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López-Legentil S, Palanisamy SK, Smith KF, McCormack G, Erwin PM. Prokaryotic symbiont communities in three ascidian species introduced in both Ireland and New Zealand. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:6805-6817. [PMID: 36002791 DOI: 10.1007/s11356-022-22652-2] [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: 01/26/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Ascidians or sea squirts are among the marine taxa with the most introduced species worldwide. These animals have a suite of biological characteristics that contribute to their successful establishment, including long reproductive seasons, rapid growth rates, and resistance to pollution. Here, we sequenced a fragment of the 16S ribosomal RNA gene to characterize symbiont diversity and host-specificity in the solitary species Syela clava and Ascidiella aspersa, and the colonial species Didemnum vexillum. Samples were collected from introduced populations in several marinas and mussel facilities around Ireland, and a marina in New Zealand. Two additional colonial species Botrylloides violaceus and Didemnum sp. were collected in Ireland, and ambient seawater was sampled from both countries for comparison. Data revealed a strong effect of host species and location on prokaryote symbiont composition, consistent with recent ascidian microbiome literature. However, a location effect did not manifest in alpha diversity metrics (e.g., the same ascidian species at different locations exhibited similar diversity) but was evident in beta diversity metrics (greater intra-specific differences across locations than within locations). Location effects were stronger than species effects only for the solitary species (i.e., A. aspersa from New Zealand was more similar to S. clava from New Zealand than to A. aspersa from Ireland). D. vexillum and A. aspersa hosted a high abundance of prokaryotic symbionts that were previously found in other ascidian species, while S. clava symbiotic community was more closely related to bacteria common in the marine environment. Further studies should aim to unravel host-microbe coevolutionary patterns and the microbial role in facilitating host establishment in different habitats.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA.
| | - Satheesh Kumar Palanisamy
- Zoology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7042, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Grace McCormack
- Zoology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
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2
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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3
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Yadav S, Koenen M, Bale N, Sinninghe Damsté JS, Villanueva L. The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:899-910. [PMID: 34668338 DOI: 10.1111/1758-2229.13012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.
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Affiliation(s)
- Subhash Yadav
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Nicole Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, P.O. Box 59, 1797AB, Den Burg, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
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4
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Undaria pinnatifida exudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02471-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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5
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Horodesky A, Castilho-Westphal GG, Pont GD, Faoro H, Balsanelli E, Tadra-Sfeir MZ, Cozer N, Pie MR, Ostrensky A. Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments. AN ACAD BRAS CIENC 2020; 92:e20180432. [PMID: 32609272 DOI: 10.1590/0001-3765202020180432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 01/16/2019] [Indexed: 11/22/2022] Open
Abstract
In this work, we identified the bacterial microbiota associated with farmed oystersin estuarine regions of four states in the north eastern region of Brazil. During the drought and rainy seasons, for eight months, twenty oysters were sampled seasonally from seven different marine farms. In the laboratory, DNA extraction, amplification, and sequencing of the 16S rRNA gene were performed to establish the taxonomic units. We identified 106 genera of bacteria belonging to 103 families, 70 orders, 39 classes, and 21 phyla. Out of the total, 40 of the genera represented bacteria potentially pathogenic to humans; of these, nine are known to cause foodborne diseases and six are potentially pathogenic to oysters. The most prevalent genera were Mycoplasma, Propionigenium, Psychrilyobacter, and Arcobacter. The results indicate the need for more systematic monitoring of bacteria of the genus Mycoplasma in oyster farming operations in the Brazilian north eastern region. Currently, Mycoplasma is not one of the microorganisms analysed and monitored by order of Brazilian legislation during the oyster production and/or commercialization process, even though this genus was the most prevalent at all sampling points and presents pathogenic potential both for oysters and for consumers.
