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Rutkoski CF, Vergara-Luis I, Urionabarrenetxea E, García-Velasco N, Zaldibar B, Anza M, Olivares M, Prieto A, Epelde L, Garbisu C, Almeida EA, Soto M. Effects of sulfamethazine and tetracycline at molecular, cellular and tissue levels in Eisenia fetida earthworms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175579. [PMID: 39154996 DOI: 10.1016/j.scitotenv.2024.175579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/24/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
Soil contamination by antibiotics is a global issue of great concern that contributes to the rise of bacterial antibiotic resistance and can have toxic effects on non-target organisms. This study evaluated the variations of molecular, cellular, and histological parameters in Eisenia fetida earthworms exposed to sulfamethazine (SMZ) and tetracycline (TC), two antibiotics commonly found in agricultural soils. The earthworms were exposed for 14 days to a series of concentrations (0, 10, 100, and 1000 mg/kg) of both antibiotics. SMZ and TC did not affect the survival of E. fetida, however, other effects at different levels of biological complexity were detected. The two highest concentrations of SMZ reduced the viability of coelomocytes. At the highest TC concentration, there was a noticeable decline in cell viability, acetylcholinesterase activity (neurotoxicity), and the relative presence of mucopolysaccharides in the epidermis (mucous production). Glutathione S-transferase activity decreased in all TC treatments and at the highest SMZ concentration. However, levels of malondialdehyde and protein carbonyls did not change, suggesting an absence of oxidative stress. Tetracycline was neurotoxic to E. fetida and changed the integrity of the epidermis. Both antibiotics altered the intestinal microbiota of E. fetida, leading to a reduction in the relative abundance of bacteria from the phyla Proteobacteria and Bacteroidetes, while causing an increase in the phylum Actinobacteroidota. All observed changes indicate that both SMZ and TC can disrupt the earthworms' immune system and gut microbiome, while fostering the growth of bacteria that harbour antibiotic resistance genes. Finally, both antibiotics exerted additional metabolic and physiological effects that increased the vulnerability of E. fetida to pathogens.
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Affiliation(s)
- C F Rutkoski
- Environmental Engineering Post-Graduation Program, University of Blumenau, Blumenau, SC, Brazil; Department of Natural Science, University of Blumenau, Blumenau, SC, Brazil
| | - I Vergara-Luis
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - E Urionabarrenetxea
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain; CBET Research Group, Dept. Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - N García-Velasco
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain; CBET Research Group, Dept. Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - B Zaldibar
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain; CBET Research Group, Dept. Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - M Anza
- NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Basque Country, Spain
| | - M Olivares
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - A Prieto
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - L Epelde
- NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Basque Country, Spain
| | - C Garbisu
- NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Basque Country, Spain
| | - E A Almeida
- Environmental Engineering Post-Graduation Program, University of Blumenau, Blumenau, SC, Brazil; Department of Natural Science, University of Blumenau, Blumenau, SC, Brazil
| | - M Soto
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain; CBET Research Group, Dept. Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
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2
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Attrah M, Schärer MR, Esposito M, Gionchetta G, Bürgmann H, Lens PNL, Fenner K, van de Vossenberg J, Robinson SL. Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase. MICROBIOME 2024; 12:164. [PMID: 39242535 PMCID: PMC11380404 DOI: 10.1186/s40168-024-01879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/23/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs. RESULTS To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs. CONCLUSIONS This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.
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Affiliation(s)
- Mustafa Attrah
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
| | - Milo R Schärer
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | - Mauro Esposito
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
| | - Giulia Gionchetta
- Department of Surface Waters - Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Department of Surface Waters - Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
| | - Piet N L Lens
- Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
- National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Kathrin Fenner
- Department of Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Department of Chemistry, University of Zürich, 8057, Zurich, Switzerland
| | - Jack van de Vossenberg
- Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, 2611 AX, Delft, The Netherlands
| | - Serina L Robinson
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland.
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Martin JD, Tisler S, Scheel M, Svendsen S, Anwar MZ, Zervas A, Ekelund F, Bester K, Hansen LH, Jacobsen CS, Ellegaard-Jensen L. Total RNA analysis of the active microbiome on moving bed biofilm reactor carriers under incrementally increasing micropollutant concentrations. FEMS Microbiol Ecol 2024; 100:fiae098. [PMID: 38986504 PMCID: PMC11385203 DOI: 10.1093/femsec/fiae098] [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: 02/28/2024] [Revised: 06/13/2024] [Accepted: 07/08/2024] [Indexed: 07/12/2024] Open
Abstract
Micropollutants are increasingly prevalent in the aquatic environment. A major part of these originates from wastewater treatment plants since traditional treatment technologies do not remove micropollutants sufficiently. Moving bed biofilm reactors (MBBRs), however, have been shown to aid in micropollutant removal when applied to conventional wastewater treatment as a polishing step. Here, we used Total RNA sequencing to investigate both the active microbial community and functional dynamics of MBBR biofilms when these were exposed to increasing micropollutant concentrations over time. Concurrently, we conducted batch culture experiments using biofilm carriers from the MBBRs to assess micropollutant degradation potential. Our study showed that biofilm eukaryotes, in particular protozoa, were negatively influenced by micropollutant exposure, in contrast to prokaryotes that increased in relative abundance. Further, we found several functional genes that were differentially expressed between the MBBR with added micropollutants and the control. These include genes involved in aromatic and xenobiotic compound degradation. Moreover, the biofilm carrier batch experiment showed vastly different alterations in benzotriazole and diclofenac degradation following the increased micropollutant concentrations in the MBBR. Ultimately, this study provides essential insights into the microbial community and functional dynamics of MBBRs and how an increased load of micropollutants influences these dynamics.
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Affiliation(s)
- Joseph Donald Martin
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Selina Tisler
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Maria Scheel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Sif Svendsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Muhammad Zohaib Anwar
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
- The Center for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, 8888 University Dr. W, Burnaby, BC V5A 1S6, Canada
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Flemming Ekelund
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Kai Bester
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Carsten Suhr Jacobsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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Godinho O, Devos DP, Quinteira S, Lage OM. The influence of the phylum Planctomycetota in the environmental resistome. Res Microbiol 2024; 175:104196. [PMID: 38467354 DOI: 10.1016/j.resmic.2024.104196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Quinteira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Rede de Investigação em Biodiversidade e Biologia Evolutiva, Laboratório Associado, Universidade do Porto, 4485-6661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; 1H-TOXRUN - One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal
| | - Olga M Lage
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
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Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
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Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
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Yao T, Ye L, Wang S, Lu J, Li H, Yu G. Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone. CHEMOSPHERE 2024; 352:141507. [PMID: 38387663 DOI: 10.1016/j.chemosphere.2024.141507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/03/2023] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.
