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Davis KM, Parfrey LW, Harley CDG, Holmes K, Schaefer O, Gehman AL. Epibiont communities on mussels in relation to parasitism and location in the rocky intertidal zone. FEMS Microbiol Ecol 2024; 100:fiae101. [PMID: 39138059 PMCID: PMC11385189 DOI: 10.1093/femsec/fiae101] [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: 02/12/2023] [Revised: 06/16/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
The factors shaping host-parasite interactions and epibiont communities in the variable rocky intertidal zone are poorly understood. California mussels, Mytilus californianus, are colonized by endolithic cyanobacterial parasites that erode the host shell. These cyanobacteria become mutualistic under certain abiotic conditions because shell erosion can protect mussels from thermal stress. How parasitic shell erosion affects or is affected by epibiotic microbial communities on mussel shells and the context dependency of these interactions is unknown. We used transplant experiments to characterize assemblages of epibiotic bacteria and endolithic parasites on mussel shells across intertidal elevation gradients. We hypothesized that living mussels, and associated epibacterial communities, could limit colonization and erosion by endolithic cyanobacteria compared with empty mussel shells. We hypothesized that shell erosion would be associated with compositional shifts in the epibacterial community and tidal elevation. We found that living mussels experienced less shell erosion than empty shells, demonstrating potential biotic regulation of endolithic parasites. Increased shell erosion was not associated with a distinct epibacterial community and was decoupled from the relative abundance of putatively endolithic taxa. Our findings suggest that epibacterial community structure is not directly impacted by the dynamic symbiosis between endolithic cyanobacteria and mussels throughout the rocky intertidal zone.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christopher D G Harley
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Keith Holmes
- Hakai Institute, PO Box 25039 Campbell River, BC V9W 0B7, Canada
| | - Olivia Schaefer
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alyssa-Lois Gehman
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Hakai Institute, PO Box 25039 Campbell River, BC V9W 0B7, Canada
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Ghaly TM, Focardi A, Elbourne LDH, Sutcliffe B, Humphreys W, Paulsen IT, Tetu SG. Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling. MICROBIOME 2023; 11:190. [PMID: 37626351 PMCID: PMC10463829 DOI: 10.1186/s40168-023-01633-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood. RESULTS Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling. CONCLUSION These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments. Video Abstract.
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Affiliation(s)
- Timothy M Ghaly
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Amaranta Focardi
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Liam D H Elbourne
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | | | - William Humphreys
- School of Biological Sciences, University of Western Australia, Perth, Australia
| | - Ian T Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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Kiama CW, Njire MM, Kambura AK, Mugweru JN, Matiru VN, Wafula EN, Kagali RN, Kuja JO. Prokaryotic diversity and composition within equatorial lakes Olbolosat and Oloiden in Kenya (Africa). CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100066. [PMID: 34841356 PMCID: PMC8610316 DOI: 10.1016/j.crmicr.2021.100066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 01/04/2023] Open
Abstract
Total community 16S rDNA was used to determine the diversity and composition of bacteria and archaea within lakes Olbolosat and Oloiden in Kenya. The V3-V4 hypervariable region of the 16S rRNA gene was targeted since it's highly conserved and has a higher resolution for lower rank taxa. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Lakes Olbolosat and Oloiden shared 280 of 10,523 Amplicon Sequence Variants (ASVs) recovered while the four sample types (water, microbial mats, dry and wet sediments) shared 4 ASVs. The composition of ASVs in lake Olbolosat was highly dependent on Cu+, Fe2+, NH4 +, and Mn2+, while L. Oloiden was dependent on Mg2+, Na+, Ca2+, and K+. All the alpha diversity indices except Simpson were highest in the dry sediment sample (EC1 and 2) both from lake Oloiden. The abundant phyla included Proteobacteria (33.8%), Firmicutes (27.3%), Actinobacteriota (21.2%), Chloroflexi (6.8%), Cyanobacteria (3.8%), Acidobacteriota (2.8%), Planctomycetota (1.9%) and Bacteroidota (1.1%). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The interaction network for prokaryotic communities within the two lakes displayed Proteobacteria to be highly positively connected with other microbes. PERMANOVA results suggest that temperature controls the functioning of the two ecosystems.
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Affiliation(s)
- Catherine Wachera Kiama
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Moses Mucugi Njire
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Anne Kelly Kambura
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300 Voi, Kenya
| | | | - Viviene Njeri Matiru
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Eliud Nalianya Wafula
- Department of Physical and Biological Sciences, Bomet University College, P.O Box 701-20400, Bomet Kenya
| | - Robert Nesta Kagali
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
| | - Josiah Ochieng Kuja
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200 Nairobi, Kenya
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Marzocchi U, Bonaglia S, Zaiko A, Quero GM, Vybernaite-Lubiene I, Politi T, Samuiloviene A, Zilius M, Bartoli M, Cardini U. Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments. Front Microbiol 2021; 11:610269. [PMID: 33542710 PMCID: PMC7851879 DOI: 10.3389/fmicb.2020.610269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.
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Affiliation(s)
- Ugo Marzocchi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Center for Water Technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anastasija Zaiko
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Grazia M. Quero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Institute for Biological Resources and Marine Biotechnologies, National Research Council of Italy, Ancona, Italy
| | | | - Tobia Politi
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | | | - Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Chemistry, Life science and Environmental Sustainability, Parma University, Parma, Italy
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
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Cleary DFR. A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01476-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Cleary DFR, Swierts T, Coelho FJRC, Polónia ARM, Huang YM, Ferreira MRS, Putchakarn S, Carvalheiro L, van der Ent E, Ueng JP, Gomes NCM, de Voogd NJ. The sponge microbiome within the greater coral reef microbial metacommunity. Nat Commun 2019; 10:1644. [PMID: 30967538 PMCID: PMC6456735 DOI: 10.1038/s41467-019-09537-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/18/2019] [Indexed: 02/03/2023] Open
Abstract
Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan.
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Francisco J R C Coelho
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Marine Recreation, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Marina R S Ferreira
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Sumaitt Putchakarn
- Institute of Marine Science, Burapha University, Chon Buri, 20131, Thailand
| | - Luis Carvalheiro
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Esther van der Ent
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Jinn-Pyng Ueng
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Aquaculture, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Newton C M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
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Cleary DFR, Polónia ARM, de Voogd NJ. Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea. MICROBIAL ECOLOGY 2018; 76:610-624. [PMID: 29470608 DOI: 10.1007/s00248-018-1156-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana R M Polónia
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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