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Sreya PK, Hari Naga Papa Rao A, Suresh G, Sasikala C, Venkata Ramana C. Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov. Syst Appl Microbiol 2024; 47:126523. [PMID: 38897058 DOI: 10.1016/j.syapm.2024.126523] [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: 02/10/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
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Affiliation(s)
- P K Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Atham Hari Naga Papa Rao
- 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
| | | | - 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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Berlinghof J, Montilla LM, Peiffer F, Quero GM, Marzocchi U, Meador TB, Margiotta F, Abagnale M, Wild C, Cardini U. Accelerated nitrogen cycling on Mediterranean seagrass leaves at volcanic CO 2 vents. Commun Biol 2024; 7:341. [PMID: 38503855 PMCID: PMC11254932 DOI: 10.1038/s42003-024-06011-0] [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: 06/02/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
Seagrass meadows form highly productive and diverse ecosystems in coastal areas worldwide, where they are increasingly exposed to ocean acidification (OA). Efficient nitrogen (N) cycling and uptake are essential to maintain plant productivity, but the effects of OA on N transformations in these systems are poorly understood. Here we show that complete N cycling occurs on leaves of the Mediterranean seagrass Posidonia oceanica at a volcanic CO2 vent near Ischia Island (Italy), with OA affecting both N gain and loss while the epiphytic microbial community structure remains largely unaffected. Daily leaf-associated N2 fixation contributes to 35% of the plant's N demand under ambient pH, while it contributes to 45% under OA. Nitrification potential is only detected under OA, and N-loss via N2 production increases, although the balance remains decisively in favor of enhanced N gain. Our work highlights the role of the N-cycling microbiome in seagrass adaptation to OA, with key N transformations accelerating towards increased N gain.
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Affiliation(s)
- Johanna Berlinghof
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.
- Department of Marine Ecology, University of Bremen, Bremen, Germany.
- Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genova, Italy.
| | - Luis M Montilla
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Friederike Peiffer
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Grazia M Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (CNR), Ancona, Italy
| | - Ugo Marzocchi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Center for water technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Travis B Meador
- Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Francesca Margiotta
- Department of Research Infrastructures for marine biological resources, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Maria Abagnale
- Department of Research Infrastructures for marine biological resources, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Christian Wild
- Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Ulisse Cardini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.
- Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genova, Italy.
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3
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Ugarelli K, Campbell JE, Rhoades OK, Munson CJ, Altieri AH, Douglass JG, Heck KL, Paul VJ, Barry SC, Christ L, Fourqurean JW, Frazer TK, Linhardt ST, Martin CW, McDonald AM, Main VA, Manuel SA, Marco-Méndez C, Reynolds LK, Rodriguez A, Rodriguez Bravo LM, Sawall Y, Smith K, Wied WL, Choi CJ, Stingl U. Microbiomes of Thalassia testudinum throughout the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico are influenced by site and region while maintaining a core microbiome. Front Microbiol 2024; 15:1357797. [PMID: 38463486 PMCID: PMC10920284 DOI: 10.3389/fmicb.2024.1357797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 03/12/2024] Open
Abstract
Plant microbiomes are known to serve several important functions for their host, and it is therefore important to understand their composition as well as the factors that may influence these microbial communities. The microbiome of Thalassia testudinum has only recently been explored, and studies to-date have primarily focused on characterizing the microbiome of plants in a single region. Here, we present the first characterization of the composition of the microbial communities of T. testudinum across a wide geographical range spanning three distinct regions with varying physicochemical conditions. We collected samples of leaves, roots, sediment, and water from six sites throughout the Atlantic Ocean, Caribbean Sea, and the Gulf of Mexico. We then analyzed these samples using 16S rRNA amplicon sequencing. We found that site and region can influence the microbial communities of T. testudinum, while maintaining a plant-associated core microbiome. A comprehensive comparison of available microbial community data from T. testudinum studies determined a core microbiome composed of 14 ASVs that consisted mostly of the family Rhodobacteraceae. The most abundant genera in the microbial communities included organisms with possible plant-beneficial functions, like plant-growth promoting taxa, disease suppressing taxa, and nitrogen fixers.