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Affiliation(s)
- Aline Horodesky
- Grupo Integrado de Aquicultura e Estudos Ambientais, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil
| | - Gisela G Castilho-Westphal
- Grupo Integrado de Aquicultura e Estudos Ambientais, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil
| | - Giorgi Dal Pont
- Grupo Integrado de Aquicultura e Estudos Ambientais, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zootecnia, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Rua Professor Algacyr Munhoz Mader, 3775, 81310-020 Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil
| | - Michelle Z Tadra-Sfeir
- Departamento de Bioquímica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil
| | - Nathieli Cozer
- Grupo Integrado de Aquicultura e Estudos Ambientais, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zootecnia, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil
| | - Marcio Roberto Pie
- Programa de Pós-Graduação em Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil
| | - Antonio Ostrensky
- Grupo Integrado de Aquicultura e Estudos Ambientais, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Coronel Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil.,Programa de Pós-Graduação em Zootecnia, Setor de Ciências Agrárias, Universidade Federal do Paraná, Rua dos Funcionários, 1540, 80035-050 Curitiba, PR, Brazil
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Selvarajan R, Sibanda T, Venkatachalam S, Ogola HJO, Christopher Obieze C, Msagati TA. Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa. Sci Rep 2019; 9:19835. [PMID: 31882618 PMCID: PMC6934600 DOI: 10.1038/s41598-019-56269-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.
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Affiliation(s)
- Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.
| | - Timothy Sibanda
- Department of Biological Sciences, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek, Namibia
| | | | - Henry J O Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.,Centre for Research, Innovation and Technology, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | | | - Titus A Msagati
- Nanotechnology and Water Sustainability Research Unit, College of Science, Engineering and Technology, University of South Africa-Science Campus, Florida, South Africa
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7
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Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem. Appl Environ Microbiol 2019; 85:AEM.01297-19. [PMID: 31324631 PMCID: PMC6752017 DOI: 10.1128/aem.01297-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/14/2019] [Indexed: 01/21/2023] Open
Abstract
Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere. Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based analyses). Of eight amino acids tested, glutamate, aspartate, and threonine were most stimulatory and yielded dissimilar fermentations facilitated by contrasting taxa (e.g., glutamate stimulated the Fusobacteriaceae and yielded H2 and formate, whereas aspartate stimulated the Aeromonadaceae and yielded succinate and propionate). A marginal Stickland fermentation was associated with the Peptostreptococcaceae and Lachnospiraceae. Ribose fermentation yielded a complex product profile facilitated primarily by the Aeromonadaceae. The transient nature of succinate was linked to its decarboxylation to propionate and the Fusobacteriaceae, whereas the transient nature of formate was linked to formate-hydrogen lyase activity and the Peptostreptococcaceae. These findings reinforce the likelihood that (i) the animal host and hosted fermentative bacteria compete for the constituents of protein and RNA in the alimentary canal and (ii) diverse gut fermenters engaged in the fermentation of these constituents produce products that can be utilized by earthworms. IMPORTANCE Animal health is linked to gut ecosystems whose primary function is normally the digestion of dietary matter. Earthworms are representative of one of the oldest known animal lineages and, despite their primitive nature, have unique environmental impact by virtue of their dietary consumption of their habitat, i.e., soil-associated matter. A resident gut community is a hallmark of many gut ecosystems of evolutionarily more advanced animals, but the alimentary canal of earthworms is dominated by ingested transient soil microbes. Protein and RNA are (i) the primary organic components of microbial cells that are subject to lysis during gut passage and (ii) fermentable dietary substrates in the alimentary canal. This study examined the gut-associated fermentation of constituents of these biopolymers to determine how their fermentation is integrated to the microbiological dynamics of the gut and might contribute to earthworm-linked transformations of organic matter in the terrestrial biosphere.
