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Wang H, Liu F, Wang M, Bettarel Y, Eissler Y, Chen F, Kan J. Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients. Microbiol Spectr 2024; 12:e0404823. [PMID: 38606959 PMCID: PMC11064499 DOI: 10.1128/spectrum.04048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental roles as primary producers and trophic links and sustain estuarine ecosystems. In this study, we investigated the detailed community structure and spatiotemporal variations of planktonic eukaryotes in the Chesapeake Bay across space and time for three consecutive years. A clear seasonal and spatial shift of total, abundant, and rare planktonic eukaryotes was evident, and the pattern recurred interannually. Multiple harmful algal species have been identified in the Bay with varied distribution patterns, such as Karlodinium, Heterosigma akashiwo, Protoperidinium sp., etc. Compared to abundant taxa, rare subcommunities were more sensitive to environmental disturbance in terms of richness, diversity, and distribution. The combined effects of temporal variation (13.3%), nutrient availability (10.0%), and spatial gradients (8.8%) structured the distribution of eukaryotic microbial communities in the Bay. Similar spatiotemporal patterns between planktonic prokaryotes and eukaryotes suggest common mechanisms of adjustment, replacement, and species interaction for planktonic microbiomes under strong estuarine gradients. To our best knowledge, this work represents the first systematic study on planktonic eukaryotes in the Bay. A comprehensive view of the distribution of planktonic microbiomes and their interactions with environmental processes is critical in understanding the underlying microbial mechanisms involved in maintaining the stability, function, and environmental health of estuarine ecosystems. IMPORTANCE Deep sequencing analysis of planktonic eukaryotes in the Chesapeake Bay reveals high community diversity with many newly recognized phytoplankton taxa. The Chesapeake Bay planktonic eukaryotes show distinct seasonal and spatial variability, with recurring annual patterns of total, abundant, and rare groups. Rare taxa mainly contribute to eukaryotic diversity compared to abundant groups, and they are more sensitive to spatiotemporal variations and environmental filtering. Temporal variations, nutrient availability, and spatial gradients significantly affect the distribution of eukaryotic microbial communities. Similar spatiotemporal patterns in prokaryotes and eukaryotes suggest common mechanisms of adjustment, substitution, and species interactions in planktonic microbiomes under strong estuarine gradients. Interannually recurring patterns demonstrate that diverse eukaryotic taxa have well adapted to the estuarine environment with a long residence time. Further investigations of how human activities impact estuarine planktonic eukaryotes are critical in understanding their essential ecosystem roles and in maintaining environmental safety and public health.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Feilong Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Yvan Bettarel
- ECOSYM (Ecologie des systèmes marins côtiers)- UMR 5119, Universite de Montpellier, Montpellier, France
| | - Yoanna Eissler
- Laboratorio de Virología, Centro de Neurobiología y Fisiopatología Integrativa, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Arizona, USA
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Jeon BS, Park MG. Morphology, phylogeny, and host range of the novel early-diverging oomycete Sirolpidium dinoletiferum sp. nov. parasitizing marine dinoflagellates. HARMFUL ALGAE 2024; 132:102567. [PMID: 38331547 DOI: 10.1016/j.hal.2024.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
Oomycetes are fungus-like heterotrophic organisms with a broad environmental distribution, including marine, freshwater, and terrestrial habitats. They function as saprotrophs that use the remains of other organisms or as parasites of a variety of eukaryotes, including protists, diatoms, dinoflagellates, macroalgae, plants, fungi, animals, and even other oomycetes. Among the protist hosts, the taxonomy, morphology, and phylogenetic positions of the oomycete parasitoids of diatoms have been well studied; however, this information concerning the oomycete parasitoids of dinoflagellates is poorly understood. During intensive sampling along the east and west coasts of Korea in May and October 2019, a new species of oomycetes was discovered and two strains of the new parasitoid were successfully established in cultures. The new oomycete parasitoid penetrated the dinoflagellate host cell and developed to form a sporangium, which was very similar to the perkinsozoan parasitoids that infect marine dinoflagellates. The most distinctive morphological feature of the new parasitoid was a central large vacuole forming several long discharge tubes. The molecular phylogenetic tree inferred based on the small subunit (SSU) ribosomal DNA (rDNA) revealed that the new parasitoid forms a distinct branch unrelated to other described species belonging to early-diverging oomycetes. It clustered with species belonging to the genus Sirolpidium with strong support values in the cytochrome c oxidase subunit 2 (cox2) tree. Cross-infection experiments showed that infections by the new parasitoid occurred in only six genera belonging to dinoflagellates among the protists tested in this study. Based on the morphological and molecular data obtained in this study, we propose to introduce a new species, Sirolpidium dinoletiferum sp. nov., for this novel parasitoid, conservatively within the genus Sirolpidium.