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Affiliation(s)
- Kelly Ugarelli
- Department of Microbiology and Cell Science, Ft. Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Justin E Campbell
- Department of Biological Sciences, Institute of Environment, Coastlines and Oceans Division, Florida International University, Miami, FL, United States
- Smithsonian Marine Station, Fort Pierce, FL, United States
| | - O Kennedy Rhoades
- Department of Biological Sciences, Institute of Environment, Coastlines and Oceans Division, Florida International University, Miami, FL, United States
- Smithsonian Marine Station, Fort Pierce, FL, United States
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Calvin J Munson
- Department of Biological Sciences, Institute of Environment, Coastlines and Oceans Division, Florida International University, Miami, FL, United States
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Andrew H Altieri
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - James G Douglass
- The Water School, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Kenneth L Heck
- Dauphin Island Sea Lab, University of South Alabama, Dauphin Island, AL, United States
| | - Valerie J Paul
- Smithsonian Marine Station, Fort Pierce, FL, United States
| | - Savanna C Barry
- University of Florida, Institute of Food and Agricultural Sciences Nature Coast Biological Station, University of Florida, Cedar Key, FL, United States
| | | | - James W Fourqurean
- Department of Biological Sciences, Institute of Environment, Coastlines and Oceans Division, Florida International University, Miami, FL, United States
| | - Thomas K Frazer
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States
| | - Samantha T Linhardt
- Dauphin Island Sea Lab, University of South Alabama, Dauphin Island, AL, United States
| | - Charles W Martin
- Dauphin Island Sea Lab, University of South Alabama, Dauphin Island, AL, United States
- University of Florida, Institute of Food and Agricultural Sciences Nature Coast Biological Station, University of Florida, Cedar Key, FL, United States
| | - Ashley M McDonald
- Smithsonian Marine Station, Fort Pierce, FL, United States
- University of Florida, Institute of Food and Agricultural Sciences Nature Coast Biological Station, University of Florida, Cedar Key, FL, United States
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vivienne A Main
- Smithsonian Marine Station, Fort Pierce, FL, United States
- International Field Studies, Inc., Andros, Bahamas
| | - Sarah A Manuel
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton Parish, Bermuda
| | - Candela Marco-Méndez
- Dauphin Island Sea Lab, University of South Alabama, Dauphin Island, AL, United States
- Center for Advanced Studies of Blanes (Spanish National Research Council), Girona, Spain
| | - Laura K Reynolds
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL, United States
| | - Alex Rodriguez
- Dauphin Island Sea Lab, University of South Alabama, Dauphin Island, AL, United States
| | | | - Yvonne Sawall
- Bermuda Institute of Ocean Sciences (BIOS), St. George's, Bermuda
| | - Khalil Smith
- Smithsonian Marine Station, Fort Pierce, FL, United States
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton Parish, Bermuda
| | - William L Wied
- Department of Biological Sciences, Institute of Environment, Coastlines and Oceans Division, Florida International University, Miami, FL, United States
- Smithsonian Marine Station, Fort Pierce, FL, United States
| | - Chang Jae Choi
- Department of Microbiology and Cell Science, Ft. Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Ulrich Stingl
- Department of Microbiology and Cell Science, Ft. Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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Egea LG, Brun FG, Jiménez-Ramos R. Dissolved organic carbon leaching from microplastics and bioavailability in coastal ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168673. [PMID: 37981166 DOI: 10.1016/j.scitotenv.2023.168673] [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: 09/15/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
The dissolved organic carbon (DOC) leached from two types of microplastics (polyethylene and polypropylene) frequently found in coastal areas were evaluated in situ. Subsequently, the bioavailability of leached DOC was assessed for microbial inocula from different coastal communities (i.e., estuarine and open-coastal waters, river-mouth waters and seagrass beds). Leached DOC was largely biodegradable (as much as 85 %). However, seagrass beds and river-mouth waters exhibited lower DOC utilization efficiency than estuarine and open-coastal waters, probably because of differences in their microbial communities. The labile/recalcitrant ratio of DOC leached from plastic was similar under illuminated and dark conditions, whereas DOC leached from polyethylene, rather than DOC leached from polypropylene, was preferentially used by microbial communities. We estimated that as many as 21,000 metric tons of DOC leached from plastics may be released into ocean annually. Our results support the need to consider the potential impacts of coastal plastic pollution on microbial communities, including consideration of the trophic webs and coastal carbon cycle.
