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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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2
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Klimek D, Herold M, Calusinska M. Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes. BMC Genomics 2024; 25:523. [PMID: 38802741 PMCID: PMC11131199 DOI: 10.1186/s12864-024-10413-z] [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: 01/26/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats. RESULTS Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides - this opens new perspectives for algal biomass valorisation in biogas processes. CONCLUSIONS Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.
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Affiliation(s)
- Dominika Klimek
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg.
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l'Université, Esch-sur-Alzette, L-4365, Luxembourg.
| | - Malte Herold
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, Belvaux, L-4422, Luxembourg
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3
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Yang S, Zuo J, Grossart HP, Dai G, Liu J, Song L, Gan N. Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123878. [PMID: 38548158 DOI: 10.1016/j.envpol.2024.123878] [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: 02/21/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.
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Affiliation(s)
- Siyu Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zuo
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Lab for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, Wenzhou University, Wenzhou, 325035, China.
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries IGB, Stechlin, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Guofei Dai
- Jiangxi Academy of Water Science and Engineering, Nanchang, 330029, China
| | - Jin Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lirong Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Nanqin Gan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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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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5
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, origin, and evolution of the ESCRT systems. mBio 2024; 15:e0033524. [PMID: 38380930 PMCID: PMC10936438 DOI: 10.1128/mbio.00335-24] [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: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.IMPORTANCEAll eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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Milke L, Kabuu M, Zschoche R, Gätgens J, Krumbach K, Carlstedt KL, Wurzbacher CE, Balluff S, Beemelmanns C, Jogler C, Marienhagen J, Kallscheuer N. A type III polyketide synthase cluster in the phylum Planctomycetota is involved in alkylresorcinol biosynthesis. Appl Microbiol Biotechnol 2024; 108:239. [PMID: 38407604 PMCID: PMC10896814 DOI: 10.1007/s00253-024-13065-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Members of the bacterial phylum Planctomycetota have recently emerged as promising and for the most part untapped sources of novel bioactive compounds. The characterization of more than 100 novel species in the last decade stimulated recent bioprospection studies that start to unveil the chemical repertoire of the phylum. In this study, we performed systematic bioinformatic analyses based on the genomes of all 131 described members of the current phylum focusing on the identification of type III polyketide synthase (PKS) genes. Type III PKSs are versatile enzymes involved in the biosynthesis of a wide array of structurally diverse natural products with potent biological activities. We identified 96 putative type III PKS genes of which 58 are encoded in an operon with genes encoding a putative oxidoreductase and a methyltransferase. Sequence similarities on protein level and the genetic organization of the operon point towards a functional link to the structurally related hierridins recently discovered in picocyanobacteria. The heterologous expression of planctomycetal type III PKS genes from strains belonging to different families in an engineered Corynebacterium glutamicum strain led to the biosynthesis of pentadecyl- and heptadecylresorcinols. Phenotypic assays performed with the heterologous producer strains and a constructed type III PKS gene deletion mutant suggest that the natural function of the identified compounds differs from that confirmed in other bacterial alkylresorcinol producers. KEY POINTS: • Planctomycetal type III polyketide synthases synthesize long-chain alkylresorcinols. • Phylogenetic analyses suggest an ecological link to picocyanobacterial hierridins. • Engineered C. glutamicum is suitable for an expression of planctomycete-derived genes.
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Affiliation(s)
- Lars Milke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Moses Kabuu
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany
| | - Renè Zschoche
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany
| | - Jochem Gätgens
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Kim-Loreen Carlstedt
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany
| | - Carmen E Wurzbacher
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany
| | - Sven Balluff
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123, Saarbrücken, Germany
| | - Christine Beemelmanns
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), 66123, Saarbrücken, Germany
- Saarland University, Saarbrücken, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University, 07743, Jena, Germany.
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7
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, Origin and Evolution of the ESCRT Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579148. [PMID: 38903064 PMCID: PMC11188069 DOI: 10.1101/2024.02.06.579148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Endosomal Sorting Complexes Required for Transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold, using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The Last Archaeal Common Ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Rzehak T, Praeg N, Zink H, Simon A, Geitner C, Illmer P. Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13215. [PMID: 38062558 PMCID: PMC10866079 DOI: 10.1111/1758-2229.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/01/2023] [Indexed: 02/15/2024]
Abstract
Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.