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Affiliation(s)
- Boo Seong Jeon
- Research Institute for Basic Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju 61186, Korea.
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Da J, Xi Y, Cheng Y, He H, Liu Y, Li H, Wu QL. The Effects of Intraguild Predation on Phytoplankton Assemblage Composition and Diversity: A Mesocosm Experiment. BIOLOGY 2023; 12:biology12040578. [PMID: 37106778 PMCID: PMC10136063 DOI: 10.3390/biology12040578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023]
Abstract
Intraguild predation (IGP) can have a significant impact on phytoplankton biomass, but its effects on their diversity and assemblage composition are not well understood. In this study, we constructed an IGP model based on the common three-trophic food chain of "fish (or shrimp)-large branchiopods (Daphnia)-phytoplankton", and investigated the effects of IGP on phytoplankton assemblage composition and diversity in outdoor mesocosms using environmental DNA high-throughput sequencing. Our results indicated that the alpha diversities (number of amplicon sequence variants and Faith's phylogenetic diversity) of phytoplankton and the relative abundance of Chlorophyceae increased with the addition of Pelteobagrus fulvidraco, while similar trends were found in alpha diversities but with a decrease in the relative abundance of Chlorophyceae in the Exopalaemon modestus treatment. When both predators were added to the community, the strength of collective cascading effects on phytoplankton alpha diversities and assemblage composition were weaker than the sum of the individual predator effects. Network analysis further showed that this IGP effect also decreased the strength of collective cascading effects in reducing the complexity and stability of the phytoplankton assemblages. These findings contribute to a better understanding of the mechanisms underlying the impacts of IGP on lake biodiversity, and provide further knowledge relevant to lake management and conservation.
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Affiliation(s)
- Jun Da
- School of Ecology and Environment, Anhui Normal University, Wuhu 050031, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yilong Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu 050031, China
| | - Yunshan Cheng
- School of Ecology and Environment, Anhui Normal University, Wuhu 050031, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hu He
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanru Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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Rasheed S, Amin A, Sarwar A, Saleem HGM, Hassan A. Evaluation of Antimicrobial Effect of Silver Nanoparticle Based Whey Emulsions and Edible Films for the Extension of Shelf Life of Fruits and Vegetables. Curr Microbiol 2023; 80:158. [PMID: 37002374 DOI: 10.1007/s00284-023-03275-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 03/19/2023] [Indexed: 04/04/2023]
Abstract
The purpose of this study was to develop and assess the antimicrobial properties of silver nanoparticles (AgNPs)-based whey emulsions and edible films for extending the shelf life of fruits and vegetables. The AgNPs were synthesized using a biological method, and their morphological and topographical characteristics were evaluated using scanning electron microscopy (SEM). The AgNPs were incorporated into the emulsions and films to increase their antimicrobial efficacy. Bacterial and fungal strains were identified by DNA regions, including 16S and 18S rRNA, TEF-1α, and RPB2 to evaluate antimicrobial activity. AgNPs-based emulsions and films were used to extend the shelf life of fruits and vegetables for up to 15 days. The results showed that the use of AgNPs in the coated samples significantly increased their effectiveness against bacterial and fungal strains. SEM analysis revealed the presence of AgNPs of varying sizes, ranging from 21 to 62 nm. The zones of inhibition were measured against Staphylococcus aureus, Escherichia coli, Salmonella enterica, Aspergillus flavus, Aspergillus tamari, and Aspergillus niger. The total viable count (log cfu/ml) decreased from 6.423 in the control group to 3.301 in the treated samples. The antioxidant activity of the treated fruits and vegetables was also significantly improved, with values of 56.12, 23.36, 26.10, 7.6, 36.04, and 33.81% for strawberry, taro root, guava, peas, green chili, and carrot, respectively (p < 0.05). The AgNPs-based whey protein emulsions were found to exhibit the highest antimicrobial activity and are therefore a promising approach to extend the shelf life of fruits and vegetables.