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Affiliation(s)
- L G Egea
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Departamento de Biología, Facultad de Ciencias del Mar y Ambientales Universidad de Cádiz, Campus Universitario de Puerto Real., 11510 Puerto Real, Cádiz, Spain
| | - F G Brun
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Departamento de Biología, Facultad de Ciencias del Mar y Ambientales Universidad de Cádiz, Campus Universitario de Puerto Real., 11510 Puerto Real, Cádiz, Spain
| | - R Jiménez-Ramos
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Departamento de Biología, Facultad de Ciencias del Mar y Ambientales Universidad de Cádiz, Campus Universitario de Puerto Real., 11510 Puerto Real, Cádiz, Spain.
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5
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Rotini A, Conte C, Winters G, Vasquez MI, Migliore L. Undisturbed Posidonia oceanica meadows maintain the epiphytic bacterial community in different environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95464-95474. [PMID: 37548791 PMCID: PMC10482771 DOI: 10.1007/s11356-023-28968-x] [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: 02/03/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Seagrasses harbour different and rich epiphytic bacterial communities. These microbes may establish intimate and symbiotic relationships with the seagrass plants and change according to host species, environmental conditions, and/or ecophysiological status of their seagrass host. Although Posidonia oceanica is one of the most studied seagrasses in the world, and bacteria associated with seagrasses have been studied for over a decade, P. oceanica's microbiome remains hitherto little explored. Here, we applied 16S rRNA amplicon sequencing to explore the microbiome associated with the leaves of P. oceanica growing in two geomorphologically different meadows (e.g. depth, substrate, and turbidity) within the Limassol Bay (Cyprus). The morphometric (leaf area, meadow density) and biochemical (pigments, total phenols) descriptors highlighted the healthy conditions of both meadows. The leaf-associated bacterial communities showed similar structure and composition in the two sites; core microbiota members were dominated by bacteria belonging to the Thalassospiraceae, Microtrichaceae, Enterobacteriaceae, Saprospiraceae, and Hyphomonadaceae families. This analogy, even under different geomorphological conditions, suggest that in the absence of disturbances, P. oceanica maintains characteristic-associated bacterial communities. This study provides a baseline for the knowledge of the P. oceanica microbiome and further supports its use as a putative seagrass descriptor.
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Affiliation(s)
- Alice Rotini
- ISPRA Istituto Superiore per la Protezione e la Ricerca Ambientale, Via Vitaliano Brancati, 48, 00144, Rome, Italy
| | - Chiara Conte
- Department of Biology, Laboratory of Ecology and Ecotoxicology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Gidon Winters
- Dead Sea and Arava Science Center (DSASC), Masada National Park, 86910, Masada, Israel
- Eilat Campus, Ben-Gurion University of the Negev, Hatmarim Blv., 8855630, Eilat, Israel
| | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianos Str.t, 3036, Limassol, Cyprus
- European University of Technology, 30 Archbishop Kyprianos Str.t, 3036, Limassol, Cyprus
| | - Luciana Migliore
- Department of Biology, Laboratory of Ecology and Ecotoxicology, University of Rome Tor Vergata, 00133, Rome, Italy.
- eCampus University, Via Isimbardi 10, 22060, Novedrate, CO, Italy.
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6
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Conte C, Apostolaki ET, Vizzini S, Migliore L. A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations. PLANTS (BASEL, SWITZERLAND) 2023; 12:350. [PMID: 36679063 PMCID: PMC9863530 DOI: 10.3390/plants12020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.