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Affiliation(s)
- Tuo Yao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Research Center of Hydrobiology, Jinan University, Guangzhou, China
| | - Lingtong Ye
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Jie Lu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Gang Yu
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Godinho O, Klimek D, Jackiewicz A, Guedes B, Almeida E, Calisto R, Vitorino IR, Santos JDN, González I, Lobo-da-Cunha A, Calusinska M, Quinteira S, Lage OM. Stieleria tagensis sp. nov., a novel member of the phylum Planctomycetota isolated from Tagus River in Portugal. Antonie Van Leeuwenhoek 2023; 116:1209-1225. [PMID: 37737556 PMCID: PMC10541342 DOI: 10.1007/s10482-023-01877-2] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023]
Abstract
A bacterial strain was isolated from a brackish water sample of Tagus river, Alcochete, Portugal and was designated TO1_6T. It forms light pink colonies on M13 medium supplemented with N-acetylglucosamine. Cells are pear-shaped to spherical, form rosettes and divide by budding. Strain TO1_6T presents a mesophilic and neutrophilic profile, with optimum growth at 20 to 25 °C and pH 7.0 to 7.5, and vitamin supplementation is not required to promote its growth. The genome of the novel isolate is 7.77 Mbp in size and has a DNA G + C content of 56.3%. Based on its 16S rRNA gene sequence, this strain is affiliated with the phylum Planctomycetota. Further taxonomic characterization using additional phylogenetic markers, namely rpoB gene sequence (encoding the β-subunit of the DNA-dependent RNA polymerase), as well as Percentage of conserved proteins, average nucleotide identity and average amino acid identity, suggest the affiliation of strain TO1_6T to the genus Stieleria, a recently described taxon in the family Pirellulaceae, order Pirellulales and class Planctomycetia. Based on the genotypic, phylogenetic and physiological characterization, we here describe a new species represented by the type strain TO1_6T (= CECT 30432T, = LMG 32465T), for which the name Stieleria tagensis sp. nov. is proposed.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| | - Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Rue du Brill 41, 4422, Belvaux, Luxembourg
- The Faculty of Science, Technology and Medicine, FSTM, University of Luxembourg, 2 Avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Adrianna Jackiewicz
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Bárbara Guedes
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Eduarda Almeida
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Rita Calisto
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - José Diogo Neves Santos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Ignacio González
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, 18016, Granada, Spain
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Rue du Brill 41, 4422, Belvaux, Luxembourg
| | - Sandra Quinteira
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- BIOPOLIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal
- TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL., Avenida Central de Gandra, 1317, 4585-116, Gandra, PRD, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
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Zou K, Zhu Y, Jiang Y, Ma S, Li M, Zhao W, Wang J. Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132161. [PMID: 37523960 DOI: 10.1016/j.jhazmat.2023.132161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
| | - Yiyi Zhu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Yun Jiang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shanshan Ma
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangzhou 510300, Guangdong Province, China
| | - Wencheng Zhao
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Jun Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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Veloso S, Amouroux D, Lanceleur L, Cagnon C, Monperrus M, Deborde J, Laureau CC, Duran R. Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130858. [PMID: 36706488 DOI: 10.1016/j.jhazmat.2023.130858] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ13C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.
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Affiliation(s)
- Sandrine Veloso
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Laurent Lanceleur
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Mathilde Monperrus
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France
| | - Jonathan Deborde
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Anglet, France; Ifremer, LITTORAL, Laboratoire Environnement Ressources des Pertuis Charentais, F-17390 La Tremblade, France
| | - Cristiana Cravo Laureau
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux, Pau, France.
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10
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Sreya P, Suresh G, Rai A, Ria B, Vighnesh L, Agre VC, Jagadeeshwari U, Sasikala C, Ramana CV. Revisiting the taxonomy of the genus Rhodopirellula with the proposal for reclassification of the genus to Rhodopirellula sensu stricto, Aporhodopirellula gen. nov., Allorhodopirellula gen. nov. and Neorhodopirellula gen. nov. Antonie Van Leeuwenhoek 2023; 116:243-264. [PMID: 36547858 DOI: 10.1007/s10482-022-01801-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The current genus Rhodopirellula consists of marine bacteria which belong to the family Pirellulaceae of the phylum Planctomycetota. Members of the genus Rhodopirellula are aerobic, mesophiles and chemoheterotrophs. The here conducted analysis built on 16S rRNA gene sequence and multi-locus sequence analysis based phylogenomic trees suggested that the genus is subdivided into four clades. Existing Rhodopirellula species were studied extensively based on phenotypic, genomic and chemotaxonomic parameters. The heterogeneity was further confirmed by overall genome-related indices (OGRI) including digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), and percentage of conserved proteins (POCP). AAI and POCP values between the clades of the genus Rhodopirellula were 62.2-69.6% and 49.5-62.5%, respectively. Comparative genomic approaches like pan-genome analysis and conserved signature indels (CSIs) also support the division of the clades. The genomic incoherence of the members of the genus is further supported by variations in phenotypic characteristics. Thus, with the here applied integrated comparative genomic and polyphasic approaches, we propose the reclassification of the genus Rhodopirellula to three new genera: Aporhodopirellula gen. nov., Allorhodopirellula gen. nov., and Neorhodopirellula gen. nov.
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Affiliation(s)
- Pannikurungottu Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Lakshmanan Vighnesh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Vaibhav Chandrakant Agre
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad, 500 085, India.
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500 046, India.
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11
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Wang A, Li X, Hao X, Luo X, Chen W, Huang Q. Ammonia level influences the assembly of dissimilatory nitrate reduction to ammonia bacterial community in soils under different heavy metal remediation treatments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156393. [PMID: 35660450 DOI: 10.1016/j.scitotenv.2022.156393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/19/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Heavy metal remediation treatments might influence functional microbial community assembly. Dissimilatory nitrate reduction to ammonia (DNRA) contributes to the nitrogen retention processes in soil ecosystems. We assumed that remediation might reduce heavy metal toxicity and increase some available nutrients for the DNRA microbes, thus balancing the deterministic and stochastic process for DNRA community assembly. Here, we investigated the process of DNRA bacterial community assembly under different heavy metal remediation treatments (including control, biochar, limestone, rice straw, rice straw + limestone, and biochar + limestone) in an Alfisol soil. The abundance of DNRA bacteria diverged across treatments. The α-diversity of the DNRA bacterial community was correlated with pH, available phosphorus (AP), ammonium (NH4+), and extractable Fe (EFe). Metal Cd and Fe significantly affected the abundance of the nrfA gene. The β-diversity was associated with pH, NH4+, and EFe. Deterministic processes dominantly drove the assembly processes of the DNRA bacterial community. NH4+ level played an essential role in the assembly processes than the other soil physicochemical properties and metal availability. High, moderate, and low levels of NH4+ could advocate stochastic process plus selection, heterogeneous selection to stochastic process, and heterogeneous selection, respectively. Network analysis highlighted a predominant role of NH4+ in regulating DNRA bacterial community assembly. However, the relative abundance of modules and some keystone species also were influenced by pH and EFe, respectively. Therefore, the DNRA bacterial community assembly under different heavy metal remediation treatments in this study was dominantly driven by nitrogen availability. pH, phosphorus, and metal availability were auxiliary regulators on DNRA bacterial community.