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Affiliation(s)
- Sunbul Rasheed
- Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan
| | - Aatif Amin
- Department of Microbiology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan.
| | - Arslan Sarwar
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Hafiz Ghulam Murtaza Saleem
- Department of Medical Laboratory Technology, College of Rehabilitation and Allied Health Sciences, Riphah International University, 28-M Quaid-e-Azam, Industrial Estate Kot Lakhpat, Lahore, 54000, Pakistan
| | - Ammara Hassan
- Food and Biotechnology Research Centre, Laboratories Complex, Pakistan Council of Scientific and Industrial Research (PCSIR), Ferozepur Road, Lahore, 54600, Pakistan
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Li C, Li Y, Tang L, Ikenaga M, Liu R, Xu G. Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective. Ecol Evol 2023; 13:e9727. [PMID: 36620424 PMCID: PMC9810793 DOI: 10.1002/ece3.9727] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in the habitat heterogeneity in the two Haloxylon species from a nutrient perspective. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0-20, 20-40, and 40-60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g., eukarya, bacteria, and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil available nitrogen, especially nitrate nitrogen, was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g., Firmicutes, Bacteroidetes, and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. Haloxylon persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea), and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.
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Affiliation(s)
- Chenhua Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina,Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina,Univerisity of Chinese Academy of SciencesBeijingChina
| | - Yan Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina,Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina,Univerisity of Chinese Academy of SciencesBeijingChina
| | - Lisong Tang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina,Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina,Univerisity of Chinese Academy of SciencesBeijingChina
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine AreaKagoshima UniversityKagoshimaJapan
| | - Ran Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina,Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina,Univerisity of Chinese Academy of SciencesBeijingChina
| | - Guiqing Xu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiangChina,Fukang Station of Desert EcologyChinese Academy of SciencesFukangXinjiangChina,Univerisity of Chinese Academy of SciencesBeijingChina
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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Parsy A, Guyoneaud R, Lot MC, Baldoni-Andrey P, Périé F, Sambusiti C. Impact of salinities, metals and organic compounds found in saline oil & gas produced water on microalgae and cyanobacteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113351. [PMID: 35255251 DOI: 10.1016/j.ecoenv.2022.113351] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
This work evaluates the impact of salinity and the toxicity of some metals and organic compounds commonly found in produced waters on the growth of model photosynthetic organisms. Five strains of marine microalgae and one cyanobacteria (i.e. Dunaliella salina, Nannochloropsis oceanica, Tetraselmis suecica, Picochlorum costavermella, Coccomyxa simplex and Synechococcus rubescens) were tested in microplates as well as the freshwater Chlorella vulgaris selected as reference. Results revealed that D.salina was able to growth at high salinity (up to 135 g·L-1). Copper was the most toxic metal for all strains (half maximal effective concentration between 0.1 and 10 mg·L-1) except for D.salina and C.simplex. These two strains were the most resistant to all metals tested. All organic compounds presented half maximal effective concentration above 10 mg·L-1, none of them being very toxic for the studied microorganisms. P.costavermella and C.simplex were the most resistant strains to organic compounds. Looking at tolerance to salinity, metals and organic compounds, D.salina appeared to be the best choice for biomass production in produced waters. In addition, growths in 80% artificial produced water supplemented with f medium confirm the feasibility to use this medium to produce biomass.
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Affiliation(s)
- Aurélien Parsy
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Environmental Microbiology and Chemistry, UMR 5254, 64000 Pau, France; TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Environmental Microbiology and Chemistry, UMR 5254, 64000 Pau, France
| | - Marie-Claire Lot
- TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Patrick Baldoni-Andrey
- TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Frédéric Périé
- TotalEnergies, CSTJF - Avenue Larribau, 64018 Pau, France
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Molecular Detection of Malpighamoeba mellificae in Honey Bees. Vet Sci 2022; 9:vetsci9030148. [PMID: 35324875 PMCID: PMC8949188 DOI: 10.3390/vetsci9030148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Malpighamoeba mellificae is a protozoan that infects the Malpighian tubules of honey bees. The amoebae, ingested as cysts, develop into trophozoites that feed upon tubule epithelia. The resulting damage of the Malpighian tubules can induce an imbalance of waste excretion and hemolymph exchange. This causes the so-called amoebiasis disease in adult bees, which may co-occur with Nosema infections. Most reports of this amoeba are from the 1960s and earlier, and knowledge of the disease and its spreading is very poor. The lack of any genetic marker for the species hampers its sensitive identification using molecular tools and gaining knowledge on its epidemiology. Here, we present a diagnostic RT-qPCR assay, consisting of two primers and one probe that were developed based on 18S rRNA sequences of the amoeba, generated with metagenomic sequencing of Malpighian tubules with and without M. mellificae cysts. The assay was initially tested and adjusted with samples microscopically tested for the presence of M. mellificae cysts. Later, it was validated and material with unknown infection status was tested. The sensitive diagnostic Malpighamoeba disease 18S assay is now ready to be applied for honey bee health monitoring purposes and to investigate the prevalence of M. mellificae in more detail.