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Affiliation(s)
- Chiara Conte
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- CoNISMa, National Interuniversity Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Roma, Italy
| | - Luciana Migliore
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, Via Isimbardi 10, 22060 Novedrate (CO), Italy
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7
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Iqbal MM, Nishimura M, Haider MN, Yoshizawa S. Microbial communities on eelgrass ( Zostera marina) thriving in Tokyo Bay and the possible source of leaf-attached microbes. Front Microbiol 2023; 13:1102013. [PMID: 36687565 PMCID: PMC9853538 DOI: 10.3389/fmicb.2022.1102013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Zostera marina (eelgrass) is classified as one of the marine angiosperms and is widely distributed throughout much of the Northern Hemisphere. The present study investigated the microbial community structure and diversity of Z. marina growing in Futtsu bathing water, Chiba prefecture, Japan. The purpose of this study was to provide new insight into the colonization of eelgrass leaves by microbial communities based on leaf age and to compare these communities to the root-rhizome of Z. marina, and the surrounding microenvironments (suspended particles, seawater, and sediment). The microbial composition of each sample was analyzed using 16S ribosomal gene amplicon sequencing. Each sample type was found to have a unique microbial community structure. Leaf-attached microbes changed in their composition depending on the relative age of the eelgrass leaf. Special attention was given to a potential microbial source of leaf-attached microbes. Microbial communities of marine particles looked more like those of eelgrass leaves than those of water samples. This finding suggests that leaf-attached microbes were derived from suspended particles, which could allow them to go back and forth between eelgrass leaves and the water column.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan,*Correspondence: Md Mehedi Iqbal,
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Md. Nurul Haider
- Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan,Susumu Yoshizawa,
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8
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A genomic overview including polyphasic taxonomy of Thalassoroseus pseudoceratinae gen. nov., sp. nov. isolated from a marine sponge, Pseudoceratina sp. Antonie van Leeuwenhoek 2022; 115:843-856. [PMID: 35587321 DOI: 10.1007/s10482-022-01738-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
A pink-coloured, salt- and alkali-tolerant planctomycetal strain (JC658T) with oval to pear-shaped, motile, aerobic, Gram-negative stained cells was isolated from a marine sponge, Pseudoceratina sp. Strain JC658T shares the highest 16S rRNA gene sequence identity with Maioricimonas rarisocia Mal4T (< 89.2%) in the family Planctomycetaceae. The genomic analysis of the new strain indicates its biotechnological potential for the production of various industrially important enzymes, notably sulfatases and carbohydrate-active enzymes (CAZymes), and also potential antimicrobial compounds. Several genes encoding restriction-modification (RM) and CRISPR-CAS systems are also present. NaCl is obligate for growth, of which strain JC658T can tolerate a concentration up to 6% (w/v). Optimum pH and temperature for growth are 8.0 (range 7.0-9.0) and 25 ºC (range 10-40 °C), respectively. The major respiratory quinone of strain JC658T is MK6. Major fatty acids are C16:1ω7c/C16:1ω6c, C18:0 and C16:0. Major polar lipids are phosphatidylcholine, phosphatidyl-dimethylethanolamine and phosphatidyl-monomethylethanolamine. The genomic size of strain JC658T is 7.36 Mb with a DNA G + C content of 54.6 mol%. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strain JC658T belongs to a novel genus and constitutes a novel species within the family Planctomycetaceae, for which we propose the name Thalassoroseus pseudoceratinae gen. nov., sp. nov. The novel species is represented by the type strain JC658T (= KCTC 72881 T = NBRC 114371 T).
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9
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Berlinghof J, Peiffer F, Marzocchi U, Munari M, Quero GM, Dennis L, Wild C, Cardini U. The role of epiphytes in seagrass productivity under ocean acidification. Sci Rep 2022; 12:6249. [PMID: 35428831 PMCID: PMC9012757 DOI: 10.1038/s41598-022-10154-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Ocean Acidification (OA), due to rising atmospheric CO2, can affect the seagrass holobiont by changing the plant's ecophysiology and the composition and functioning of its epiphytic community. However, our knowledge of the role of epiphytes in the productivity of the seagrass holobiont in response to environmental changes is still very limited. CO2 vents off Ischia Island (Italy) naturally reduce seawater pH, allowing to investigate the adaptation of the seagrass Posidonia oceanica L. (Delile) to OA. Here, we analyzed the percent cover of different epiphytic groups and the epiphytic biomass of P. oceanica leaves, collected inside (pH 6.9–7.9) and outside (pH 8.1–8.2) the CO2 vents. We estimated the contribution of epiphytes to net primary production (NPP) and respiration (R) of leaf sections collected from the vent and ambient pH sites in laboratory incubations. Additionally, we quantified net community production (NCP) and community respiration (CR) of seagrass communities in situ at vent and ambient pH sites using benthic chambers. Leaves at ambient pH sites had a 25% higher total epiphytic cover with encrusting red algae (32%) dominating the community, while leaves at vent pH sites were dominated by hydrozoans (21%). Leaf sections with and without epiphytes from the vent pH site produced and respired significantly more oxygen than leaf sections from the ambient pH site, showing an average increase of 47 ± 21% (mean ± SE) in NPP and 50 ± 4% in R, respectively. Epiphytes contributed little to the increase in R; however, their contribution to NPP was important (56 ± 6% of the total flux). The increase in productivity of seagrass leaves adapted to OA was only marginally reflected by the results from the in situ benthic chambers, underlining the complexity of the seagrass community response to naturally occurring OA conditions.
