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Goffredi SK, Appy RG, Hildreth R, deRogatis J. Marine vampires: Persistent, internal associations between bacteria and blood-feeding marine annelids and crustaceans. Front Microbiol 2023; 13:1113237. [PMID: 36713196 PMCID: PMC9876621 DOI: 10.3389/fmicb.2022.1113237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Persistent bacterial presence is believed to play an important role in host adaptation to specific niches that would otherwise be unavailable, including the exclusive consumption of blood by invertebrate parasites. Nearly all blood-feeding animals examined so far host internal bacterial symbionts that aid in some essential aspect of their nutrition. Obligate blood-feeding (OBF) invertebrates exist in the oceans, yet symbiotic associations between them and beneficial bacteria have not yet been explored. This study describes the microbiome of 6 phylogenetically-diverse species of marine obligate blood-feeders, including leeches (both fish and elasmobranch specialists; e.g., Pterobdella, Ostreobdella, and Branchellion), isopods (e.g., Elthusa and Nerocila), and a copepod (e.g., Lernanthropus). Amplicon sequencing analysis revealed the blood-feeding invertebrate microbiomes to be low in diversity, compared to host fish skin surfaces, seawater, and non-blood-feeding relatives, and dominated by only a few bacterial genera, including Vibrio (100% prevalence and comprising 39%-81% of the average total recovered 16S rRNA gene sequences per OBF taxa). Vibrio cells were localized to the digestive lumen in and among the blood meal for all taxa examined via fluorescence microscopy. For Elthusa and Branchellion, Vibrio cells also appeared intracellularly within possible hemocytes, suggesting an interaction with the immune system. Additionally, Vibrio cultivated from four of the obligate blood-feeding marine taxa matched the dominant amplicons recovered, and all but one was able to effectively lyse vertebrate blood cells. Bacteria from 2 additional phyla and 3 families were also regularly recovered, albeit in much lower abundances, including members of the Oceanospirillaceae, Flavobacteriacea, Porticoccaceae, and unidentified members of the gamma-and betaproteobacteria, depending on the invertebrate host. For the leech Pterobdella, the Oceanospirillaceae were also detected in the esophageal diverticula. For two crustacean taxa, Elthusa and Lernanthropus, the microbial communities associated with brooded eggs were very similar to the adults, indicating possible direct transmission. Virtually nothing is known about the influence of internal bacteria on the success of marine blood-feeders, but this evidence suggests their regular presence in marine parasites from several prominent groups.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, United States,*Correspondence: Shana K. Goffredi, ✉
| | - Ralph G. Appy
- Cabrillo Marine Aquarium, San Pedro, CA, United States
| | - Rebecca Hildreth
- Department of Biology, Occidental College, Los Angeles, CA, United States
| | - Julia deRogatis
- Department of Biology, Occidental College, Los Angeles, CA, United States
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Shabana BM, Elkenany RM, Younis G. Sequencing and multiple antimicrobial resistance of Pseudomonas fluorescens isolated from Nile tilapia fish in Egypt. BRAZ J BIOL 2022; 84:e257144. [PMID: 35293547 DOI: 10.1590/1519-6984.257144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/08/2022] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas fluorescens is one of the main causes of septicemic diseases among freshwater fish, causing severe economic losses and decreasing farm efficiency. Thus, this research was aimed to investigate the occurrence of P. fluorescens in Nile Tilapia (O. niloticus) fish in Egypt, gene sequencing of 16SrDNA gene, and antimicrobial susceptibility. P. fluorescens strains were detected in 32% (128\400) of apparently healthy (9%; 36\400) and diseased (23%; 92\400) Nile tilapia fish. The highest prevalence was observed in gills of fish, 31.3% followed by intestine 26.9%, liver 24.2%, and kidneys 17.6%. The PCR results for the 16SrDNA gene of P. fluorescens showed 16SrDNA gene in 30% of examined isolates. Moreover, Homogeny and a strong relationship between strains of P. fluorescens was confirmed using 16SrDNA sequences. Beside the responsibility of 16SrDNA gene on the virulence of P. fluorescens. The results of antimicrobial susceptibility tests revealed that all strains were resistant to piperacillin (100%), followed by ceftazidime (29.7%), and cefepime (25.8%). The strains of P. fluorescence were highly sensitive to cefotaxime (74.2%), followed by ceftriaxone and levofloxacin (70.3% each). Interestingly, 29.7% of strains of P. fluorescens were multiple antimicrobial-resistant (MAR).
