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Salomaki ED, Terpis KX, Rueckert S, Kotyk M, Varadínová ZK, Čepička I, Lane CE, Kolisko M. Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans. BMC Biol 2021; 19:77. [PMID: 33863338 PMCID: PMC8051059 DOI: 10.1186/s12915-021-01007-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/19/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria. RESULTS Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines. CONCLUSIONS Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.
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Affiliation(s)
- Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kristina X Terpis
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, Scotland, UK
| | - Michael Kotyk
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA.
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic.
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2
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Xu Z, Fan W, Shi Z, Tan C, Cui M, Tang S, Qiu G, Feng X. Mercury and methylmercury bioaccumulation in a contaminated bay. MARINE POLLUTION BULLETIN 2019; 143:134-139. [PMID: 31789148 DOI: 10.1016/j.marpolbul.2019.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/04/2019] [Accepted: 04/12/2019] [Indexed: 06/10/2023]
Abstract
The bioaccumulation and the main source of total Hg (THg) and methylmercury (MMHg) in the deposit-feeding polychaete Neanthes japonica collected in Jinzhou Bay, China, were investigated. Compared with the historical data, THg bioaccumulation in polychaetes collected in sediment of Jinzhou Bay was distinctly higher due to higher sediment THg concentration, but MMHg bioaccumulation was significantly lower. THg accumulation in polychaetes mainly derived from its accumulation in sediment. However, MMHg bioaccumulation in polychaetes did not correlate with Hg concentration in sediment. Besides sediment ingestion, MMHg accumulation in polychaetes may partially source from the process of in vivo transformation. The in vivo Hg methylation may take place in polychaetes, according to the excellent correlation between MMHg concentration and THg and inorganic Hg concentration in polychaetes. The biochemical characters in polychaete body, the oxidation-reduction environment and the microbial activity in polychaete gut may be beneficial to in vivo Hg methylation.
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Affiliation(s)
- Zhizhen Xu
- Key Laboratory of Occupational Safety and Health, Beijing Municipal Institute of Labor Protection, Beijing 100054, PR China
| | - Wenhong Fan
- School of Space and Environment, Beihang University, Beijing 100191, PR China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, PR China.
| | - Zhiwei Shi
- School of Space and Environment, Beihang University, Beijing 100191, PR China
| | - Cheng Tan
- School of Space and Environment, Beihang University, Beijing 100191, PR China
| | - Minming Cui
- School of Space and Environment, Beihang University, Beijing 100191, PR China
| | - Shichuan Tang
- Key Laboratory of Occupational Safety and Health, Beijing Municipal Institute of Labor Protection, Beijing 100054, PR China
| | - Guangle Qiu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China.
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3
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Dale H, Solan M, Lam P, Cunliffe M. Sediment microbial assemblage structure is modified by marine polychaete gut passage. FEMS Microbiol Ecol 2019; 95:5426820. [DOI: 10.1093/femsec/fiz047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/02/2019] [Indexed: 01/13/2023] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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4
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Marine Invertebrates: Underexplored Sources of Bacteria Producing Biologically Active Molecules. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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5
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Isolation and Characterization of a Shewanella Phage-Host System from the Gut of the Tunicate, Ciona intestinalis. Viruses 2017; 9:v9030060. [PMID: 28327522 PMCID: PMC5371815 DOI: 10.3390/v9030060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/08/2017] [Accepted: 03/17/2017] [Indexed: 01/16/2023] Open
Abstract
Outnumbering all other biological entities on earth, bacteriophages (phages) play critical roles in structuring microbial communities through bacterial infection and subsequent lysis, as well as through horizontal gene transfer. While numerous studies have examined the effects of phages on free-living bacterial cells, much less is known regarding the role of phage infection in host-associated biofilms, which help to stabilize adherent microbial communities. Here we report the cultivation and characterization of a novel strain of Shewanella fidelis from the gut of the marine tunicate Ciona intestinalis, inducible prophages from the S. fidelis genome, and a strain-specific lytic phage recovered from surrounding seawater. In vitro biofilm assays demonstrated that lytic phage infection affects biofilm formation in a process likely influenced by the accumulation and integration of the extracellular DNA released during cell lysis, similar to the mechanism that has been previously shown for prophage induction.