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8
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Wolff D, Krah D, Dötsch A, Ghattas AK, Wick A, Ternes TA. Insights into the variability of microbial community composition and micropollutant degradation in diverse biological wastewater treatment systems. WATER RESEARCH 2018; 143:313-324. [PMID: 29986241 DOI: 10.1016/j.watres.2018.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/02/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
The biological potential of conventional wastewater treatment plants to remove micropollutants mainly depends on process conditions and the predominant microbial community. To explore this dependence and to connect the occurrence of genera with operating conditions, five pilot-scale reactors with different process conditions were combined into two reactor cascades and fed with the effluent of the primary clarifier of a municipal WWTP. All reactors and the WWTP were analyzed for the removal of 33 micropollutants by LC-MS/MS and the presence of the microbial community using 16S rRNA gene sequencing. The overall removal of the micropollutants was slightly improved (ca. 20%) by the reactor cascades in comparison to the WWTP while certain compounds such as diatrizoate, venlafaxine or diclofenac showed an enhanced removal (ca. 70% in one or both cascades). To explore the diverse bacteria in more detail, the general community was divided into a core and a specialized community. Despite their profoundly different operating parameters (especially redox conditions), the different treatments share a core community consisted of 143 genera (9% of the overall community). Furthermore, the alpha- and beta-biodiversity as well as the occurrence of several genera belonging to the specialized microbial community could be linked to the prevalent process conditions of the individual treatments. Members of the specialized community also correlated with the removal of certain groups of micropollutants. Hence, the comparison of the specialized community with micropollutant removal and operating conditions via correlation analysis is a valuable tool for an extended evaluation of prevalent process conditions. Based on an extended data set this approach could also be used to identify organisms as indicators for operating conditions which are beneficial for an improved removal of specific micropollutants.
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Affiliation(s)
- David Wolff
- Federal Institute of Hydrology (BfG), D-56068, Koblenz, Am Mainzer Tor 1, Germany
| | - Daniel Krah
- Federal Institute of Hydrology (BfG), D-56068, Koblenz, Am Mainzer Tor 1, Germany
| | - Andreas Dötsch
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), D-76344, Eggenstein-Leopoldshafen, Hermann-von-Helmholtz-Platz 1, Germany
| | - Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068, Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068, Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068, Koblenz, Am Mainzer Tor 1, Germany.
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9
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Rzeznik-Orignac J, Puisay A, Derelle E, Peru E, Le Bris N, Galand PE. Co-occurring nematodes and bacteria in submarine canyon sediments. PeerJ 2018; 6:e5396. [PMID: 30083476 PMCID: PMC6074754 DOI: 10.7717/peerj.5396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/17/2018] [Indexed: 01/17/2023] Open
Abstract
In submarine canyon sediments, bacteria and nematodes dominate the benthic biomass and play a key role in nutrient cycling and energy transfer. The diversity of these communities remains, however, poorly studied. This work aims at describing the composition of bacteria and nematode communities in the Lacaze-Duthiers submarine canyon in the north-western Mediterranean Sea. We targeted three sediment depths for two consecutive years and investigated the communities using nuclear markers (18S rRNA and 16S rRNA genes). High throughput sequencing combined to maximal information coefficient (MIC) statistical analysis allowed us to identify, for the first time, at the same small scale, the community structures and the co-occurrence of nematodes and bacteria Operational Taxonomic Units across the sediment cores. The associations detected by MIC revealed marked patterns of co-occurrences between the bacteria and nematodes in the sediment of the canyon and could be linked to the ecological requirements of individual bacteria and nematodes. For the bacterial community, Delta- and Gammaproteobacteria sequences were the most abundant, as seen in some canyons earlier, although Acidobacteria, Actinobacteria and Planctomycetes have been prevalent in other canyon sediments. The 20 identified nematode genera included bacteria feeders as Terschellingia, Eubostrichus, Geomonhystera, Desmoscolex and Leptolaimus. The present study provides new data on the diversity of bacterial and nematodes communities in the Lacaze-Duthiers canyon and further highlights the importance of small-scale sampling for an accurate vision of deep-sea communities.