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Affiliation(s)
- B M Shabana
- Mansoura University, Faculty of Veterinary Medicine, Department of Bacteriology, Mycology and Immunology, Mansoura, Egypt
| | - R M Elkenany
- Mansoura University, Faculty of Veterinary Medicine, Department of Bacteriology, Mycology and Immunology, Mansoura, Egypt
| | - G Younis
- Mansoura University, Faculty of Veterinary Medicine, Department of Bacteriology, Mycology and Immunology, Mansoura, Egypt
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Chakaroun RM, Massier L, Heintz-Buschart A, Said N, Fallmann J, Crane A, Schütz T, Dietrich A, Blüher M, Stumvoll M, Musat N, Kovacs P. Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery. Genome Med 2021; 13:105. [PMID: 34158092 PMCID: PMC8218394 DOI: 10.1186/s13073-021-00919-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardiometabolic disease, and blunted response to metabolic interventions. In this aspect, thorough next-generation sequencing-based and contaminant-aware approaches are lacking. To address this, we tested whether bacterial DNA could be amplified in the blood of subjects with obesity and high metabolic risk under strict experimental and analytical control and whether a putative bacterial signature is related to metabolic improvement after bariatric surgery. METHODS Subjects undergoing bariatric surgery were recruited into sex- and BMI-matched subgroups with (n = 24) or without T2D (n = 24). Bacterial DNA in the blood was quantified and prokaryotic 16S rRNA gene amplicons were sequenced. A contaminant-aware approach was applied to derive a compositional microbial signature from bacterial sequences in all subjects at baseline and at 3 and 12 months after surgery. We modeled associations between bacterial load and composition with host metabolic and anthropometric markers. We further tested whether compositional shifts were related to weight loss response and T2D remission. Lastly, bacteria were visualized in blood samples using catalyzed reporter deposition (CARD)-fluorescence in situ hybridization (FISH). RESULTS The contaminant-aware blood bacterial signature was associated with metabolic health. Based on bacterial phyla and genera detected in the blood samples, a metabolic syndrome classification index score was derived and shown to robustly classify subjects along their actual clinical group. T2D was characterized by decreased bacterial richness and loss of genera associated with improved metabolic health. Weight loss and metabolic improvement following bariatric surgery were associated with an early and stable increase of these genera in parallel with improvements in key cardiometabolic risk parameters. CARD-FISH allowed the detection of living bacteria in blood samples in obesity. CONCLUSIONS We show that the circulating bacterial signature reflects metabolic disease and its improvement after bariatric surgery. Our work provides contaminant-aware evidence for the presence of living bacteria in the blood and suggests a putative crosstalk between components of the blood and metabolism in metabolic health regulation.
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Affiliation(s)
- Rima M Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
| | - Lucas Massier
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Medicine (H7), Karolinska Institutet, C2-94, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Helmholtz Centre for Environmental Research GmbH - UFZ, Halle, Germany
| | - Nedal Said
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Joerg Fallmann
- Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Alyce Crane
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Tatjana Schütz
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Arne Dietrich
- Department of Visceral, Transplantation, Thoracic and Vascular Surgery, Section of Bariatric Surgery, Leipzig University Hospital, Leipzig, Germany
| | - Matthias Blüher
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung, Neuherberg, Germany
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Goffredi SK, Tilic E, Mullin SW, Dawson KS, Keller A, Lee RW, Wu F, Levin LA, Rouse GW, Cordes EE, Orphan VJ. Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage. SCIENCE ADVANCES 2020; 6:eaay8562. [PMID: 32284974 PMCID: PMC7124940 DOI: 10.1126/sciadv.aay8562] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/09/2020] [Indexed: 06/11/2023]
Abstract
Deep-sea cold seeps are dynamic sources of methane release and unique habitats supporting ocean biodiversity and productivity. Here, we describe newly discovered animal-bacterial symbioses fueled by methane, between two species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct aerobic methane-oxidizing bacteria belonging to the Methylococcales, localized to the host respiratory crown. Worm tissue δ13C of -44 to -58‰ are consistent with methane-fueled nutrition for both species, and shipboard stable isotope labeling experiments revealed active assimilation of 13C-labeled methane into animal biomass, which occurs via the engulfment of methanotrophic bacteria across the crown epidermal surface. These worms represent a new addition to the few animals known to intimately associate with methane-oxidizing bacteria and may further explain their enigmatic mass occurrence at 150-million year-old fossil seeps. High-resolution seafloor surveys document significant coverage by these symbioses, beyond typical obligate seep fauna. These findings uncover novel consumers of methane in the deep sea and, by expanding the known spatial extent of methane seeps, may have important implications for deep-sea conservation.