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Affiliation(s)
- Achen Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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12
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Vitorino IR, Lobo-da-Cunha A, Vasconcelos V, Vicente F, Lage OM. Isolation, diversity and antimicrobial activity of planctomycetes from the Tejo river estuary (Portugal). FEMS Microbiol Ecol 2022; 98:6609431. [PMID: 35709427 DOI: 10.1093/femsec/fiac066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/18/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022] Open
Abstract
The discovery of new bioactive compounds is an invaluable aid to the development of new drugs. Strategies for finding novel molecules can focus on the exploitation of less studied organisms and ecosystems such as planctomycetes and brackish habitats. The unique cell biology of the underexplored Planctomycetota mean it is of particular interest. In this study, we aimed to isolate planctomycetes from the estuary of the Tejo river (Portugal). To reach this goal, macroalgae, water and sediments were sampled and diverse media and isolation techniques applied. Sixty-nine planctomycetal strains were brought into pure culture. An analysis of the 16S rRNA genes found that the majority of the isolates were affiliated to the genus Rhodopirellula. Putative novel taxa belonging to genera Stieleria and Rhodopirellula were also isolated and characterized morphologically. Enterobacterial Repetitive Intergenic Consensus fingerprinting analyses showed higher diversity and different genotypes within close strains. Relevant biosynthetic gene clusters were found in most isolates and acetone extracts from representative strains exhibited mild antimicrobial activities against Escherichia coli and Staphylococcus aureus. Our work has not only enlarged the number and diversity of cultured planctomycetes but also shown the potential for the discovery of bioactive compounds from the novel taxa.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n°, 4169-007 Porto, Portugal.,CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Vasconcelos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n°, 4169-007 Porto, Portugal.,CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n°, 4169-007 Porto, Portugal.,CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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13
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Gamoń F, Cema G, Ziembińska-Buczyńska A. The influence of antibiotics on the anammox process - a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:8074-8090. [PMID: 34845633 PMCID: PMC8776664 DOI: 10.1007/s11356-021-17733-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/20/2021] [Indexed: 04/15/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is one of the most promising processes for the treatment of ammonium-rich wastewater. It is more effective, cheaper, and more environmentally friendly than the conventional process currently in use for nitrogen removal. Unfortunately, anammox bacteria are sensitive to various substances, including heavy metals and organic matter commonly found in the wastewater treatment plants (WWTPs). Of these deleterious substances, antibiotics are recognized to be important. For decades, the increasing consumption of antibiotics has led to the increased occurrence of antibiotics in the aquatic environment, including wastewater. One of the most important issues related to antibiotic pollution is the generation and transfer of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Here, we will discuss the effect of short- and long-term exposure of the anammox process to antibiotic pollutants; with a special focus on the activity of the anammox bacteria, biomass properties, community structures, the presence of antibiotic resistance genes and combined effect of antibiotics with other substances commonly found in wastewater. Further, the defense mechanisms according to which bacteria adapt against antibiotic stress are speculated upon. This review aims to facilitate a better understanding of the influence of antibiotics and other co-pollutants on the anammox process and to highlight future avenues of research to target gaps in the knowledge.
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Affiliation(s)
- Filip Gamoń
- Environmental Biotechnology Department, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland.
| | - Grzegorz Cema
- Environmental Biotechnology Department, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland
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14
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Kallscheuer N, Jogler C, Peeters SH, Boedeker C, Jogler M, Heuer A, Jetten MSM, Rohde M, Wiegand S. Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands. Antonie van Leeuwenhoek 2022; 115:407-420. [PMID: 35050438 PMCID: PMC8882080 DOI: 10.1007/s10482-021-01707-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
For extending the current collection of axenic cultures of planctomycetes, we describe in this study the isolation and characterisation of strain Pan265T obtained from a red biofilm in the hydrothermal vent system close to the Lipari Islands in the Tyrrhenian Sea, north of Sicily, Italy. The strain forms light pink colonies on solid medium and grows as a viscous colloid in liquid culture, likely as the result of formation of a dense extracellular matrix observed during electron microscopy. Cells of the novel isolate are spherical, motile and divide by binary fission. Strain Pan265T is mesophilic (temperature optimum 30-33 °C), neutrophilic (pH optimum 7.0-8.0), aerobic and heterotrophic. The strain has a genome size of 3.49 Mb and a DNA G + C content of 63.9%. Phylogenetically, the strain belongs to the family Phycisphaeraceae, order Phycisphaerales, class Phycisphaerae. Our polyphasic analysis supports the delineation of strain Pan265T from the known genera in this family. Therefore, we conclude to assign strain Pan265T to a novel species within a novel genus, for which we propose the name Mucisphaera calidilacus gen. nov., sp. nov. The novel species is the type species of the novel genus and is represented by strain Pan265T (= DSM 100697T = CECT 30425T) as type strain.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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15
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Sulfuriroseicoccus oceanibius gen. nov., sp. nov., a representative of the phylum Verrucomicrobia with a special cytoplasmic membrane. Antonie van Leeuwenhoek 2022; 115:337-352. [PMID: 35044567 DOI: 10.1007/s10482-021-01689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/18/2021] [Indexed: 10/19/2022]
Abstract
Here, we describe a novel bacterial strain, designated T37T, which was isolated from the marine sediment of Xiaoshi Island, PR China. Growth of strain T37T occurs at 15-40 °C (optimum 37 °C), pH 6.0-9.0 (optimum 7.5), and in the presence of 0.5-5.5% (w/v) NaCl (optimum 1.5%). Characteristic biochemical traits of the novel strain include MK-9 as the major menaquinone. The major fatty acids identified were iso-C14:0 and C16:1 ω9c (oleic acid). Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphoglycolipids were the major cellular polar lipids. The G + C content of genomic DNA was 58.4 mol%. Unusual outer membrane features deduced from the analysis of cell morphology point towards the formation of an enlarged periplasmic space putatively used for the digestion of macromolecules. Phylogenetic analyses based on 16S rRNA genes and the genome indicated that strain T37T represents a novel species and genus affiliated with a distinct family level lineage of the verrucomicrobial subdivision 1. Our polyphasic taxonomy approach places the novel strain in a new genus within the current family Verrucomicrobiaceae, order Verrucomicrobiales, class Verrucomicrobiae. Strain T37T (= KCTC 72799 T = MCCC 1H00391T) is the type strain of a novel species, for which the name Sulfuriroseicoccus oceanibius gen. nov., sp. nov. is proposed.
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16
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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17
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Lee S, Kim JY, Yi MH, Lee IY, Yong D, Yong TS. Reduced production of the major allergens Bla g 1 and Bla g 2 in Blattella germanica after antibiotic treatment. PLoS One 2021; 16:e0257114. [PMID: 34813599 PMCID: PMC8610280 DOI: 10.1371/journal.pone.0257114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/06/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Allergens present in the feces or frass of cockroaches can cause allergic sensitization in humans. The use of fecal and frass extracts for immunotherapy has been previously investigated but has not yet been fully standardized. Here, we treated cockroaches with ampicillin to produce extracts with reduced amounts of total bacteria. METHODS We performed targeted high-throughput sequencing of 16S rDNA to compare the microbiomes of ampicillin-treated and untreated (control) cockroaches. RNA-seq was performed to identify differentially expressed genes (DEGs) in ampicillin-treated cockroaches. RESULTS Analysis of the microbiome revealed that alpha diversity was lower in the ampicillin-treated group than in the control group. Beta diversity analysis indicated that ampicillin treatment altered bacterial composition in the microbiome of cockroaches. Quantitative polymerase chain reaction revealed that almost all bacteria were removed from ampicillin-treated cockroaches. RNA-seq analysis revealed 1,236 DEGs in ampicillin-treated cockroaches (compared to untreated cockroaches). Unlike bacterial composition, the DEGs varied between the two groups. Among major allergens, the expression of Bla g 2 decreased significantly in ampicillin-treated cockroaches (compared to untreated group). CONCLUSIONS In this study, the reduced level of allergens observed in cockroaches may be related to lower amounts of total bacteria caused by treatment with antibiotics. It is possible to make a protein extract with few bacteria for use in immunotherapy.