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Affiliation(s)
- Jadwiga Rzeznik-Orignac
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Antoine Puisay
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France.,Criobe, Laboratoire d'Excellence "Corail", PSL Research University: EPHE-UPVD-CNRS, Papetoai, French Polynesia
| | - Evelyne Derelle
- Laboratoire de Biologie Intégrative des Organismes Marins, Sorbonne Université, CNRS, Banyuls-sur-Mer, France.,LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, IUEM, Plouzané, France
| | - Erwan Peru
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Nadine Le Bris
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Pierre E Galand
- Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
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10
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Hundt PJ, Hundt MJ, Staley C, Sadowsky MJ, Simons AM. The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies,Chasmodes saburraeandScartella cristata. COPEIA 2017. [DOI: 10.1643/ci-16-505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Ngangbam AK, Baten A, Waters DLE, Whalan S, Benkendorff K. Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod. PLoS One 2015; 10:e0140725. [PMID: 26488885 PMCID: PMC4619447 DOI: 10.1371/journal.pone.0140725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/28/2015] [Indexed: 11/19/2022] Open
Abstract
Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita.
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Affiliation(s)
- Ajit Kumar Ngangbam
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Steve Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
- * E-mail:
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12
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Roalkvam I, Bredy F, Baumberger T, Pedersen RB, Steen IH. Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field. Int J Syst Evol Microbiol 2015; 65:4521-4525. [PMID: 26373292 DOI: 10.1099/ijsem.0.000606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91 % 16S rRNA gene sequence similarity). The cells of the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20-55 °C (optimally at 48 °C), with 1-6 % (w/v) NaCl (optimally with 2 %), and at pH 5.3-8.0 (optimally at pH 6.0-8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7 mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T ( = DSM 100055 = JCM 30901).
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Affiliation(s)
- Irene Roalkvam
- Center for Geobiology, University of Bergen, Allégaten 41, 5007 Bergen, Norway.,Department of Biology, University of Bergen, Thormøhlensgate 53A/B, 5006 Bergen, Norway
| | - Florian Bredy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Tamara Baumberger
- Center for Geobiology, University of Bergen, Allégaten 41, 5007 Bergen, Norway.,Department of Earth Science, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Rolf-B Pedersen
- Center for Geobiology, University of Bergen, Allégaten 41, 5007 Bergen, Norway.,Department of Earth Science, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Ida Helene Steen
- Center for Geobiology, University of Bergen, Allégaten 41, 5007 Bergen, Norway.,Department of Biology, University of Bergen, Thormøhlensgate 53A/B, 5006 Bergen, Norway
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Aida AA, Kuroda K, Yamamoto M, Nakamura A, Hatamoto M, Yamaguchi T. Diversity Profile of Microbes Associated with Anaerobic Sulfur Oxidation in an Upflow Anaerobic Sludge Blanket Reactor Treating Municipal Sewage. Microbes Environ 2015; 30:157-63. [PMID: 25817585 PMCID: PMC4462926 DOI: 10.1264/jsme2.me14105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors.
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Affiliation(s)
- Azrina A Aida
- Department of Environmental Systems Engineering, Nagaoka University of Technology
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14
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Graue J, Engelen B, Cypionka H. Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes. THE ISME JOURNAL 2012; 6:660-9. [PMID: 21918576 PMCID: PMC3280128 DOI: 10.1038/ismej.2011.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 07/29/2011] [Accepted: 07/29/2011] [Indexed: 11/08/2022]
Abstract
To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with (13)C-labeled Spirulina biomass (130 mg per 21 g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output reached its maximum (55 μW), while primary fermentation products were formed (in μmol) as follows: acetate 440, ethanol 195, butyrate 128, propionate 112, H(2) 127 and smaller amounts of valerate, propanol and butanol. Sulfate was depleted within 7 days. Thereafter, methanogenesis was observed and secondary fermentation proceeded. H(2) and alcohols disappeared completely, whereas fatty acids decreased in concentration. Three main degraders were identified by RNA-based SIP and denaturant gradient gel electrophoresis. After 12 h, two phylotypes clearly enriched in (13)C: (i) Psychrilyobacter atlanticus, a fermenter known to produce hydrogen and acetate and (ii) bacteria distantly related to Propionigenium. A Cytophaga-related bacterium was highly abundant after day 3. Sulfate reduction appeared to be performed by incompletely oxidizing species, as only sulfate-reducing bacteria related to Desulfovibrio were labeled as long as sulfate was available.