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Affiliation(s)
| | - Ekin Tilic
- Scripps Institution of Oceanography, La Jolla, CA, USA
- University of Bonn, Bonn, Germany
| | | | | | | | | | - Fabai Wu
- California Institute of Technology, Pasadena, CA, USA
| | - Lisa A. Levin
- Scripps Institution of Oceanography, La Jolla, CA, USA
| | - Greg W. Rouse
- Scripps Institution of Oceanography, La Jolla, CA, USA
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Abstract
PhageFISH uses the power of fluorescence in situ hybridization to monitor intracellular phage infections at single cell level. It combines host cell identification via rRNA probes and phage identification via phage-specific gene probes, allowing for the quantification of the infected cell fraction and the discrimination between infection stages. This book chapter covers all aspects of the procedure, from phage probe design and synthesis, to the phageFISH protocol itself, to microscopy and image analysis.
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Borrero-Santiago AR, DelValls TÁ, Inmaculada Riba M. Bacterial community responses during a possible CO 2 leaking from sub-seabed storage in marine polluted sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:116-123. [PMID: 28342412 DOI: 10.1016/j.scitotenv.2017.03.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/16/2017] [Accepted: 03/16/2017] [Indexed: 06/06/2023]
Abstract
Carbon capture and storage (CCS) is a viable option to reduce high concentrations of CO2 and mitigate their negative effects. This option has associated risks such as possible CO2 leakage from the storage sites. So far, negative effects deriving from a CO2 release have been reported for benthic macrofauna in both polluted and nonpolluted sediments. However, bacterial communities has no considered. In this work, risk assessment was carried out in order to evaluate the possible effects in a contaminated area considering bacterial responses (total number of cells, respiring activity, changes in the bacterial community composition and diversity). Four microcosms were placed into an integrated CO2 injection system with a non-pressurized chamber to simulate four different pH treatments (pH control 7.8, 7, 6.5 and 6). Results showed an impact on bacterial communities because of the CO2 treatment. Changes in respiring activity, community composition groups and diversity were found. This study highlights the use of respiring bacteria activity not only as bioindicator for environmental risk assessment and monitoring purposes but also as a bioindicador during a CO2 leakage event or CO2 enrichment process among all the responses studied.
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Affiliation(s)
- Ana R Borrero-Santiago
- UNESCO/UNITWIN Wicop, Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain.
| | - T Ángel DelValls
- UNESCO/UNITWIN Wicop, Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| | - M Inmaculada Riba
- UNESCO/UNITWIN Wicop, Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
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Borrero-Santiago AR, Bautista-Chamizo E, DelValls TÁ, Riba I. A possible CO 2 leakage event: Can the marine microbial community be recovered? MARINE POLLUTION BULLETIN 2017; 117:380-385. [PMID: 28202276 DOI: 10.1016/j.marpolbul.2017.02.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Bacterial communities have been studied to a much lesser degree than macrofauna in the case of a CO2 release. The resistance capacity of marine bacteria is well known, but their possible responses and their ability to recover after a CO2 release has not been investigated. Therefore, this work evaluated the responses of a marine bacterial community after 96h of CO2 exposure under diverse pH treatments (7.8 as control without CO2, 7.0, 6.5, and 6.0) and 24h after CO2 exposure. Results showed that the respiration activity and the diversity of the community were affected in all pH treatments. However, after 24h without CO2 enrichment, the respiration activity and diversity increased, showing a partial recovery. Consequently, bacterial responses have the potential to be used as a monitoring tool for risk assessment related to carbon capture and storage techniques or in any similar CO2 enrichment situations.
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Affiliation(s)
- A R Borrero-Santiago
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain.
| | - E Bautista-Chamizo
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
| | - T Á DelValls
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
| | - I Riba
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
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Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas-specific and rpoD genes. 3 Biotech 2016; 6:80. [PMID: 28330150 PMCID: PMC4764612 DOI: 10.1007/s13205-016-0386-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationship of 22 FLPs was
revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and Pseudomonas-specific gene region phylogenies were generally similar, but rpoD gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes. rpoD provided comparable phylogenetic resolution to that of the 16S rRNA and Pseudomonas-specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoD could complement and better justify the information provided by the 16S rRNA gene. Hence rpoD can be used further as an evolutionary chronometer for species-level identification.