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Affiliation(s)
- Seogwon Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Korea
| | - Ju Yeong Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Korea
| | - Myung-Hee Yi
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Korea
| | - In-Yong Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Korea
- Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, Incheon, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Tai-Soon Yong
- Department of Environmental Medical Biology, Institute of Tropical Medicine and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, Korea
- * E-mail:
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Kruppa OC, Gerlach D, Fan R, Czermak P. Development of a chemically defined medium for Planctopirus limnophila to increase biomass production. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kallscheuer N, Jogler C. The bacterial phylum Planctomycetes as novel source for bioactive small molecules. Biotechnol Adv 2021; 53:107818. [PMID: 34537319 DOI: 10.1016/j.biotechadv.2021.107818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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Dang BT, Bui XT, Itayama T, Ngo HH, Jahng D, Lin C, Chen SS, Lin KYA, Nguyen TT, Nguyen DD, Saunders T. Microbial community response to ciprofloxacin toxicity in sponge membrane bioreactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145041. [PMID: 33940712 DOI: 10.1016/j.scitotenv.2021.145041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
This study aims to offer insights into how ciprofloxacin (CIP) impact bacterial community structures in the Sponge-MBR process when CIP is spiked into hospital wastewater. We found that the CIP toxicity decreased richness critical phylotypes such as phylum class ẟ-, β-, ɣ-proteobacteria, and Flavobacteria that co-respond to suppress denitrification and cake fouling to 37% and 28% respectively. Cluster analysis shows that the different community structures were formed under the influence of CIP toxicity. CIP decreased attached growth biomass by 2.3 times while increasing the concentration of permeate nitrate by 3.8 times, greatly affecting TN removal by up to 26%. Ammonia removal was kept stable by inflating the ammonia removal rate (p < 0.003), with the wealthy Nitrospira genus guaranteeing the nitrification activity. In addition, we observed an increasing richness of Chloroflexi and Planctomycetes, which may play a role in fouling reduction in the Sponge-MBR. Therefore, if the amount of antibiotics in hospital wastewater continues to increase, it is so important to extend biomass retention for denitrification recovery.
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Affiliation(s)
- Bao-Trong Dang
- Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan; Ho Chi Minh City University of Technology (HUTECH) 475A, Dien Bien Phu, Ward 25, Binh Thanh District, Ho Chi Minh City, Viet Nam
| | - Xuan-Thanh Bui
- Key Laboratory of Advanced Waste Treatment Technology, Vietnam National University Ho Chi Minh (VNU-HCM), Linh Trung ward, Thu Duc district, Viet Nam; Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Viet Nam.
| | - Tomoaki Itayama
- Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Huu Hao Ngo
- Center for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Australia
| | - Deokjin Jahng
- Department of Environmental Engineering and Energy, Myongji University, Republic of Korea
| | - Chitsan Lin
- College of Maritime, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan.
| | - Shiao-Shing Chen
- Institute of Environmental Engineering and Management, National Taipei University of Technology, Taipei, Taiwan
| | - Kun-Yi Andrew Lin
- Department of Environmental Engineering, National Chung Hsing University, No. 250 Kuo-Kuang Road, Taichung 402, Taiwan
| | - Thanh-Tin Nguyen
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet Nam
| | - Dinh Duc Nguyen
- Department of Environmental Energy Engineering, Kyonggi University, 442-760, Republic of Korea
| | - Todd Saunders
- Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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Lee TCH, Chan PL, Tam NFY, Xu SJL, Lee FWF. Establish axenic cultures of armored and unarmored marine dinoflagellate species using density separation, antibacterial treatments and stepwise dilution selection. Sci Rep 2021; 11:202. [PMID: 33420310 PMCID: PMC7794416 DOI: 10.1038/s41598-020-80638-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
Academic research on dinoflagellate, the primary causative agent of harmful algal blooms (HABs), is often hindered by the coexistence with bacteria in laboratory cultures. The development of axenic dinoflagellate cultures is challenging and no universally accepted method suit for different algal species. In this study, we demonstrated a promising approach combined density gradient centrifugation, antibiotic treatment, and serial dilution to generate axenic cultures of Karenia mikimotoi (KMHK). Density gradient centrifugation and antibiotic treatments reduced the bacterial population from 5.79 ± 0.22 log10 CFU/mL to 1.13 ± 0.07 log10 CFU/mL. The treated KMHK cells were rendered axenic through serial dilution, and algal cells in different dilutions with the absence of unculturable bacteria were isolated. Axenicity was verified through bacterial (16S) and fungal internal transcribed spacer (ITS) sequencing and DAPI epifluorescence microscopy. Axenic KMHK culture regrew from 1000 to 9408 cells/mL in 7 days, comparable with a normal culture. The established methodology was validated with other dinoflagellate, Alexandrium tamarense (AT6) and successfully obtained the axenic culture. The axenic status of both cultures was maintained more than 30 generations without antibiotics. This efficient, straightforward and inexpensive approach suits for both armored and unarmored dinoflagellate species.
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Affiliation(s)
- Thomas Chun-Hung Lee
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Ho Man Tin, Hong Kong
| | - Ping-Lung Chan
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Ho Man Tin, Hong Kong
| | - Nora Fung-Yee Tam
- Department of Chemistry, City University of Hong Kong, Kowloon Bay, Hong Kong
| | - Steven Jing-Liang Xu
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Ho Man Tin, Hong Kong
| | - Fred Wang-Fat Lee
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Ho Man Tin, Hong Kong.
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Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
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Ozumchelouei EJ, Hamidian AH, Zhang Y, Yang M. A critical review on the effects of antibiotics on anammox process in wastewater. REV CHEM ENG 2020. [DOI: 10.1515/revce-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains.
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Affiliation(s)
- Elnaz Jafari Ozumchelouei
- School of Chemical Engineering , University College of Engineering, University of Tehran , Tehran , Iran
| | - Amir Hossein Hamidian
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Min Yang
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
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Jogler C, Wiegand S, Boedeker C, Heuer A, Peeters SH, Jogler M, Jetten MSM, Rohde M, Kallscheuer N. Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago. Antonie Van Leeuwenhoek 2020; 113:1889-1900. [PMID: 32399714 PMCID: PMC7716859 DOI: 10.1007/s10482-020-01424-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).
