=BCRC 81159T=LMG 30926T=KCTC 62870T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, No. 142, Hai-Chuan Rd. Nan-Tzu, Taiwan, ROC
| | - Tzu-Ying Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, No. 142, Hai-Chuan Rd. Nan-Tzu, Taiwan, ROC
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, No. 142, Hai-Chuan Rd. Nan-Tzu, Taiwan, ROC
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