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6
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Li M, Gu JD. The diversity and distribution of anammox bacteria in the marine aquaculture zones. Appl Microbiol Biotechnol 2016; 100:8943-53. [PMID: 27368740 DOI: 10.1007/s00253-016-7690-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 01/15/2023]
Abstract
The accumulation of toxic inorganic nitrogen is one of the major water quality problems in intensive aquaculture systems, thus the N removal in aquaculture systems is an important issue for the sustainable development of aquaculture. To understand one of the major microbial N removal processes, anaerobic ammonium oxidation (anammox), phylogenetic diversity, and distribution of anammox bacteria in sediments of four different marine aquaculture zones in Hong Kong (HK) were investigated. The 16S rRNA genes analysis indicated that sequences detected from Cheung Sha Wan (CSW) and Sok Kwu Wan (SKW) were closely related to several clusters within the Scalindua genus of anammox bacteria, including a new habitat-specific group, while only several sequences related to Scalindua and Kuenenia were detected in Sham Wan (SW) and Yim Tin Tsai East (YTTE). Most of the sequences obtained in SW and YTTE with the same PCR primers showed a low similarity to the known anammox bacteria, forming several novel groups within the Planctomycetes. However, results from the hydrazine oxidoreductase (HZO) encoding gene showed that only sequences from SW were related to the genus of Kuenenia, and sequences from other three sites were closely related to the genus of Scalindua. The community analysis showed that CSW and SKW share similar anammox bacterial community structures while SW and YTTE contain a unique anammox bacterial community. Furthermore, correlations reflect that organic matter is positively correlated with Kuenenia-like anammox bacteria, while the redox potential is significantly correlated with Scalindua-like anammox bacteria in marine aquaculture zones. Our results extend the knowledge of anammox bacteria in marine aquaculture systems and highlight the importance of environmental factors in shaping the community structures of anammox bacteria.
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Affiliation(s)
- Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
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7
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Abstract
The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.
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Affiliation(s)
- Rita Aghnatios
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
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8
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Zhou Z, Chen J, Cao H, Han P, Gu JD. Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes. Front Microbiol 2015; 5:789. [PMID: 25774150 PMCID: PMC4343527 DOI: 10.3389/fmicb.2014.00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 106 copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 106 copies per gram dry weight) was observed, but higher abundance (6.9 × 106 to 1.02 × 108 copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 105 copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 105 copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 108 copies per gram dry weight) and pmoA gene (1.56 × 107 copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Jing Chen
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong China
| | - Ping Han
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong Hong Kong, China
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9
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Dishaw LJ, Cannon JP, Litman GW, Parker W. Immune-directed support of rich microbial communities in the gut has ancient roots. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 47:36-51. [PMID: 24984114 PMCID: PMC4146740 DOI: 10.1016/j.dci.2014.06.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/30/2014] [Accepted: 06/21/2014] [Indexed: 05/12/2023]
Abstract
The animal gut serves as a primary location for the complex host-microbe interplay that is essential for homeostasis and may also reflect the types of ancient selective pressures that spawned the emergence of immunity in metazoans. In this review, we present a phylogenetic survey of gut host-microbe interactions and suggest that host defense systems arose not only to protect tissue directly from pathogenic attack but also to actively support growth of specific communities of mutualists. This functional dichotomy resulted in the evolution of immune systems much more tuned for harmonious existence with microbes than previously thought, existing as dynamic but primarily cooperative entities in the present day. We further present the protochordate Ciona intestinalis as a promising model for studying gut host-bacterial dialogue. The taxonomic position, gut physiology and experimental tractability of Ciona offer unique advantages in dissecting host-microbe interplay and can complement studies in other model systems.
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Affiliation(s)
- Larry J Dishaw
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA.
| | - John P Cannon
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL 33701, USA; Department of Molecular Genetics, All Children's Hospital-Johns Hopkins Medicine, 501 6th Avenue South, St. Petersburg, FL 33701, USA
| | - William Parker
- Department of Surgery, Duke University Medical Center, Box 2605, Durham, NC 27710, USA
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10
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The gut of geographically disparate Ciona intestinalis harbors a core microbiota. PLoS One 2014; 9:e93386. [PMID: 24695540 PMCID: PMC3973685 DOI: 10.1371/journal.pone.0093386] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 03/04/2014] [Indexed: 02/07/2023] Open
Abstract
It is now widely understood that all animals engage in complex interactions with bacteria (or microbes) throughout their various life stages. This ancient exchange can involve cooperation and has resulted in a wide range of evolved host-microbial interdependencies, including those observed in the gut. Ciona intestinalis, a filter-feeding basal chordate and classic developmental model that can be experimentally manipulated, is being employed to help define these relationships. Ciona larvae are first exposed internally to microbes upon the initiation of feeding in metamorphosed individuals; however, whether or not these microbes subsequently colonize the gut and whether or not Ciona forms relationships with specific bacteria in the gut remains unknown. In this report, we show that the Ciona gut not only is colonized by a complex community of bacteria, but also that samples from three geographically isolated populations reveal striking similarity in abundant operational taxonomic units (OTUs) consistent with the selection of a core community by the gut ecosystem.