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Affiliation(s)
- Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
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Rivas-Marin E, Wiegand S, Kallscheuer N, Jogler M, Peeters SH, Heuer A, Jetten MSM, Boedeker C, Rohde M, Devos DP, Jogler C. Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island. Antonie Van Leeuwenhoek 2020; 113:1915-1926. [PMID: 32583191 PMCID: PMC7716918 DOI: 10.1007/s10482-020-01437-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Access to axenic cultures is crucial to extend the knowledge of the biology, lifestyle or metabolic capabilities of bacteria from different phyla. The phylum Planctomycetes is an excellent example since its members display an unusual cell biology and complex lifestyles. As a contribution to the current collection of axenic planctomycete cultures, here we describe strain Mal48T isolated from phytoplankton material sampled at the coast of S'Arenal close to Palma de Mallorca (Spain). The isolated strain shows optimal growth at pH 7.0-7.5 and 30 °C and exhibits typical features of Planctomycetes. Cells of the strain are spherical to pear-shaped, divide by polar budding with daughter cells showing the same shape as the mother cell, tend to aggregate, display a stalk and produce matrix or fimbriae. Strain Mal48T showed 95.8% 16S rRNA gene sequence similarity with the recently described Thalassoglobus neptunius KOR42T. The genome sequence of the novel isolate has a size of 6,357,355 bp with a G+C content of 50.3%. A total of 4874 protein-coding genes, 41 tRNA genes and 2 copies of the 16S rRNA gene are encoded in the genome. Based on phylogenetic, morphological and physiological analyses, we conclude that strain Mal48T (= DSM 100737T = LMG 29019T) should be classified as the type strain of a new species in the genus Thalassoglobus, for which the name Thalassoglobus polymorphus sp. nov. is proposed.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany.
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Stieleria varia sp. nov., isolated from wood particles in the Baltic Sea, constitutes a novel species in the family Pirellulaceae within the phylum Planctomycetes. Antonie van Leeuwenhoek 2020; 113:1953-1963. [PMID: 32797359 PMCID: PMC7717043 DOI: 10.1007/s10482-020-01456-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Species belonging to the bacterial phylum Planctomycetes are ubiquitous members of the microbial communities in aquatic environments and are frequently isolated from various biotic and abiotic surfaces in marine and limnic water bodies. Planctomycetes have large genomes of up to 12.4 Mb, follow complex lifestyles and display an uncommon cell biology; features which motivate the investigation of members of this phylum in greater detail. As a contribution to the current collection of axenic cultures of Planctomycetes, we here describe strain Pla52T isolated from wood particles in the Baltic Sea. Phylogenetic analysis places the strain in the family Pirellulaceae and suggests two species of the recently described genus Stieleria as current closest neighbours. Strain Pla52nT shows typical features of members of the class Planctomycetia, including division by polar budding and the presence of crateriform structures. Colonies of strain Pla52nT have a light orange colour, which is an unusual pigmentation compared to the majority of members in the phylum, which show either a pink to red pigmentation or entirely lack pigmentation. Optimal growth of strain Pla52nT at 33 °C and pH 7.5 indicates a mesophilic (i.e. with optimal growth between 20 and 45 °C) and neutrophilic growth profile. The strain is an aerobic heterotroph with motile daughter cells. Its genome has a size of 9.6 Mb and a G + C content of 56.0%. Polyphasic analyses justify delineation of the strain from described species within the genus Stieleria. Therefore, we conclude that strain Pla52nT = LMG 29463T = VKM B-3447T should be classified as the type strain of a novel species, for which we propose the name Stieleria varia sp. nov.
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Caulifigura coniformis gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from a red biofilm sampled in a hydrothermal area. Antonie van Leeuwenhoek 2020; 113:1927-1937. [PMID: 32583190 PMCID: PMC7717036 DOI: 10.1007/s10482-020-01439-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023]
Abstract
Pan44T, a novel strain belonging to the phylum Planctomycetes, was isolated from a red biofilm in a hydrothermal area close to the island Panarea in the Tyrrhenian Sea north of Sicily, Italy. The strain forms white colonies on solid medium and displays the following characteristics: cell division by budding, formation of rosettes, presence of matrix or fimbriae and long stalks. The cell surface has an interesting and characteristic texture made up of triangles and rectangles, which leads to a pine cone-like morphology of the strain. Strain Pan44T is mesophilic (temperature optimum 26 °C), slightly alkaliphilic (pH optimum 8.0), aerobic and heterotrophic. The strain has a genome size of 6.76 Mb with a G + C content of 63.2%. Phylogenetically, the strain is a member of the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. Our analysis supports delineation of strain Pan44T from all known genera in this family, hence, we propose to assign it to a novel species within a novel genus, for which we propose the name Caulifigura coniformis gen. nov., sp. nov., represented by Pan44T (DSM 29405T = LMG 29788T) as the type strain.
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Pu Q, Zhao LX, Li YT, Su JQ. Manure fertilization increase antibiotic resistance in soils from typical greenhouse vegetable production bases, China. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122267. [PMID: 32062545 DOI: 10.1016/j.jhazmat.2020.122267] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 05/21/2023]
Abstract
A large quantity of manure is applied in greenhouse vegetable production (GVP) soils, while manure fertilization often leads to the proliferation of antibiotic resistance genes (ARGs) in soils. However, comprehensive study on the effects of different types of manure on ARGs in GVP soils remains unknown, and the baseline level of ARGs in GVP soil is poorly quantified. This study conducted a comprehensive survey of ARGs in GVP soils using high-throughput quantitative PCR. We found elevated ARG diversity and absolute abundance in fertilized soil, whereas no significant difference in soil ARGs amended with different types of manure. Redundancy analysis indicated that the change of bacterial community compositions and environmental factors contributed partially to the shift in ARG profiles. Bipartite network analysis indicated that one ARG was detected in non-manured soils, while 50 ARGs and 4 mobile gene elements were exclusively detected in fertilized soils, suggesting introduction of ARGs from manure into soils largely explained the increased ARG diversity in fertilized soil. By comparison of ARG absolute abundance between manured and non-manured soil, we estimated the typical level of ARG absolute abundance in non-manured soil, which provided the first rough baseline level of ARGs to assess ARG contamination in GVP soils.
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Affiliation(s)
- Qiang Pu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Li-Xia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yong-Tao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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Aureliella helgolandensis gen. nov., sp. nov., a novel Planctomycete isolated from a jellyfish at the shore of the island Helgoland. Antonie Van Leeuwenhoek 2020; 113:1839-1849. [PMID: 32219667 PMCID: PMC7716919 DOI: 10.1007/s10482-020-01403-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/06/2020] [Indexed: 11/02/2022]
Abstract
A novel planctomycetal strain, designated Q31aT, was isolated from a jellyfish at the shore of the island Helgoland in the North Sea. The strain forms lucid white colonies on solid medium and displays typical characteristics of planctomycetal strains, such as division by budding, formation of rosettes, presence of crateriform structures, extracellular matrix or fibre and a holdfast structure. Q31aT is mesophilic (temperature optimum 27 °C), neutrophilic (pH optimum 7.5), aerobic and heterotrophic. A maximal growth rate of 0.017 h- 1 (generation time of 41 h) was observed. Q31aT has a genome size of 8.44 Mb and a G + C content of 55.3%. Phylogenetically, the strain represents a novel genus and species in the recently introduced family Pirellulaceae, order Pirellulales, class Planctomycetia. We propose the name Aureliella helgolandensis gen. nov., sp. nov. for the novel species, represented by Q31aT (= DSM 103537T = LMG 29700T) as the type strain.