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Affiliation(s)
- Johanna Berlinghof
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy. .,Department of Marine Ecology, University of Bremen, Bremen, Germany.
| | - Friederike Peiffer
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.,Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Ugo Marzocchi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.,Department of Biology, Center for Water Technology - WATEC, Aarhus University, Aarhus, Denmark.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Marco Munari
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Grazia M Quero
- Institute for Marine Biological Resources and Biotechnology, National Research Council (IRBIM-CNR), Ancona, Italy
| | - Laura Dennis
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - Christian Wild
- Department of Marine Ecology, University of Bremen, Bremen, Germany
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy.
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10
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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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11
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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: 20] [Impact Index Per Article: 10.0] [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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12
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Rubio-Portillo E, Martin-Cuadrado AB, Ramos-Esplá AÁ, Antón J. Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes). mSystems 2021; 6:e0086621. [PMID: 34519521 PMCID: PMC8547425 DOI: 10.1128/msystems.00866-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.
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Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | | | - Alfonso Ángel Ramos-Esplá
- Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
- CIMAR, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
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13
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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: 16] [Impact Index Per Article: 5.3] [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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14
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The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator. WATER 2021. [DOI: 10.3390/w13040406] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.
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15
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Kallscheuer N, Rast P, Jogler M, Wiegand S, Kohn T, Boedeker C, Jeske O, Heuer A, Quast C, Glöckner FO, Rohde M, Jogler C. Analysis of bacterial communities in a municipal duck pond during a phytoplankton bloom and isolation of Anatilimnocola aggregata gen. nov., sp. nov., Lacipirellula limnantheis sp. nov. and Urbifossiella limnaea gen. nov., sp. nov. belonging to the phylum Planctomycetes. Environ Microbiol 2021; 23:1379-1396. [PMID: 33331109 DOI: 10.1111/1462-2920.15341] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/24/2020] [Indexed: 11/26/2022]
Abstract
Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant on the surfaces of marine macroscopic phototrophs; however, less data are available on their ecological roles in limnic environments. In this study, we followed a cultivation-independent deep sequencing approach to study the bacterial community composition during a cyanobacterial bloom event in a municipal duck pond. In addition to cyanobacteria, which caused the bloom event, members of the phylum Planctomycetes were significantly enriched in the cyanobacteria-attached fraction compared to the free-living fraction. Separate datasets based on isolated DNA and RNA point towards considerable differences in the abundance and activity of planctomycetal families, indicating different activity peaks of these families during the cyanobacterial bloom. Motivated by the finding that the sampling location harbours untapped bacterial diversity, we included a complementary cultivation-dependent approach and isolated and characterized three novel limnic strains belonging to the phylum Planctomycetes.
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Affiliation(s)
| | | | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.,Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Germany
| | - Timo Kohn
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | | | - Olga Jeske
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Christian Quast
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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16
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Kallscheuer N, Wiegand S, Kohn T, Boedeker C, Jeske O, Rast P, Müller RW, Brümmer F, Heuer A, Jetten MSM, Rohde M, Jogler M, Jogler C. Cultivation-Independent Analysis of the Bacterial Community Associated With the Calcareous Sponge Clathrina clathrus and Isolation of Poriferisphaera corsica Gen. Nov., Sp. Nov., Belonging to the Barely Studied Class Phycisphaerae in the Phylum Planctomycetes. Front Microbiol 2020; 11:602250. [PMID: 33414774 PMCID: PMC7783415 DOI: 10.3389/fmicb.2020.602250] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022] Open
Abstract
Marine ecosystems serve as global carbon sinks and nutrient source or breeding ground for aquatic animals. Sponges are ancient parts of these important ecosystems and can be found in caves, the deep-sea, clear waters, or more turbid environments. Here, we studied the bacterial community composition of the calcareous sponge Clathrina clathrus sampled close to the island Corsica in the Mediterranean Sea with an emphasis on planctomycetes. We show that the phylum Planctomycetes accounts for 9% of the C. clathrus-associated bacterial community, a 5-fold enrichment compared to the surrounding seawater. Indeed, the use of C. clathrus as a yet untapped source of novel planctomycetal strains led to the isolation of strain KS4T. The strain represents a novel genus and species within the class Phycisphaerae in the phylum Planctomycetes and displays interesting cell biological features, such as formation of outer membrane vesicles and an unexpected mode of cell division.