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Affiliation(s)
- Theresa Rzehak
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Nadine Praeg
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
| | - Harald Zink
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Alois Simon
- Department of Forest PlanningOffice of the Tyrolean GovernmentInnsbruckAustria
| | - Clemens Geitner
- Department of GeographyUniversität InnsbruckInnsbruckAustria
| | - Paul Illmer
- Department of MicrobiologyUniversität InnsbruckInnsbruckAustria
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Vitorino IR, Pinto E, Martín J, Mackenzie TA, Ramos MC, Sánchez P, de la Cruz M, Vicente F, Vasconcelos V, Reyes F, Lage OM. Uncovering the biotechnological capacity of marine and brackish water Planctomycetota. Antonie Van Leeuwenhoek 2024; 117:26. [PMID: 38261060 PMCID: PMC10805854 DOI: 10.1007/s10482-023-01923-z] [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: 09/14/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
An appealing strategy for finding novel bioactive molecules in Nature consists in exploring underrepresented and -studied microorganisms. Here, we investigated the antimicrobial and tumoral anti-proliferative bioactivities of twenty-three marine and estuarine bacteria of the fascinating phylum Planctomycetota. This was achieved through extraction of compounds produced by the Planctomycetota cultured in oligotrophic medium followed by an antimicrobial screening against ten relevant human pathogens including Gram-positive and Gram-negative bacteria, and fungi. Cytotoxic effects of the extracts were also evaluated against five tumoral cell lines. Moderate to potent activities were obtained against Enterococcus faecalis, methicillin-sensitive and methicillin-resistant Staphylococcus aureus and vancomycin-sensitive and vancomycin-resistant Enterococcus faecium. Anti-fungal effects were observed against Trichophyton rubrum, Candida albicans and Aspergillus fumigatus. The highest cytotoxic effects were observed against human breast, pancreas and melanoma tumoral cell lines. Novipirellula caenicola and Rhodopirellula spp. strains displayed the widest spectrum of bioactivities while Rubinisphaera margarita ICM_H10T affected all Gram-positive bacteria tested. LC-HRMS analysis of the extracts did not reveal the presence of any known bioactive natural product, suggesting that the observed activities are most likely caused by novel molecules, that need identification. In summary, we expanded the scope of planctomycetal species investigated for bioactivities and demonstrated that various strains are promising sources of novel bioactive compounds, which reenforces the potential biotechnological prospects offered by Planctomycetota.
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Affiliation(s)
- Inês R Vitorino
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal.
| | - Eugénia Pinto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Jesús Martín
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Thomas A Mackenzie
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Maria C Ramos
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Pilar Sánchez
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Vítor Vasconcelos
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
| | - Fernando Reyes
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
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Kumar G, Kallscheuer N, Kashif M, Ahamad S, Jagadeeshwari U, Pannikurungottu S, Haufschild T, Kabuu M, Sasikala C, Jogler C, Ramana CV. Gemmata algarum, a Novel Planctomycete Isolated from an Algal Mat, Displays Antimicrobial Activity. Mar Drugs 2023; 22:10. [PMID: 38276648 PMCID: PMC10817699 DOI: 10.3390/md22010010] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Axenic cultures of two strains, JC673T and JC717, both belonging to the phylum Planctomycetota, were isolated from distinct geographical locations in India. Strain JC673T was obtained from algal mats of a wetland situated in the state of Kerala, India, while strain JC717 originated from the Central Marine Fisheries Research Institute (CMFRI), state of Tamil Nadu, India. The two strains share 99.9% 16S rRNA gene sequence similarity and are most closely related to Gemmata obscuriglobus UQM 2246T (99.3% 16S rRNA gene sequence identity). The newly isolated strains are Gram-negative, grow aerobically and tolerate up to 4% (w/v) NaCl and a pH of up to 9.0. Cells are spherical and form pink-pigmented colonies. The respiratory quinone is MK-6. Major fatty acids are C18:0, C16:1ω5c and C16:0. Polar lipids include phosphatidylcholine, phosphatidylethanolamine, several unidentified amino lipids, unidentified phospholipids, additional unidentified lipids, and an unidentified choline lipid. The polyamine spermidine is produced by the two strains. The strains have a genome size of about 8.2 Mb with a DNA G+C content of 67.6%. Solvent-based culture extracts of the isolates showed antimicrobial activity against three bacterial test strains. Their phylogenetic position along with differences in morphological, physiological, and genomic features support the classification as a new species of the genus Gemmata, for which we propose the name Gemmata algarum sp. nov. Strain JC673T (=KCTC 72851T = NBRC 114340T) and JC717 are the type and non-type strain of the new species, respectively.