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Affiliation(s)
- Jutta Graue
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
| | - Bert Engelen
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
| | - Heribert Cypionka
- Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky Universität Oldenburg, Niedersachsen, Germany
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15
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Zhao JS, Manno D, Hawari J. Psychrilyobacter atlanticus gen. nov., sp. nov., a marine member of the phylum Fusobacteria that produces H2 and degrades nitramine explosives under low temperature conditions. Int J Syst Evol Microbiol 2009; 59:491-7. [PMID: 19244428 DOI: 10.1099/ijs.0.65263-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative and obligately anaerobic marine bacterium, strain HAW-EB21(T), was isolated in a previous study from marine sediment from the Atlantic Ocean, near Halifax Harbor, Canada, and found to have the potential to degrade both hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine. In the present study, phylogenetic analyses showed that strain HAW-EB21(T) was only distantly related to the genera Propionigenium and Ilyobacter with 6.6-7.5 % and 8.2-10.5 % dissimilarity as measured by 16S rRNA and 23S rRNA gene sequence analyses, respectively. Strain HAW-EB21(T) displayed unique properties in being psychrotrophic (18.5 degrees C optimum) and unable to utilize any of the carbon substrates (succinate, l-tartrate, 3-hydroxybutyrate, quinate or shikimate) used for isolating members of the genera Propionigenium and Ilyobacter. Strain HAW-EB21(T) utilized glucose, fructose, maltose, N-acetyl-d-glucosamine, citrate, pyruvate, fumarate and Casitone as carbon sources and produced H(2) and acetate as the major fermentation products. Cells grown at 10 degrees C produced C(15 : 1) (30 %), C(16 : 1)omega7 (15 %) and C(16 : 0) (16 %) as major membrane fatty acids. The novel strain had a genomic DNA G+C content of 28.1 mol%, lower than the values of the genera Ilyobacter and Propionigenium. Based on the present results, the novel isolate is suggested to be a member of a new genus for which the name Psychrilyobacter atlanticus gen. nov., sp. nov. is proposed. The type strain of the type species is HAW-EB21(T) (=DSM 19335(T)=JCM 14977(T)).
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Affiliation(s)
- Jian-Shen Zhao
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave, Montreal, Quebec H4P 2R2, Canada.
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Janssen PH, Liesack W, Kluge C, Seeliger S, Schink B, Harfoot CG. Sodium-dependent succinate decarboxylation by a new anaerobic bacterium belonging to the genus Peptostreptococcus. Antonie Van Leeuwenhoek 1996; 70:11-20. [PMID: 8836437 DOI: 10.1007/bf00393565] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An anaerobic bacterium was isolated from a polluted sediment, with succinate and yeast extract as carbon and energy sources. The new strain was Gram-positive, the cells were coccal shaped, the mol% G+G content of the genomic DNA was 29, and the peptidoglycan was of the L-ornithine-D-glutamic acid type. Comparative sequence analysis of the 16S rRNA gene showed the new strain to belong to the genus Peptostreptococcus. Succinate, fumarate, pyruvate, 3-hydroxybutyrate and lysine supported growth. Succinate was degraded to propionate and presumably CO2, with a stoichiometric cell yield. Key enzymes of the methylmalonyl-CoA decarboxylase pathway were present. The methylmalonyl-CoA decarboxylase activity was avidin-sensitive and sodium dependent, and about 5 mM Na+ was required for maximal activity. Whole cells, however, required at least 50 mM sodium for maximal succinate decarboxylation activity and to support the maximum growth rate. Sodium-dependent energy conservation coupled to succinate decarboxylation is shown for the first time to occur in a bacterium belonging to the group of Gram-positive bacteria containing the peptostreptococci and their relatives.
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Affiliation(s)
- P H Janssen
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
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