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Wang H, Pijl A, Liu B, Wamelink W, Korthals GW, Costa OYA, Kuramae EE. A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil. Microorganisms 2024; 12:760. [PMID: 38674704 PMCID: PMC11051824 DOI: 10.3390/microorganisms12040760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.
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Affiliation(s)
- Han Wang
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China;
| | - Wieger Wamelink
- Biodiversity and Policy, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Gerard W. Korthals
- Bioindications and Plant Health, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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Pascoal F, Tomasino MP, Piredda R, Quero GM, Torgo L, Poulain J, Galand PE, Fuhrman JA, Mitchell A, Tinta T, Turk Dermastia T, Fernandez-Guerra A, Vezzi A, Logares R, Malfatti F, Endo H, Dąbrowska AM, De Pascale F, Sánchez P, Henry N, Fosso B, Wilson B, Toshchakov S, Ferrant GK, Grigorov I, Vieira FRJ, Costa R, Pesant S, Magalhães C. Inter-comparison of marine microbiome sampling protocols. ISME COMMUNICATIONS 2023; 3:84. [PMID: 37598259 PMCID: PMC10439934 DOI: 10.1038/s43705-023-00278-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 08/21/2023]
Abstract
Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169- 007, Porto, Portugal
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Roberta Piredda
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grazia Marina Quero
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Largo Fiera della Pesca 2, 60125, Ancona, Italy
| | - Luís Torgo
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Alex Mitchell
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Tinkara Tinta
- National Institute of Biology, Marine Biology Station Piran, Piran, Slovenia
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Vezzi
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC. Passeig Marítim de la Barceloneta, 37-49, ES08003, Barcelona, Spain
| | | | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Anna Maria Dąbrowska
- Department of Marine Ecology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Fabio De Pascale
- Department of Biology, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Pablo Sánchez
- Institute of Marine Sciences (ICM), CSIC. Passeig Marítim de la Barceloneta, 37-49, ES08003, Barcelona, Spain
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, UMR 7144, Roscoff, France
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Bruno Fosso
- Department of Biosciences, Biotechnologies and Environment, University of Bari, 70126, Bari, Italy
| | - Bryan Wilson
- Department of Biology, John Krebs Field Station, University of Oxford, Wytham, OX2 8QJ, UK
| | | | | | - Ivo Grigorov
- Technical University of Denmark, National Institute of Aquatic Resources, Kgs. Lyngby, Denmark
| | | | - Rodrigo Costa
- Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Institute for Bioengineering and Biosciences (iBB) and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Stéphane Pesant
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169- 007, Porto, Portugal.
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Morales Medina WR, Eramo A, Fahrenfeld NL. Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion. MICROBIAL ECOLOGY 2022; 83:583-595. [PMID: 34117524 PMCID: PMC8195243 DOI: 10.1007/s00248-021-01775-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/13/2021] [Indexed: 05/11/2023]
Abstract
Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.
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Affiliation(s)
- William R Morales Medina
- Microbiology & Molecular Genetics, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA
| | - Alessia Eramo
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA
| | - N L Fahrenfeld
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA.
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Silva DP, Epstein HE, Vega Thurber RL. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. Front Microbiol 2022; 13:1007877. [PMID: 36891260 PMCID: PMC9987214 DOI: 10.3389/fmicb.2022.1007877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/30/2022] [Indexed: 02/22/2023] Open
Abstract
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
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Affiliation(s)
- Denise P Silva
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Hannah E Epstein
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Lebrun M, Miard F, Bucci A, Trupiano D, Nandillon R, Naclerio G, Scippa GS, Morabito D, Bourgerie S. Evaluation of direct and biochar carrier-based inoculation of Bacillus sp. on As- and Pb-contaminated technosol: effect on metal(loid) availability, Salix viminalis growth, and soil microbial diversity/activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:11195-11204. [PMID: 33111230 DOI: 10.1007/s11356-020-11355-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Phytomanagement manipulates the soil-plant system to lower the risk posed by contaminated soils. In this process, the addition of amendments, such as biochar, and bacteria can improve the fertility of poor contaminated soils and consequently ameliorate plant growth. A number of studies based on the inoculation of soil with microorganisms of the genus Bacillus, previously isolated from contaminated sites, revealed positive effects on soil properties and plant growth. Furthermore, when the Bacillus isolates were used in association with biochar, better results were obtained, as biochar can ameliorate soil properties and serve as habitat for microorganisms. Accordingly, a mesocosm study was set-up using a mining technosol amended with biochar and inoculated with an endogenous Bacillus isolate, to evaluate the effect of inoculation on soil properties, metal(loid) immobilization, and Salix viminalis growth. Two inoculation methods were compared: (1) direct inoculation of bacteria (Bacillus sp.) and (2) inoculation using biochar as a carrier. Results showed that the Bacillus isolate modified soil properties and ameliorated plant growth, while having a reduced effect on metal(loid) accumulation. The microbial activity was also stimulated, and the community composition was shifted, more importantly when biochar was used as a carrier. In conclusion, this research revealed an improvement of the plant growth and microbial activity after the addition of the endogenous bacterium to the analyzed former mining soil, with better results recorded when a carrier was used.