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, 07743 Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Mohammad Kashif
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Shabbir Ahamad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Sreya Pannikurungottu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
| | - Tom Haufschild
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Moses Kabuu
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, 07743 Jena, Germany
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India; (G.K.)
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11
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Zhang H, Zhou X, Li Z, Bartlam M, Wang Y. Anthropogenic original DOM is a critical factor affecting LNA bacterial community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166169. [PMID: 37562635 DOI: 10.1016/j.scitotenv.2023.166169] [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: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
We investigated the geographical and environmental distance-decay relationships for both of the two bacteria in the Haihe River, Tianjin, China. HNA bacteria exhibited a stronger geographical variation-dependent pattern while LNA bacteria exhibited a stronger environmental variation-dependent pattern. Variance partition analysis (VPA), Mantel test, and partial mantel test validated the discrepant impacts of geographical distance and environmental factors on their two communities. The heterogeneous selection dominated community assembly of LNA bacteria demonstrates their greater sensitivity to environmental conditions. As the deterministic environmental factor, anthropogenic original dissolved organic matter (DOM) functions exclusively on LNA bacteria, and it is the critical factor leading to the discrepant biogeographical patterns of LNA and HNA bacteria. LNA bacteria interact with HNA bacteria and mediate the DOM driving total bacteria assembly. The LNA keystone taxa, Pseudomonas, Rheinheimera, Candidatus Aquiluna, and hgcl clade are capable to compete with HNA bacteria for anthropogenic original DOM, and are potential indicators of anthropogenic pollution. Our research reveals the non-negligible effect of the LNA bacteria in regulating the ecological response of total bacteria.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Xinzhu Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Zun Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300071, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China.
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12
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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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13
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Kumar G, Kallscheuer N, Jogler M, Wiegand S, Heuer A, Boedeker C, Rohde M, Jogler C. Stratiformator vulcanicus gen. nov., sp. nov., a marine member of the family Planctomycetaceae isolated from a red biofilm in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie Van Leeuwenhoek 2023; 116:995-1007. [PMID: 37584762 PMCID: PMC10509075 DOI: 10.1007/s10482-023-01860-x] [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: 07/21/2023] [Indexed: 08/17/2023]
Abstract
A novel planctomycetal strain, designated Pan189T, was isolated from biofilm material sampled close to Panarea Island in the Tyrrhenian Sea. Cells of strain Pan189T are round grain rice-shaped, form pink colonies and display typical planctomycetal characteristics including asymmetric cell division through polar budding and presence of crateriform structures. Cells bear a stalk opposite to the division pole and fimbriae cover the cell surface. Strain Pan189T has a mesophilic (optimum at 24 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. Under laboratory-scale cultivation conditions, it reached a generation time of 102 h (µmax = 0.0068 h-1), which places the strain among the slowest growing members of the phylum Planctomycetota characterized so far. The genome size of the strain is with 5.23 Mb at the lower limit among the family Planctomycetaceae (5.1-8.9 Mb). Phylogenetically, the strain represents a novel genus and species in the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. We propose the name Stratiformator vulcanicus gen. nov., sp. nov. for the novel taxon, that is represented by the type strain Pan189T (= DSM 101711 T = CECT 30699 T).
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Affiliation(s)
- Gaurav Kumar
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, 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
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
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14
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Lalitha N, Ronald BSM, Chitra MA, Jangam AK, Katneni VK, Suganya PN, Senthilnayagam H, Senthilkumar TMA, Muralidhar M. Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing. Lett Appl Microbiol 2023; 76:ovad087. [PMID: 37541955 DOI: 10.1093/lambio/ovad087] [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: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.