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Taşkan B, Taşkan E. Sustainable bioelectricity generation using Cladophora sp. as a biocathode in membrane-less microbial fuel cell. BIORESOURCE TECHNOLOGY 2022; 347:126704. [PMID: 35031436 DOI: 10.1016/j.biortech.2022.126704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
In this study, the Cladophora sp. is used to provide oxygen to the cathode of the photosynthetic biocathode membrane-less microbial fuel cell (PB-MLMFC). Non-aerated (NA-MLMFC) and mechanically-aerated (MA-MLMFC) MLMFCs are operated under similar operating conditions to evaluate the performance of PB-MLMFC with the presence of Cladophora sp. The PB-MLMFC exhibits the highest dissolved oxygen (DO) concentration, which results in a more efficient oxygen reduction reaction and a significant improvement in the electricity generation performance. The maximum power density of PB-MLMFC is 619.1 mW m-2, which is the highest power density known to be reported for algal cathode MFCs in the literature. The electrochemical analysis shows that theCladophora sp.reduces the charge (Rct) and mass transfer (Rmt) resistances of the PB-MLMFC, and improves the bioelectrochemical activity of the anode microorganisms. The study reveals that Cladophora sp. provides a cost-effective and renewable approach for practical applications of MLMFCs.
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Affiliation(s)
- Banu Taşkan
- Firat University, Department of Environmental Engineering, 23119 Elazig, Turkey.
| | - Ergin Taşkan
- Firat University, Department of Environmental Engineering, 23119 Elazig, Turkey
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Zou S, Fu R, Deng H, Zhang Q, Gentekaki E, Gong J. Coupling between Ribotypic and Phenotypic Traits of Protists across Life Cycle Stages and Temperatures. Microbiol Spectr 2021; 9:e0173821. [PMID: 34817220 PMCID: PMC8612162 DOI: 10.1128/spectrum.01738-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023] Open
Abstract
Relationships between ribotypic and phenotypic traits of protists across life cycle stages remain largely unknown. Herein, we used single cells of two soil and two marine ciliate species to examine phenotypic and ribotypic traits and their relationships across lag, log, plateau, cystic stages and temperatures. We found that Colpoda inflata and Colpoda steinii demonstrated allometric relationships between 18S ribosomal DNA (rDNA) copy number per cell (CNPC), cell volume (CV), and macronuclear volume across all life cycle stages. Integrating previously reported data of Euplotes vannus and Strombidium sulcatum indicated taxon-dependent rDNA CNPC-CV functions. Ciliate and prokaryote data analysis revealed that the rRNA CNPC followed a unified power-law function only if the rRNA-deficient resting cysts were not considered. Hence, a theoretical framework was proposed to estimate the relative quantity of resting cysts in the protistan populations with total cellular rDNA and rRNA copy numbers. Using rDNA CNPC was a better predictor of growth rate at a given temperature than rRNA CNPC and CV, suggesting replication of redundant rDNA operons as a key factor that slows cell division. Single-cell high-throughput sequencing and analysis after correcting sequencing errors revealed multiple rDNA and rRNA variants per cell. Both encystment and temperature affected the number of rDNA and rRNA variants in several cases. The divergence of rDNA and rRNA sequence in a single cell ranged from 1% to 10% depending on species. These findings have important implications for inferring cell-based biological traits (e.g., species richness, abundance and biomass, activity, and community structure) of protists using molecular approaches. IMPORTANCE Based on phenotypic traits, traditional surveys usually characterize organismal richness, abundance, biomass, and growth potential to describe diversity, organization, and function of protistan populations and communities. The rRNA gene (rDNA) and its transcripts have been widely used as molecular markers in ecological studies of protists. Nevertheless, the manner in which these molecules relate to cellular (organismal) and physiological traits remains poorly understood, which could lead to misinterpretations of protistan diversity and ecology. The current research highlights the dynamic nature of cellular rDNA and rRNA contents, which tightly couple with multiple phenotypic traits in ciliated protists. We demonstrate that quantity of resting cysts and maximum growth rate of a population can be theoretically estimated using ribotypic trait-based models. The intraindividual sequence polymorphisms of rDNA and rRNA can be influenced by encystment and temperature, which should be considered when interpreting species-level diversity and community structure of microbial eukaryotes.