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Affiliation(s)
- Manhattan Lebrun
- University of Orléans, INRA USC1328, LBLGC EA1207, Orleans, France
- Department of Biosciences and Territory, University of Molise, Pesche, IS, Italy
| | - Florie Miard
- University of Orléans, INRA USC1328, LBLGC EA1207, Orleans, France
| | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Pesche, IS, Italy
| | - Dalila Trupiano
- Department of Biosciences and Territory, University of Molise, Pesche, IS, Italy
| | - Romain Nandillon
- University of Orléans, INRA USC1328, LBLGC EA1207, Orleans, France
- French Geological Survey (BRGM), Orleans, France
- IDDEA, Environmental consulting engineering, Olivet, France
- ISTO, UMR 7327, CNRS/Orleans University, Orleans, France
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Pesche, IS, Italy
| | - Gabriella S Scippa
- Department of Biosciences and Territory, University of Molise, Pesche, IS, Italy
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Carvalho VRD, Wilcken SRS, Wilcken CF, Castro BMDCE, Soares MA, Zanuncio JC. Technical and economic efficiency of methods for extracting genomic DNA from Meloidogyne javanica. J Microbiol Methods 2018; 157:108-112. [PMID: 30593846 DOI: 10.1016/j.mimet.2018.12.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/21/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
Abstract
Plant parasitic nematodes reduce the production of agricultural crops. Species diagnosis is essential to predict losses, determine economic damage levels and develop integrated pest management programs. DNA extraction techniques need to be improved for precise and rapid molecular diagnosis of nematodes. The objective of the present study was to evaluate the efficiency of DNA extraction and amplification by PCR, cost and execution time by Chelex, Worm Lysis Buffer Method (WLB), Holterman Lysis Buffer Method (HLB) and FastDNA methods for nematodes of the Meloidogyne genus. The qualitative and quantitative efficiency of DNA extraction varied between methods. The band size of the amplified PCR product with WLB, Chelex and HLB methods was 590 bp. Extraction with the FastDNA is not recommended for DNA extraction from nematodes because it results in a low DNA concentration without bands in PCR amplification, besides presenting high cost. The efficiency of the WLB method to extracting DNA from Meloidogyne javanica was greater, ensuring a higher concentration and purity of the extracted material and guaranteeing lower costs and greater ease of PCR amplification.