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Description of the novel planctomycetal genus Bremerella, containing Bremerella volcania sp. nov., isolated from an active volcanic site, and reclassification of Blastopirellula cremea as Bremerella cremea comb. nov. Antonie van Leeuwenhoek 2020; 113:1823-1837. [DOI: 10.1007/s10482-019-01378-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023]
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Kallscheuer N, Wiegand S, Heuer A, Rensink S, Boersma AS, Jogler M, Boedeker C, Peeters SH, Rast P, Jetten MSM, Rohde M, Jogler C. Blastopirellula retiformator sp. nov. isolated from the shallow-sea hydrothermal vent system close to Panarea Island. Antonie van Leeuwenhoek 2020; 113:1811-1822. [PMID: 31894497 DOI: 10.1007/s10482-019-01377-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Aquatic bacteria belonging to the deep-branching phylum Planctomycetes play a major role in global carbon and nitrogen cycles. However, their uncommon morphology and physiology, and their roles and survival on biotic surfaces in marine environments, are only partially understood. Access to axenic cultures of different planctomycetal genera is key to study their complex lifestyles, uncommon cell biology and primary and secondary metabolism in more detail. Here, we describe the characterisation of strain Enr8T isolated from a marine biotic surface in the seawater close to the shallow-sea hydrothermal vent system off Panarea Island, an area with high temperature and pH gradients, and high availability of different sulphur and nitrogen sources resulting in a great microbial diversity. Strain Enr8T showed typical planctomycetal traits such as division by polar budding, aggregate formation and presence of fimbriae and crateriform structures. Growth was observed at ranges of 15-33 °C (optimum 30 °C), pH 6.0-8.0 (optimum 7.0) and at NaCl concentrations from 100 to 1200 mM (optimum 350-700 mM). Strain Enr8T forms white colonies on solid medium and white flakes in liquid culture. Its genome has a size of 6.20 Mb and a G + C content of 59.2%. Phylogenetically, the strain belongs to the genus Blastopirellula. We propose the name Blastopirellula retiformator sp. nov. for the novel species, represented by the type strain Enr8T (DSM 100415T = LMG 29081T).
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Affiliation(s)
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stephanie Rensink
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Alje S Boersma
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.,Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Patrick Rast
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.,Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands. .,Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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33
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Description of three bacterial strains belonging to the new genus Novipirellula gen. nov., reclassificiation of Rhodopirellula rosea and Rhodopirellula caenicola and readjustment of the genus threshold of the phylogenetic marker rpoB for Planctomycetaceae. Antonie van Leeuwenhoek 2019; 113:1779-1795. [DOI: 10.1007/s10482-019-01374-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023]
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Three novel Rubripirellula species isolated from plastic particles submerged in the Baltic Sea and the estuary of the river Warnow in northern Germany. Antonie van Leeuwenhoek 2019; 113:1767-1778. [DOI: 10.1007/s10482-019-01368-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
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35
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Kaboré OD, Aghnatios R, Godreuil S, Drancourt M. Escherichia coli Culture Filtrate Enhances the Growth of Gemmata spp. Front Microbiol 2019; 10:2552. [PMID: 31781064 PMCID: PMC6851166 DOI: 10.3389/fmicb.2019.02552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/22/2019] [Indexed: 12/05/2022] Open
Abstract
Background Planctomycetes bacteria are known to be difficult to isolate, we hypothesized this may be due to missing iron compounds known to be important for other bacteria. We tested the growth-enhancement effect of complementing two standard media with Escherichia coli culture filtrate on two cultured strains of Gemmata spp. Also, the acquisition of iron by Gemmata spp. was evaluated by measuring various molecules involved in iron metabolism. Materials and Methods Gemmata obscuriglobus and Gemmata massiliana were cultured in Caulobacter and Staley’s medium supplemented or not with E. coli culture filtrate, likely containing siderophores and extracellular ferrireductases. We performed iron metabolism studies with FeSO4, FeCl3 and deferoxamine in the cultures with the E. coli filtrate and the controls. Results and Discussion The numbers of G. obscuriglobus and G. massiliana colonies on Caulobacter medium or Staley’s medium supplemented with E. coli culture filtrate were significantly higher than those on the standard medium (p < 0.0001). Agar plate assays revealed that the Gemmata colonies near E. coli colonies were larger than the more distant colonies, suggesting the diffusion of unknown growth promoting molecules. The inclusion of 10–4 to 10–3 M FeSO4 resulted in rapid Gemmata spp. growth (4–5 days compared with 8–9 days for the controls), suggesting that both species can utilize FeSO4 to boost their growth. In contrast, deferoxamine slowed down and prevented Gemmata spp. growth. Further studies revealed that the complementation of Caulobacter medium with E. coli culture filtrate and 10–4 M FeSO4 exerted a significant growth-enhancement effect compared with that obtained with Caulobacter medium supplemented with E. coli culture filtrate alone (p < 0.0122). Moreover, the intracellular iron concentrations in G. obscuriglobus and G. massiliana cultures in iron-depleted broth supplemented with the E. coli filtrate were 0.63 ± 0.16 and 0.78 ± 0.12 μmol/L, respectively, whereas concentrations of 1.72 ± 0.13 and 1.56± 0.11 μmol/L were found in the G. obscuriglobus and G. massiliana cultures grown in broth supplemented with the E. coli filtrate and FeSO4. The data reported here indicated that both E. coli culture filtrate and FeSO4 act as growth factors for Gemmata spp. via a potentiation mechanism.
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Affiliation(s)
- Odilon D Kaboré
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rita Aghnatios
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Département de Bactériologie-Virologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Kaboré OD, Godreuil S, Drancourt M. Improved culture of fastidious Gemmata spp. bacteria using marine sponge skeletons. Sci Rep 2019; 9:11707. [PMID: 31406238 PMCID: PMC6690866 DOI: 10.1038/s41598-019-48293-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023] Open
Abstract
Gemmata are Planctomycetes bacteria recalcitrant to traditional cultivation in the clinical microbiology laboratory and they have been seldom documented in patients. Based on previously known relationships of Planctomycetes with marine sponges, we designed a new culture medium A incorporating marine sponge skeleton of Spongia sp. to the standard culture medium; and culture medium B incorporating Spongia sp. skeleton heat aqueous filtrate into medium A; and inoculating the three culture media (standard, A and B) with Gemmata obscuriglobus DSM 5831T and Gemmata massiliana DSM 26013T in the presence of negative controls. Cultures were observed by naked eyes for 7 days and bacterial growth was quantified by microscopic observations and culture-based enumerations. Macroscopic observations at day-3 revealed a pink bacterial pellet in medium B tubes while standard medium tubes remained limpid until day-8. Growing Gemmata spp. bacteria in medium A yielded air bubbles released by bacterial respiration, whereas control tubes remained bubble-free. The number of colonies in standard medium (1.363 ± 115 for G. obscuriglobus, 1.288 ± 83 for G. massiliana) was significantly lower than those counted from medium B (2.552 ± 128 for G. obscuriglobus, 1.870 ± 112 for G. massiliana) and from medium A (2.851 ± 137 for G. obscuriglobus, 2.035 ± 163 for G. massiliana) (p < 0.10-4) at day-2 incubation. At day-3 incubation, the number of colonies counted from supplemented media A and B increased up to one log than those counted from the control medium (p < 0.10-4). Along the following day-4-7 incubation, the number of colonies counted from media A and B remained significantly higher compared to standard medium (p < 0.10-4). These data indicate that incorporation of spongin-based marine sponge skeleton and heat aqueous filtrate of sponge skeleton significantly improved growth of Gemmata spp. bacteria. These observations pave the way towards improved isolation and culture of Gemmata spp. from environmental and clinical specimens.