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Bistolas KSI, Sakamoto RI, Fernandes JAM, Goffredi SK. Symbiont polyphyly, co-evolution, and necessity in pentatomid stinkbugs from Costa Rica. Front Microbiol 2014; 5:349. [PMID: 25076943 PMCID: PMC4097960 DOI: 10.3389/fmicb.2014.00349] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022] Open
Abstract
Interdomain symbioses with bacteria allow insects to take advantage of underutilized niches and provide the foundation for their evolutionary success in neotropical ecosystems. The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylogenies. Like other families within the Pentatomomorpha, these insects (within seven genera—Antiteuchus, Arvelius, Edessa, Euschistus, Loxa, Mormidea, and Sibaria) house near-monocultures of gamma-proteobacteria in midgut crypts, comprising three distinct lineages within the family Enterobacteriaceae. Identity of the dominant bacteria (78–100% of the recovered 16S rRNA genes) was partially congruent with insect phylogeny, at the level of subfamily and tribe, with bacteria closely related to Erwinia observed in six species of the subfamily Pentatominae, and bacteria in a novel clade of Enterobacteriaceae for seven species within the subfamilies Edessinae and Discocephalinae. Symbiont replacement (i.e., bacterial “contamination” from the environment) may occur during maternal transmission by smearing of bacteria onto the egg surfaces during oviposition. This transmission strategy was experimentally confirmed for Sibaria englemani, and suspected for four species from two subfamilies, based on observation of egg probing by nymphs. Symbiont-deprived S. englemani, acquired via egg surface sterilization, exhibited significantly extended second instars (9.1 days compared with 7.9 days for symbiotic nymphs; p = 0.0001, Wilcoxon's rank with Bonferroni correction), slower linearized growth rates (p = 0.005, Welch 2-sample t-test), and qualitative differences in ceca morphology, including increased translucency of crypts, elongation of extracellular cavities, and distribution of symbionts, compared to symbiotic nymphs. Combined, these results suggest a role of the symbiont in host development, the reliable transference of symbionts via egg surfaces, and a suggestion of co-evolution between symbiont and tropical pentatomid host insects.
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Affiliation(s)
| | | | - José A M Fernandes
- Instituto de Ciências Biológicas, Universidade Federal do Pará Belém-Pará, Brazil
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Goffredi SK, Gregory A, Jones WJ, Morella NM, Sakamoto RI. Ontogenetic variation in epibiont community structure in the deep-sea yeti crab, Kiwa puravida: convergence among crustaceans. Mol Ecol 2013; 23:1457-1472. [PMID: 23952239 DOI: 10.1111/mec.12439] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/29/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023]
Abstract
Recent investigations have demonstrated that unusually 'hairy' yeti crabs within the family Kiwaidae associate with two predominant filamentous bacterial families, the Epsilon and Gammaproteobacteria. These analyses, however, were based on samples collected from a single body region, the setae of pereopods. To more thoroughly investigate the microbiome associated with Kiwa puravida, a yeti crab species from Costa Rica, we utilized barcoded 16S rRNA amplicon pyrosequencing, as well as microscopy and terminal restriction fragment length polymorphism analysis. Results indicate that, indeed, the bacterial community on the pereopods is far less diverse than on the rest of the body (Shannon indices ranged from 1.30-2.02 and 2.22-2.66, respectively). Similarly, the bacterial communities associated with juveniles and adults were more complex than previously recognized, with as many as 46 bacterial families represented. Ontogenetic differences in the microbial community, from egg to juvenile to adult, included a dramatic under-representation of the Helicobacteraceae and higher abundances of both Thiotrichaceae and Methylococcaceae for the eggs, which paralleled patterns observed in another bacteria-crustacean symbiosis. The degree to which abiotic and biotic feedbacks influence the bacterial community on the crabs is still not known, but predictions suggest that both the local environment and host-derived factors influence the establishment and maintenance of microbes associated with the surfaces of aquatic animals.