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Affiliation(s)
- Vanessa Rafaela de Carvalho
- Instituto de Biotecnologia (IBTEC), Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, São Paulo, Brazil
| | - Sílvia Renata Siciliano Wilcken
- Faculdade de Ciências Agronômicas (FCA), Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, São Paulo, Brazil
| | - Carlos Frederico Wilcken
- Faculdade de Ciências Agronômicas (FCA), Universidade Estadual Paulista (UNESP), Campus de Botucatu, Botucatu, São Paulo, Brazil
| | | | - Marcus Alvarenga Soares
- Programa de Pós-Graduação em Produção Vegetal, Universidade Federal dos Vales Jequitinhonha e Mucuri (UFVJM), Diamantina 39100-000, Minas Gerais, Brazil
| | - José Cola Zanuncio
- Departamento de Entomologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570-900, Minas Gerais, Brazil
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Ma T, Zhou W, Chen L, Wu L, Christie P, Liu W. Toxicity of phthalate esters to lettuce (Lactuca sativa) and the soil microbial community under different soil conditions. PLoS One 2018; 13:e0208111. [PMID: 30571793 PMCID: PMC6301558 DOI: 10.1371/journal.pone.0208111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/12/2018] [Indexed: 01/22/2023] Open
Abstract
Phthalate esters (PAEs) are globally used plasticizers and typical endocrine disruptors that can readily accumulate in agricultural products and represent a substantial risk to human health via the food chain. The range of soil properties has an important influence on the expression of PAE toxicity, and the mechanisms by which soil physical and chemical properties affect the expression of toxicity of target PAEs to plants and microorganisms requires further investigation. Important soil factors affecting the eco-toxicological effects of two typical PAEs, di-n-butyl phthalate (DnBP) and bis (2-ethylhexyl) phthalate (DEHP), on lettuce (Lactuca sativa) in a spiked soil were investigated in the present study. Soil at various pH values was spiked with three PAE concentrations (1, 5 and 20 mg DnBP or DEHP kg-1 soil), organic matter contents and water holding contents to simulate the greenhouse soil environment for 30 days. Their influence on the biomass, photosynthetic pigment contents, various physiological changes and soil microbial communities was determined as endpoints. The toxicity to lettuce of DnBP was higher than that of DEHP in the soil and soil pH was the most important factor affecting their single toxicity, followed by soil organic matter content and soil moisture content in agreement with the Biolog test results. Under different soil conditions total protein, total soluble sugar and free amino acid contents were positively correlated with concentrations of the target PAEs, but leaf area, biomass, •O2- activity, vitamin C content and soil microbial diversity indices showed the opposite trend. Chlorophyll a and carotenoid contents were more inhibited by DnBP together with impacts on indices of soil microbial diversity. The results suggest that soil conditions in greenhouses directly explain the patterns of pollutant toxicity displayed and impact the quantity, quality and food safety of vegetables produced using highly intensive production systems.
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Affiliation(s)
- Tingting Ma
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture / Tianjin Key Laboratory of Agro-environment and Safe-product, Tianjin, China
- Institute of Hanjiang, Hubei University of Arts and Science, Xiangyang, China
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wei Zhou
- School of Civil Engineering and Architecture, Hubei University of Arts and Science, Xiangyang, China
| | - Like Chen
- Shanghai Research Institute of Chemical Industry, Shanghai, China
| | - Longhua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Godoy-Vitorino F, Ruiz-Diaz CP, Rivera-Seda A, Ramírez-Lugo JS, Toledo-Hernández C. The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico. PeerJ 2017; 5:e3717. [PMID: 28875073 PMCID: PMC5580386 DOI: 10.7717/peerj.3717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/29/2017] [Indexed: 01/04/2023] Open
Abstract
Background Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes. Methods Six A. cervicornis fragments from different individuals were collected at two different depths (three at 1.5 m and three at 11 m) from a reef 3.2 km off the northeastern coast of Puerto Rico. We characterized the microbial communities by sequencing the 16S rRNA gene region V4 with the Illumina platform. Results A total of 173,137 good-quality sequences were binned into 803 OTUs with a 97% similarity. We uncovered eight bacterial phyla at both depths with a dominance of 725 Rickettsiales OTUs (Proteobacteria). A fewer number (38) of low dominance OTUs varied by depth and taxa enriched in shallow water corals included Proteobacteria (e.g. Rhodobacteraceae and Serratia) and Firmicutes (Streptococcus). Those enriched in deeper water corals featured different Proteobacterial taxa (Campylobacterales and Bradyrhizobium) and Firmicutes (Lactobacillus). Discussion Our results confirm that the microbiota of A. cervicornis inhabiting the northeastern region of Puerto Rico is dominated by a Rickettsiales-like bacterium and that there are significant changes in less dominant taxa at different water depths. These changes in less dominant taxa may potentially impact the coral’s physiology, particularly with respect to its ability to respond to future increases in temperature and CO2.