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Affiliation(s)
- Odilon D Kaboré
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm 1058, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Meng Y, Sheng B, Meng F. Changes in nitrogen removal and microbiota of anammox biofilm reactors under tetracycline stress at environmentally and industrially relevant concentrations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:379-388. [PMID: 30852214 DOI: 10.1016/j.scitotenv.2019.02.389] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/24/2019] [Accepted: 02/24/2019] [Indexed: 06/09/2023]
Abstract
Anammox-related processes are often applied for the wastewater treatment which contains both ammonium and antibiotics. Herein, the long-term effects of tetracycline (TC), at environmentally and industrially relevant concentrations, on the performance, anammox activity and microbial community of anammox reactors were investigated for 518 days. The control reactor (without TC exposure) was stable for nitrogen removal during the long-term operation (a nitrogen removal rate of 0.56 ± 0.05 kg-N·m-3·d-1). In the TC-added reactor, the nitrogen removal efficiency increased slightly at low TC levels (1-100 μg/L), whereas poor anammox performance occurred at high TC concentration (1000 μg/L). Furthermore, the concentrations of extracellular polymeric substances (EPS) were much higher at 10 μg/L than those in the control reactor (P < 0.01), whereas rapidly decreased at 1000 μg-TC/L. Furthermore, the reactor performance was highly consistent with the variations of the heme c contents. Consistently, exposure to TC changed the abundance of anammox bacteria, e.g., an increase in Candidatus Jettenia abundance occurred from 2.20 ± 0.97% (0-10 μg/L) to 12.13 ± 1.66% (100 μg/L). Similarly, the genus Denitratisoma, the most predominant denitrification bacteria, also had a higher abundance at a TC concentration of 100 μg/L (15.60 ± 6.42%) than other TC concentrations (5.40 ± 2.50% and 7.65 ± 0.55% at concentrations of 10 and 1000 μg/L, respectively). The results can explain why the exposure of anammox bacteria to a lower TC concentration (100 μg/L) resulted in a better nitrogen removal rate. In contrast, exposure to a high TC level (1000 μg/L) led to a decline in the abundance of anammox bacteria and denitrifiers (1.53 ± 0.64% and 8.18 ± 0.63%, respectively) but an increased abundance in the nitrifier population (8.07 ± 1.21%; P < 0.01). Therefore, this study can aid in the design and operation of anammox-based processes treating sewage and industrial wastewater.
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Affiliation(s)
- Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China
| | - Binbin Sheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, China.
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38
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Antibiotic susceptibility of marine Planctomycetes. Antonie van Leeuwenhoek 2019; 112:1273-1280. [DOI: 10.1007/s10482-019-01259-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
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39
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Kaboré OD, Loukil A, Godreuil S, Drancourt M. Co-culture models illustrate the digestion of Gemmata spp. by phagocytes. Sci Rep 2018; 8:13311. [PMID: 30190504 PMCID: PMC6127157 DOI: 10.1038/s41598-018-31667-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/10/2018] [Indexed: 11/25/2022] Open
Abstract
Gemmata spp. bacteria thrive in the same aquatic environments as free-living amoebae. DNA-based detection of Gemmata spp. sequences in the microbiota of the human digestive tract and blood further questioned the susceptibility of Gemmata spp. to phagocytes. Here, Gemmata obscuriglobus and Gemmata massiliana were co-cultured with the amoebae Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba griffini and THP-1 macrophage-like phagocytes. All experiments were performed in five independant replicates. The ratio amoeba/bacteria was 1:20 and the ratio THP-1/bacteria was 1:10. After a 2-hour co-culture, extracellular bacteria were killed by kanamycin or amikacin and eliminated. The intracellular location of Gemmata bacteria was specified by confocal microscopy. Microscopic enumerations and culture-based enumerations of colony-forming units were performed at T = 0, 1, 2, 3, 4, 8, 16, 24, 48 and 72 hours post-infection. Then, Gemmata bacteria were engulfed into the phagocytes’ cytoplasmic vacuoles, more than (98 ± 2)% of Gemmata bacteria, compared to controls, were destroyed by phagocytic cells after a 48-h co-culture according to microscopy and culture results, and no positive culture was observed at T = 72-hours. Under our co-culture conditions, Gemmata bacteria were therefore susceptible to the environmental and host phagocytes here investigated. These data suggest that these Acanthamoeba species and THP-1 cells cannot be used to isolate G. massiliana and G. obscuriglobus under the co-culture conditions applied in this study. Although the THP-1 response can point towards potential responses that might occur in vivo, these responses should first bevalidated by in vivo studies to draw definite conclusions.
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Affiliation(s)
- Odilon D Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, 1058, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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40
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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41
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Rosas T, García-Ferris C, Domínguez-Santos R, Llop P, Latorre A, Moya A. Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota. FEMS Microbiol Ecol 2018; 94:4794938. [DOI: 10.1093/femsec/fiy002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/08/2018] [Indexed: 02/04/2023] Open
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van Teeseling MCF, Benz R, de Almeida NM, Jetten MSM, Mesman RJ, van Niftrik L. Characterization of the first planctomycetal outer membrane protein identifies a channel in the outer membrane of the anammox bacterium Kuenenia stuttgartiensis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:767-776. [PMID: 29288627 DOI: 10.1016/j.bbamem.2017.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/30/2017] [Accepted: 12/25/2017] [Indexed: 01/27/2023]
Abstract
Planctomycetes are a bacterial phylum known for their complex intracellular compartmentalization. While most Planctomycetes have two compartments, the anaerobic ammonium oxidizing (anammox) bacteria contain three membrane-enclosed compartments. In contrast to a long-standing consensus, recent insights suggested the outermost Planctomycete membrane to be similar to a Gram-negative outer membrane (OM). One characteristic component that differentiates OMs from cytoplasmic membranes (CMs) is the presence of outer membrane proteins (OMPs) featuring a β-barrel structure that facilitates passage of molecules through the OM. Although proteomic and genomic evidence suggested the presence of OMPs in several Planctomycetes, no experimental verification existed of the pore-forming function and localization of these proteins in the outermost membrane of these exceptional microorganisms. Here, we show via lipid bilayer assays that at least two typical OMP-like channel-forming proteins are present in membrane preparations of the anammox bacterium Kuenenia stuttgartiensis. One of these channel-forming proteins, the highly abundant putative OMP Kustd1878, was purified to homogeneity. Analysis of the channel characteristics via lipid bilayer assays showed that Kustd1878 forms a moderately cation-selective channel with a high current noise and an average single-channel conductance of about 170-190pS in 1M KCl. Antibodies were raised against the purified protein and immunogold localization indicated Kustd1878 to be present in the outermost membrane. Therefore, this work clearly demonstrates the presence of OMPs in anammox Planctomycetes and thus firmly adds to the emerging view that Planctomycetes have a Gram-negative cell envelope.