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Affiliation(s)
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, Netherlands.,Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Timo Kohn
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Olga Jeske
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Ralph-Walter Müller
- Faculty for Energy-, Process- and Bioengineering, University of Stuttgart, Stuttgart, Germany
| | - Franz Brümmer
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands.,Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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17
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Wiegand S, Jogler M, Boedeker C, Heuer A, Peeters SH, Kallscheuer N, Jetten MSM, Kaster AK, Rohde M, Jogler C. Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana. Antonie Van Leeuwenhoek 2020; 113:1979-1997. [PMID: 33151460 PMCID: PMC7717034 DOI: 10.1007/s10482-020-01486-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Eight novel strains of the phylum Planctomycetes were isolated from different aquatic habitats. Among these habitats were the hydrothermal vent system close to Panarea Island, a public beach at Mallorca Island, the shore of Costa Brava (Spain), and three sites with brackish water in the Baltic Sea. The genome sizes of the novel strains range from 4.33 to 6.29 Mb with DNA G+C contents between 52.8 and 66.7%. All strains are mesophilic (Topt 24-30 °C) and display generation times between 17 and 94 h. All eight isolates constitute novel species of either already described or novel genera within the family Lacipirellulaceae. Two of the novel species, Posidoniimonas polymericola (type strain Pla123aT = DSM 103020T = LMG 29466T) and Bythopirellula polymerisocia (type strain Pla144T = DSM 104841T = VKM B-3442T), belong to established genera, while the other strains represent the novel genera Aeoliella gen. nov., Botrimarina gen. nov., Pirellulimonas gen. nov. and Pseudobythopirellula gen. nov. Based on our polyphasic analysis, we propose the species Aeoliella mucimassa sp. nov. (type strain Pan181T = DSM 29370T = LMG 31346T = CECT 9840T = VKM B-3426T), Botrimarina colliarenosi sp. nov. (type strain Pla108T = DSM 103355T = LMG 29803T), Botrimarina hoheduenensis sp. nov. (type strain Pla111T = DSM 103485T = STH00945T, Jena Microbial Resource Collection JMRC), Botrimarina mediterranea sp. nov. (type strain Spa11T = DSM 100745T = LMG 31350T = CECT 9852T = VKM B-3431T), Pirellulimonas nuda sp. nov. (type strain Pla175T = DSM 109594T = CECT 9871T = VKM B-3448T) and Pseudobythopirellula maris sp. nov. (type strain Mal64T = DSM 100832T = LMG 29020T).
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Affiliation(s)
- 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
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
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18
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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. Maioricimonas rarisocia gen. nov., sp. nov., a novel planctomycete isolated from marine sediments close to Mallorca Island. Antonie Van Leeuwenhoek 2020; 113:1901-1913. [PMID: 32583192 PMCID: PMC7716917 DOI: 10.1007/s10482-020-01436-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Planctomycetes are ubiquitous bacteria with environmental and biotechnological relevance. Axenic cultures of planctomycetal strains are the basis to analyse their unusual biology and largely uncharacterised metabolism in more detail. Here, we describe strain Mal4T isolated from marine sediments close to Palma de Mallorca, Spain. Strain Mal4T displays common planctomycetal features, such as division by polar budding and the presence of fimbriae and crateriform structures on the cell surface. Cell growth was observed at ranges of 10-39 °C (optimum at 31 °C) and pH 6.5-9.0 (optimum at 7.5). The novel strain shows as pear-shaped cells of 2.0 ± 0.2 × 1.4 ± 0.1 µm and is one of the rare examples of orange colony-forming Planctomycetes. Its genome has a size of 7.7 Mb with a G+C content of 63.4%. Phylogenetically, we conclude that strain Mal4T (= DSM 100296T = LMG 29133T) is the type strain representing the type species of a novel genus, for which we propose the name Maioricimonas rarisocia gen. nov., sp. nov.
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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
| | | | - 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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19
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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: 9] [Impact Index Per Article: 2.3] [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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21
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2020; 70:5596-5600. [DOI: 10.1099/ijsem.0.004484] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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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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