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Affiliation(s)
- Filipa Godoy-Vitorino
- Department of Natural Sciences, Microbial Ecology and Genomics Lab, Inter American University of Puerto Rico, San Juan, PR, USA
| | - Claudia P Ruiz-Diaz
- Department of Environmental Sciences, University of Puerto Rico Rio Piedras Campus, San Juan, PR, USA.,Sociedad Ambiente Marino, San Juan, PR, USA
| | - Abigail Rivera-Seda
- Department of Natural Sciences, Microbial Ecology and Genomics Lab, Inter American University of Puerto Rico, San Juan, PR, USA
| | - Juan S Ramírez-Lugo
- Department of Biology, University of Puerto Rico Rio Piedras Campus, San Juan, PR, USA
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Weber L, DeForce E, Apprill A. Optimization of DNA extraction for advancing coral microbiota investigations. MICROBIOME 2017; 5:18. [PMID: 28179023 PMCID: PMC5299696 DOI: 10.1186/s40168-017-0229-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/04/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition. During phase I, total DNA was extracted from seven coral species in a replicated experimental design using four different MO BIO Laboratories, Inc., DNA Isolation kits: PowerSoil®, PowerPlant® Pro, PowerBiofilm®, and UltraClean® Tissue & Cells (with three homogenization permutations). Technical performance of the treatments was evaluated using DNA yield and amplification efficiency of small subunit ribosomal RNA (SSU ribosomal RNA (rRNA)) genes. During phase II, potential extraction biases were examined via microbial community analysis of SSU rRNA gene sequences amplified from the most successful DNA extraction treatments. RESULTS In phase I of the study, the PowerSoil® and PowerPlant® Pro extracts contained low DNA concentrations, amplified poorly, and were not investigated further. Extracts from PowerBiofilm® and UltraClean® Tissue and Cells permutations were further investigated in phase II, and analysis of sequences demonstrated that overall microbial community composition was dictated by coral species and not extraction treatment. Finer pairwise comparisons of sequences obtained from Orbicella faveolata, Orbicella annularis, and Acropora humilis corals revealed subtle differences in community composition between the treatments; PowerBiofilm®-associated sequences generally had higher microbial richness and the highest coverage of dominant microbial groups in comparison to the UltraClean® Tissue and Cells treatments, a result likely arising from using a combination of different beads during homogenization. CONCLUSIONS Both the PowerBiofilm® and UltraClean® Tissue and Cells treatments are appropriate for large-scale analyses of coral microbiota. However, studies interested in detecting cryptic microbial members may benefit from using the PowerBiofilm® DNA treatment because of the likely enhanced lysis efficiency of microbial cells attributed to using a variety of beads during homogenization. Consideration of the methodology involved with microbial DNA extraction is particularly important for studies investigating complex host-associated microbiota.
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Affiliation(s)
- Laura Weber
- Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, MA 02139 USA
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
| | | | - Amy Apprill
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543 USA
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10
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Santos HF, Carmo FL, Martirez N, Duarte GAS, Calderon EN, Castro CB, Pires DO, Rosado AS, Peixoto RS. Cyanobacterial and microeukaryotic profiles of healthy, diseased, and dead Millepora alcicornis from the South Atlantic. DISEASES OF AQUATIC ORGANISMS 2016; 119:163-172. [PMID: 27137074 DOI: 10.3354/dao02972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Coral reefs are at risk due to events associated with human activities, which have resulted in the increasing occurrence of coral diseases. Corals live in symbiotic relationships with different microorganisms, such as cyanobacteria, a very important group. Members of the phylum Cyanobacteria are found in great abundance in the marine environment and may play an essential role in keeping corals healthy but may also be pathogenic. Furthermore, some studies are showing a rise in cyanobacterial abundance in coral reefs as a result of climate change. The current study aimed to improve our understanding of the relationship between cyanobacteria and coral health. Our results revealed that the cyanobacterial genus GPI (Anabaena) is a possible opportunistic pathogen of the coral species Millepora alcicornis in the South Atlantic Ocean. Furthermore, the bacterial and microeukaryotic profile of healthy, diseased, and post-disease (skeletal) regions of affected coral indicated that a microbial consortium composed of Anabaena sp., Prosthecochloris sp., and microeukaryotes could be involved in this pathogenicity or could be taking advantage of the diseased state.