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Affiliation(s)
- Muriel C F van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands.
| | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Naomi M de Almeida
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands.
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Seeger C, Butler MK, Yee B, Mahajan M, Fuerst JA, Andersson SGE. Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes. Int J Syst Evol Microbiol 2017; 67:4923-4929. [PMID: 29087267 PMCID: PMC5845749 DOI: 10.1099/ijsem.0.002271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1T displays modest salt tolerance and grows optimally at pH values of 7.5–8.0 and at temperatures of 32–36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1T (=CCUG 69661T=DSM 105045T).
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Affiliation(s)
- Christian Seeger
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Margaret K Butler
- Australian Center for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Yee
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Mayank Mahajan
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siv G E Andersson
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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Bondoso J, Godoy-Vitorino F, Balagué V, Gasol JM, Harder J, Lage OM. Epiphytic Planctomycetes communities associated with three main groups of macroalgae. FEMS Microbiol Ecol 2017; 93:fiw255. [PMID: 28087803 DOI: 10.1093/femsec/fiw255] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2016] [Indexed: 01/18/2023] Open
Abstract
Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season. This pattern was confirmed by clone libraries of winter and summer samples: we obtained 720 16S rRNA gene sequences that represented 44 operational taxonomic units (OTUs) within the phylum Planctomycetes. Most of the OTUs belonged to Blastopirellula, followed by Rhodopirellula, Planctomyces, the Pir4 lineage and the uncultured class OM190 (this last one nearly 30% of the OTUs). Ulva sp. and C. crispus had more diverse planctomycetal communities than F. spiralis. Analysis of beta diversity showed that the planctomycetal microbiome was host specific. We hypothesize that the specific association of Planctomycetes and their macroalgal hosts is likely determined by nutritional molecules provided by the algae and the set of sulfatases inherent to each Planctomycetes species.
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Affiliation(s)
- Joana Bondoso
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n° 4169-007 Porto, Portugal.,CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental - Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Microbial Ecology and Genomics Lab, College of Sciences and Technology, Inter American University of Puerto Rico-Metropolitan Campus, San Juan, PR 00919, USA
| | - Vanessa Balagué
- Institut de Ciències del Mar-CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Josep M Gasol
- Institut de Ciències del Mar-CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n° 4169-007 Porto, Portugal.,CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental - Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
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van Niftrik L, Devos DP. Editorial: Planctomycetes-Verrucomicrobia-Chlamydiae Bacterial Superphylum: New Model Organisms for Evolutionary Cell Biology. Front Microbiol 2017; 8:1458. [PMID: 28824586 PMCID: PMC5539593 DOI: 10.3389/fmicb.2017.01458] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/20/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Laura van Niftrik
- Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud UniversityNijmegen, Netherlands
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo-CSIC, Universidad Pablo de OlavideSeville, Spain
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Feijoo-Siota L, Rama JLR, Sánchez-Pérez A, Villa TG. Considerations on bacterial nucleoids. Appl Microbiol Biotechnol 2017; 101:5591-5602. [PMID: 28664324 DOI: 10.1007/s00253-017-8381-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Abstract
The classic genome organization of the bacterial chromosome is normally envisaged with all its genetic markers linked, thus forming a closed genetic circle of duplex stranded DNA (dsDNA) and several proteins in what it is called as "the bacterial nucleoid." This structure may be more or less corrugated depending on the physiological state of the bacterium (i.e., resting state or active growth) and is not surrounded by a double membrane as in eukayotic cells. The universality of the closed circle model in bacteria is however slowly changing, as new data emerge in different bacterial groups such as in Planctomycetes and related microorganisms, species of Borrelia, Streptomyces, Agrobacterium, or Phytoplasma. In these and possibly other microorganisms, the existence of complex formations of intracellular membranes or linear chromosomes is typical; all of these situations contributing to weakening the current cellular organization paradigm, i.e., prokaryotic vs eukaryotic cells.
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Affiliation(s)
- Lucía Feijoo-Siota
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - José Luis R Rama
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Angeles Sánchez-Pérez
- Discipline of Physiology and Bosch Institute, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain.
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48
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Kohn T, Heuer A, Jogler M, Vollmers J, Boedeker C, Bunk B, Rast P, Borchert D, Glöckner I, Freese HM, Klenk HP, Overmann J, Kaster AK, Rohde M, Wiegand S, Jogler C. Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. Front Microbiol 2016; 7:2079. [PMID: 28066393 PMCID: PMC5177795 DOI: 10.3389/fmicb.2016.02079] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/08/2016] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11T shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11T was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 “giant genes” were found within the genome of NH11T. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in “giant genes”. Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11T from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
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Affiliation(s)
- Timo Kohn
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anja Heuer
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Mareike Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - John Vollmers
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Boedeker
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Ines Glöckner
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Heike M Freese
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anne-Kristin Kaster
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infectious Disease Braunschweig, Germany
| | - Sandra Wiegand
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
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49
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Bacterial Communities and Antibiotic Resistance Communities in a Full-Scale Hospital Wastewater Treatment Plant by High-Throughput Pyrosequencing. WATER 2016. [DOI: 10.3390/w8120580] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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50
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Rivas-Marín E, Canosa I, Devos DP. Evolutionary Cell Biology of Division Mode in the Bacterial Planctomycetes- Verrucomicrobia- Chlamydiae Superphylum. Front Microbiol 2016; 7:1964. [PMID: 28018303 PMCID: PMC5147048 DOI: 10.3389/fmicb.2016.01964] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/23/2016] [Indexed: 11/30/2022] Open
Abstract
Bacteria from the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum are exceptions to the otherwise dominant mode of division by binary fission, which is based on the interaction between the FtsZ protein and the peptidoglycan (PG) biosynthesis machinery. Some PVC bacteria are deprived of the FtsZ protein and were also thought to lack PG. How these bacteria divide is still one of the major mysteries of microbiology. The presence of PG has recently been revealed in Planctomycetes and Chlamydiae, and proteins related to PG synthesis have been shown to be implicated in the division process in Chlamydiae, providing important insights into PVC mechanisms of division. Here, we review the historical lack of observation of PG in PVC bacteria, its recent detection in two phyla and its involvement in chlamydial cell division. Based on the detection of PG-related proteins in PVC proteomes, we consider the possible evolution of the diverse division mechanisms in these bacteria. We conclude by summarizing what is known and what remains to be understood about the evolutionary cell biology of PVC division modes.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide Seville, Spain
| | - Inés Canosa
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide Seville, Spain
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