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Affiliation(s)
- Shana K Goffredi
- Biology Department, Occidental College, Los Angeles, CA, 90041, USA
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Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
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Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
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12
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Goffredi SK, Morella NM, Pulcrano ME. Affiliations between bacteria and marine fish leeches (Piscicolidae), with emphasis on a deep-sea species from Monterey Canyon, CA. Environ Microbiol 2012; 14:2429-44. [PMID: 22681178 DOI: 10.1111/j.1462-2920.2012.02798.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Leeches within the Piscicolidae are of great numerical and taxonomic importance, yet little is known about bacteria that associate with this diverse group of blood-feeding marine parasites of fish and elasmobranchs. We focused primarily on the bacteria from a deep-sea leech species of unknown identity, collected at ∼ 600 m depth in Monterey Canyon, CA, along with two shallow-living leech genera, Austrobdella and Branchellion, from Los Angeles Harbor, CA. Molecular analysis of all five leech species revealed a dominance of gammaproteobacteria, which were distinct from each other and from previously reported freshwater leech symbionts. Bacteria related to members of the genus Psychromonas (99% similarity in 16S rRNA) were dominant in the deep-sea leech species (80-94% of recovered ribotypes) collected over 19 months from two different locations. Psychromonas was not detected in cocoons or 2-16 week-old juveniles, suggesting that acquisition is via the environment at a later stage. Transmission electron microscopy did, however, reveal abundant bacteria-like cells near areas of thinning of the juvenile epithelial surface, as well as Psychromonas sparsely distributed internally. Electron and fluorescence in situ microscopy of adults also showed Psychromonas-like bacteria concentrated within the crop. Despite the apparent non-transient nature of the association between Psychromonas and the deep-sea leech, their functional role, if any, is not known. The prevalence, however, of an abundant bacterial genus in one piscicolid leech species, as well as the presence of a dominant bacterial species in singular observations of four additional marine species, suggests that members of the Piscicolidae, possibly basal within the class Hirudinea, form specific alliances with microbes.
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Affiliation(s)
- S K Goffredi
- Biology Department, Occidental College, Los Angeles, CA, USA.
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Pandey J, Chauhan A, Jain RK. Integrative approaches for assessing the ecological sustainability ofin situbioremediation. FEMS Microbiol Rev 2009; 33:324-75. [PMID: 19178567 DOI: 10.1111/j.1574-6976.2008.00133.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Pilhofer M, Pavlekovic M, Lee NM, Ludwig W, Schleifer KH. Fluorescence in situ hybridization for intracellular localization of nifH mRNA. Syst Appl Microbiol 2009; 32:186-92. [PMID: 19217232 DOI: 10.1016/j.syapm.2008.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/01/2008] [Accepted: 12/09/2008] [Indexed: 11/18/2022]
Abstract
Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.
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Affiliation(s)
- Martin Pilhofer
- Technische Universität München, Lehrstuhl für Mikrobiologie, Am Hochanger 4, 85350 Freising, Germany.
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In situ hybridization of microcolonies using catalyzed reporter deposition with tetramethylbenzidine: a method for detecting low numbers of bacterial cells in drinking water. Eur Food Res Technol 2008. [DOI: 10.1007/s00217-007-0811-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Goffredi SK, Jones WJ, Erhlich H, Springer A, Vrijenhoek RC. Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta. Environ Microbiol 2008; 10:2623-34. [DOI: 10.1111/j.1462-2920.2008.01684.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Martín M, Gibello A, Lobo C, Nande M, Garbi C, Fajardo C, Barra-Caracciolo A, Grenni P, Martínez-Iñigo MJ. Application of fluorescence in situ hybridization technique to detect simazine-degrading bacteria in soil samples. CHEMOSPHERE 2008; 71:703-710. [PMID: 18082866 DOI: 10.1016/j.chemosphere.2007.10.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 10/19/2007] [Accepted: 10/26/2007] [Indexed: 05/25/2023]
Abstract
We propose a new approach to evaluate the natural attenuation capacity of soil by using fluorescence in situ hybridization (FISH). A specific oligonucleotide probe AtzB1 was designed based on the sequence data of the atzB gene involved in the hydrolytic deamination of s-triazines; this gene, located in a multiple copy plasmid was detected by the optimized FISH protocol. Two agricultural soils (Lodi and Henares) with a history of simazine treatments, and two natural soils (Soto and Monza), without previous exposure to simazine, were studied. AtzB1 probe-target cells were found only in the agricultural soils and, in a greater percentage, in the Lodi soil, compared to the Henares one. Moreover, the greatest percentage of AtzB1 probe-target cells in Lodi was accompanied by a greater mineralization rate, compared to the Henares soil. The FISH method used in this study was suitable for the detection of simazine-degrading bacteria and could be a useful indicator of the potential of soil bioremediation.