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Affiliation(s)
- Henrique F Santos
- LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil
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11
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Fragoso Ados Santos H, Duarte GAS, Rachid CTDC, Chaloub RM, Calderon EN, Marangoni LFDB, Bianchini A, Nudi AH, do Carmo FL, van Elsas JD, Rosado AS, Castro CBE, Peixoto RS. Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota. Sci Rep 2015; 5:18268. [PMID: 26658023 PMCID: PMC4677405 DOI: 10.1038/srep18268] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/11/2015] [Indexed: 12/21/2022] Open
Abstract
Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.
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Affiliation(s)
- Henrique Fragoso Ados Santos
- BIOINOVAR/LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Caio TavoraCoelho da Costa Rachid
- BIOINOVAR/LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Moreira Chaloub
- Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil.,Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emiliano Nicolas Calderon
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil
| | | | - Adalto Bianchini
- Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil.,Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Adriana Haddad Nudi
- Laboratório de Estudos Marinhos e Ambientais, PUC, Rio de Janeiro, RJ, Brazil
| | - Flávia Lima do Carmo
- BIOINOVAR/LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Alexandre Soares Rosado
- BIOINOVAR/LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil
| | - Clovis Barreira E Castro
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil
| | - Raquel Silva Peixoto
- BIOINOVAR/LEMM - Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Instituto Coral Vivo, Rio de Janeiro, RJ, Brazil
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12
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Duarte G, Calderon EN, Pereira CM, Marangoni LFB, Santos HF, Peixoto RS, Bianchini A, Castro CB. A novel marine mesocosm facility to study global warming, water quality, and ocean acidification. Ecol Evol 2015; 5:4555-66. [PMID: 26668722 PMCID: PMC4670062 DOI: 10.1002/ece3.1670] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/12/2022] Open
Abstract
We describe a completely randomizable flow‐through outdoor mesocosm for climate change and ecotoxicology studies that was built with inexpensive materials. The 16 raceway tanks allow up to 6× water renewal per hour, avoiding changes in natural abiotic seawater conditions. We use an open‐source hardware board (Arduino) that was adapted to control heaters and an innovative CO2 injection system. This system reduced seawater pH up to −0.9 units and increased temperature up to +6°C in three treatments and a control. Treatments can be continuously compared with the control and vary according to diel fluctuations, thus following the diel range observed in the sea. The mesocosm facility also includes an integrated secondary system of 48 aquaria for ecotoxicology studies. We validated the reproducibility and relevance of our experimental system by analyzing the variation of the total DNA of the microbial community extracted from corals in three elevated temperature scenarios during a 40‐day experiment. We also present data from temperature, acidification, and copper contamination trials, which allowed continuous, reliable, and consistent treatment manipulations.
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Affiliation(s)
- Gustavo Duarte
- Instituto Coral Vivo Rio de Janeiro Brazil ; Museu Nacional Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | | | | | - Laura F B Marangoni
- Instituto Coral Vivo Rio de Janeiro Brazil ; Pós-Graduação em Oceanografia Biológica Instituto de Oceanografia Universidade Federal do Rio Grande Rio Grande Brazil
| | - Henrique F Santos
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Microbiologia Paulo de Góes UFRJ Rio de Janeiro Brazil
| | - Raquel S Peixoto
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Microbiologia Paulo de Góes UFRJ Rio de Janeiro Brazil
| | - Adalto Bianchini
- Instituto Coral Vivo Rio de Janeiro Brazil ; Instituto de Ciências Biológicas Universidade Federal do Rio Grande Rio Grande Brazil
| | - Clovis B Castro
- Instituto Coral Vivo Rio de Janeiro Brazil ; Museu Nacional Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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13
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Climate change affects key nitrogen-fixing bacterial populations on coral reefs. ISME JOURNAL 2014; 8:2272-9. [PMID: 24830827 DOI: 10.1038/ismej.2014.70] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/17/2014] [Accepted: 03/23/2014] [Indexed: 11/08/2022]
Abstract
Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.
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