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11
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Markande AR, Mikaelyan A, Nayak BB, Patel KD, Vachharajani NB, Vennila A, Rajendran KV, Purushothaman CS. Analysis of Midgut Bacterial Community Structure of <i>Neanthes chilkaensis</i> from Polluted Mudflats of Gorai, Mumbai, India. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aim.2014.413101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Kohl KD, Cary TL, Karasov WH, Dearing MD. Restructuring of the amphibian gut microbiota through metamorphosis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:899-903. [PMID: 24249298 DOI: 10.1111/1758-2229.12092] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/03/2013] [Indexed: 05/21/2023]
Abstract
Vertebrates maintain complex symbioses with a diverse community of microbes residing within their guts. The microbial players in these symbioses differ between major taxa of vertebrates, such that fish and amniotes maintain notably different communities. To date, there has not been a culture-independent inventory of an amphibian gut microbial community. Here, we compared gut microbial communities of tadpoles and frogs of the Northern leopard frog (Lithobates pipiens). We utilized Illumina sequencing, which allowed us to inventory more than 450 000 microbial sequences. We found that tadpoles and frogs differ markedly in the composition of their gut microbial communities, with tadpoles maintaining a community more similar to fish, whereas the frog community resembles that of amniotes. Additionally, frogs maintain a community with lower phylogenetic diversity compared with tadpoles. The significant restructuring of the microbiota is likely due to changes in diet as well as the large reorganization of the intestinal organ during metamorphosis. Overall, we propose that amphibians represent an important system in which to study regulation and selection of gut microbial communities.
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Affiliation(s)
- Kevin D Kohl
- Department of Biology, University of Utah, 257 S. 1400 East, Salt Lake City, UT, 84112, USA
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13
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Aharon Y, Pasternak Z, Ben Yosef M, Behar A, Lauzon C, Yuval B, Jurkevitch E. Phylogenetic, metabolic, and taxonomic diversities shape mediterranean fruit fly microbiotas during ontogeny. Appl Environ Microbiol 2013; 79:303-13. [PMID: 23104413 PMCID: PMC3536086 DOI: 10.1128/aem.02761-12] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022] Open
Abstract
The Mediterranean fruit fly (medfly) (Ceratitis capitata) lays eggs in fruits, where larvae subsequently develop, causing large-scale agricultural damage. Within its digestive tract, the fly supports an extended bacterial community that is composed of multiple strains of a variety of enterobacterial species. Most of these bacteria appear to be functionally redundant, with most strains sustaining diazotrophy and/or pectinolysis. At least some of these bacteria were shown to be vertically inherited, but colonization, structural, and metabolic aspects of the community's dynamics have not been investigated. We used fluorescent in situ hybridization, metabolic profiling, plate cultures, and pyrosequencing to show that an initial, egg-borne, diverse community expands throughout the fly's life cycle. While keeping "core" diazotrophic and pectinolytic functions, it also harbors diverse and fluctuating populations that express varied metabolic capabilities. We suggest that the metabolic and compositional plasticity of the fly's microbiota provides potential adaptive advantages to the medfly host and that its acquisition and dynamics are affected by mixed processes that include stochastic effects, host behavior, and molecular barriers.
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Affiliation(s)
- Yael Aharon
- Departments of Microbiology
- Entomology, Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Michael Ben Yosef
- Departments of Microbiology
- Entomology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Behar
- Departments of Microbiology
- Entomology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Carol Lauzon
- Department of Biological Sciences, California State University, Hayward, California, USA
| | - Boaz Yuval
- Entomology, Hebrew University of Jerusalem, Rehovot, Israel
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Analysis of stomach and gut microbiomes of the eastern oyster (Crassostrea virginica) from coastal Louisiana, USA. PLoS One 2012; 7:e51475. [PMID: 23251548 PMCID: PMC3520802 DOI: 10.1371/journal.pone.0051475] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/05/2012] [Indexed: 01/02/2023] Open
Abstract
We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.
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15
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Neave MJ, Streten-Joyce C, Glasby CJ, McGuinness KA, Parry DL, Gibb KS. The bacterial community associated with the marine polychaete Ophelina sp.1 (Annelida: Opheliidae) is altered by copper and zinc contamination in sediments. MICROBIAL ECOLOGY 2012; 63:639-650. [PMID: 22038035 DOI: 10.1007/s00248-011-9966-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Accepted: 10/05/2011] [Indexed: 05/31/2023]
Abstract
Tolerant species of polychaete worms can survive in polluted environments using various resistance mechanisms. One aspect of resistance not often studied in polychaetes is their association with symbiotic bacteria, some of which have resistance to metals and may help the organism to survive. We used "next generation" 454 sequencing of bacterial 16S rRNA sequences associated with polychaetes from a copper- and zinc-polluted harbor and from a reference site to determine bacterial community structure. We found changes in the bacteria at the polluted site, including increases in the abundance of bacteria from the order Alteromonadales. These changes in the bacteria associated with polychaetes may be relatively easy to detect and could be a useful indicator of metal pollution.
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