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Affiliation(s)
- Margarita Martín
- Complutense University, Avenida Puerta de Hierro s/n, 28040 Madrid, Spain.
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18
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Goffredi SK, Johnson SB, Vrijenhoek RC. Genetic diversity and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Appl Environ Microbiol 2007; 73:2314-23. [PMID: 17277220 PMCID: PMC1855680 DOI: 10.1128/aem.01986-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 01/20/2007] [Indexed: 11/20/2022] Open
Abstract
We investigated the genetic diversity of symbiotic bacteria associated with two newly discovered species of Osedax from Monterey Canyon, CA, at 1,017-m (Osedax Monterey Bay sp. 3 "rosy" [Osedax sp. MB3]) and 381-m (Osedax Monterey Bay sp. 4 "yellow collar") depths. Quantitative PCR and clone libraries of 16S rRNA gene sequences identified differences in the compositions and abundances of bacterial phylotypes associated with the newly discovered host species and permitted comparisons between adult Osedax frankpressi and juveniles that had recently colonized whalebones implanted at 2,891 m. The newly discovered Osedax species hosted Oceanospirillales symbionts that are related to Gammaproteobacteria associated with the previously described O. frankpressi and Osedax rubiplumus (S. K. Goffredi, V. J. Orphan, G. W. Rouse, L. Jahnke, T. Embaye, K. Turk, R. Lee, and R. C. Vrijenhoek, Environ. Microbiol. 7:1369-1378, 2005). In addition, Osedax sp. MB3 hosts a diverse and abundant population of additional bacteria dominated by Epsilonproteobacteria. Ultrastructural analysis of symbiont-bearing root tissues verified the enhanced microbial diversity of Osedax sp. MB3. Root tissues from the newly described host species and O. frankpressi all exhibited collagenolytic enzyme activity, which covaried positively with the abundance of symbiont DNA and negatively with mean adult size of the host species. Members of this unusual genus of bone-eating worms may form variable associations with symbiotic bacteria that allow for the observed differences in colonization and success in whale fall environments throughout the world's oceans.
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Affiliation(s)
- Shana K Goffredi
- California Institute of Technology, Pasadena, California 91125, USA.
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19
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Eek KM, Sessions AL, Lies DP. Carbon-isotopic analysis of microbial cells sorted by flow cytometry. GEOBIOLOGY 2007; 5:85-95. [PMID: 36298877 DOI: 10.1111/j.1472-4669.2006.00094.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
One of the outstanding current problems in both geobiology and environmental microbiology is the quantitative analysis of in situ microbial metabolic activities. Techniques capable of such analysis would have wide application, from quantifying natural rates of biogeochemical cycling to identifying the metabolic activity of uncultured organisms. We describe here a method that represents one step towards that goal, namely the high-precision measurement of 13 C in specific populations of microbial cells that are purified by fluorescence-activated cell sorting (FACS). Sorted cells are concentrated on a Teflon membrane filter, and their 13 C content is measured by coupling an isotope ratio mass spectrometer (IRMS) with a home-built spooling wire microcombustion (SWiM) apparatus. The combined instrumentation provides measurements of δ13 C in whole cells with precision better than 0.2‰ for samples containing as little as 25 ng of carbon. When losses associated with sample handling are taken into account, isotopic analyses require sorting roughly 104 eukaryotic or 107 bacterial cells per sample. Coupled with 13 C-labelled substrate additions, this approach has the potential to directly quantify uptake of metabolites in specific populations of sorted cells. The high precision afforded by SWiM-IRMS also permits useful studies of natural abundance variations in 13 C. The approach is equally applicable to specific populations of cells sorted from multicellular organisms.
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Affiliation(s)
- K M Eek
- Division of Geological and Planetary Sciences, California Institute of Technology, MC 100-23, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - A L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, MC 100-23, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - D P Lies
- Division of Geological and Planetary Sciences, California Institute of Technology, MC 100-23, 1200 E. California Blvd, Pasadena, CA 91125, USA
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Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 2006; 73:278-88. [PMID: 17071787 PMCID: PMC1797146 DOI: 10.1128/aem.01177-06] [Citation(s) in RCA: 352] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.
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Affiliation(s)
- Rebecca J Case
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Biofouling and Bio-Innovation, University of New South Wales, Randwick, Sydney NSW 2052, Australia
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