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Affiliation(s)
- Natarajan Lalitha
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Murugesan Ananda Chitra
- Centre for Animal Health Studies, Madhavaram Milk Colony, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Ashok Kumar Jangam
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Vinaya Kumar Katneni
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Panjan Nathamuni Suganya
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Hemalatha Senthilnayagam
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Moturi Muralidhar
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
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15
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Alba C, Sansano-Maestre J, Cid Vázquez MD, Martínez-Herrero MDC, Garijo-Toledo MM, Azami-Conesa I, Moraleda Fernández V, Gómez-Muñoz MT, Rodríguez JM. Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks. MICROBIAL ECOLOGY 2023; 85:1541-1551. [PMID: 35385973 PMCID: PMC10167124 DOI: 10.1007/s00248-022-02002-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/18/2022] [Indexed: 05/10/2023]
Abstract
Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.
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Affiliation(s)
- Claudio Alba
- Department of Nutrition and Food Science, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | - José Sansano-Maestre
- Department of Animal Production and Public Health, Faculty of Veterinary and Experimental Sciences, Catholic University of Valencia, Valencia, Spain
| | - María Dolores Cid Vázquez
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | - María Del Carmen Martínez-Herrero
- Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, Faculty of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - María Magdalena Garijo-Toledo
- Department of Animal Production and Health, Public Veterinary Health and Food Science and Technology, Faculty of Veterinary Medicine, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Iris Azami-Conesa
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
| | | | - María Teresa Gómez-Muñoz
- Department of Animal Health, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain.
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Faculty of Veterinary Sciences, University Complutense of Madrid, Madrid, Spain
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16
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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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17
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Thompson AW, Sweeney CP, Sutherland KR. Selective and differential feeding on marine prokaryotes by mucous mesh feeders. Environ Microbiol 2023; 25:880-893. [PMID: 36594240 DOI: 10.1111/1462-2920.16334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth's dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, Oregon, USA
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Vitorino IR, Klimek D, Calusinska M, Lobo-da-Cunha A, Vasconcelos V, Lage OM. Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments. Microorganisms 2022; 10:2151. [PMID: 36363743 PMCID: PMC9692418 DOI: 10.3390/microorganisms10112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 09/23/2023] Open
Abstract
The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.
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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
| | - Dominika Klimek
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
| | - 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
| | - 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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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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Vitorino IR, Lobo-da-Cunha A, Vasconcelos V, Lage OM. Rubinisphaera margarita sp. nov., a novel planctomycete isolated from marine sediments collected in the Portuguese north coast. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phylum
Planctomycetota
is constituted by bacteria with unique features that are well adapted to a vast range of habitats. Here, we describe a novel planctomycete isolated from marine sediments collected on a beach in Matosinhos (Portugal) using an iChip-based culturing technique. Strain ICM_H10T forms beige-coloured colonies in modified M14 medium and its cells are spherical to ovoid in shape, stalked, rosette-forming and showing motility in a phase of the life cycle. Transmission electron microscopy observations showed a typical planctomycetal cell plan and cell division by budding. This strain requires salt for growth and grows in the range of 2.0–5.0 % (w/v) NaCl, from 20 to 37 °C, within a pH of 6.0–9.0 and is able to use diverse nitrogen and carbon sources. It is heterotrophic, aerobic and capable of microaerobic growth. This strain has a genome size of approximately 6.0 Mb and a G+C content of 58.1 mol%. A 16S rRNA gene-based phylogenetic analysis supports the association of strain ICM_H10T to the phylum
Planctomycetota
and the family
Planctomycetaceae
, as it shares only 96.8 and 96.4% similarity to its closest relatives
Rubinisphaera italica
Pan54T and
Rubinisphaera brasiliensis
IFAM 1448T, respectively. Other phylogenetic markers also support the separation of this strain into a novel species. Morphological, physiological and genomic comparisons between strain ICM_H10T and its closest relatives strongly suggest that ICM_H10T represents a new species of the genus
Rubinisphaera
, for which we propose the name Rubinisphaera margarita sp. nov., with ICM_H10T (=CECT 30326T=LMG 32234T) as type strain.
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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
- 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
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Olga Maria Lage
- 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
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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