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Affiliation(s)
- Songbao Zou
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Huzhou, China
- Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Rao Fu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Huiwen Deng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Barreiro-Vescovo S, González-Fernández C, de Godos I. Characterization of communities in a microalgae-bacteria system treating domestic wastewater reveals dominance of phototrophic and pigmented bacteria. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Ortiz-Ardila AE, Díez B, Celis C, Jenicek P, Labatut R. Microaerobic conditions in anaerobic sludge promote changes in bacterial composition favouring biodegradation of polymeric siloxanes. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1182-1197. [PMID: 34302159 DOI: 10.1039/d1em00143d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Volatile organic silicon compounds (VOSiC) are harmful pollutants to the biota and ecological dynamics as well as biogas-based energy conversion systems. However, there is a lack of understanding regarding the source of VOSiCs in biogas, especially arising from the biochemical conversion of siloxane polymers such as polydimethylsiloxanes (PDMS). The biodegradation of PDMS was evaluated under anaerobic/microaerobic conditions (PO2 = 0, 1, 3, 5%), using wastewater treatment plant (WWTP) sludge as an inoculum and PDMS as a co-substrate (0, 50, 100, 500 ppm). On average, strictly anaerobic treatments produced significantly less methane than the 3 and 5% microaerated ones, which show the highest PMDS biodegradation at 50 ppm. Thauera sp. and Rhodococcus sp. related phylotypes were identified as the most abundant bacterial groups in microaerated treatments, and siloxane-related molecules were identified as remnants of PDMS catabolism. Our study demonstrates that microaeration promotes changes to the native bacterial community which favour the biological degradation of PDMS. This confirms that the presence of VOSiC (e.g., D4-D6) in biogas is not only due to its direct input in wastewaters, but also to the PDMS microbial catabolism. Microaerobic conditions enhance both PDMS and (subsequent) VOSiC degradation in the liquid phase, increasing the concentrations of D4 and D5 in biogas, and the production of less toxic siloxane-based derivatives in the liquid phase. This study suggests that microaeration of the anaerobic sludge can significantly decrease the concentration of PDMSs in the WWTP effluent. However, for WWTPs to become effective barriers for the emission of these ecotoxic contaminants to the environment, such a strategy needs to be coupled with an efficient biodegradation of VOSiCs from the biogas.
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Affiliation(s)
- A E Ortiz-Ardila
- Department of Hydraulic and Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Liu Q, Zhao Q, Jiang Y, Li Y, Zhang C, Li X, Yu X, Huang L, Wang M, Yang G, Chen H, Tian J. Diversity and co-occurrence networks of picoeukaryotes as a tool for indicating underlying environmental heterogeneity in the Western Pacific Ocean. MARINE ENVIRONMENTAL RESEARCH 2021; 170:105376. [PMID: 34091097 DOI: 10.1016/j.marenvres.2021.105376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Picoeukaryotes are an essential component of microbial communities and play key roles in marine ecosystems. In this study, surface water picoeukaryotes were investigated at 32 stations along a latitudinal cross-section of the Western Pacific (WP) in 2015. Multivariate analyses demonstrated that there were clear spatial patterns in picoeukaryotic community structures which were consistent with the distributions of environmental variables. The spatial patterns of community structures and diversity indices were all significantly correlated with multiple environmental parameters, especially nutrients. Co-occurrence networks linked community variability to environmental heterogeneity. In summary, the construction of picoeukaryotic communities in the WP was significantly affected by numerous environmental variables, and certain variables were revealed as key forcing factors responsible for the main similarities between picoeukaryotic communities. This study details the relationships between the picoeukaryotes and environmental parameters in the WP, and provides insight for application of using picoeukaryotes as indicator in future bioassessment for open waters.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China; Frontiers Science Center for Deep Ocean Multiphases and Earth System, Ocean University of China, Qingdao, China; College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Qiannan Zhao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Yong Jiang
- Frontiers Science Center for Deep Ocean Multiphases and Earth System, Ocean University of China, Qingdao, China; College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Yan Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Chenru Zhang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Xianrong Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Liyang Huang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Min Wang
- Frontiers Science Center for Deep Ocean Multiphases and Earth System, Ocean University of China, Qingdao, China; College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Guipeng Yang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China.
| | - Hongtao Chen
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China.
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
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Long-Term Cultivation of a Native Arthrospira platensis (Spirulina) Strain in Pozo Izquierdo (Gran Canaria, Spain): Technical Evidence for a Viable Production of Food-Grade Biomass. Processes (Basel) 2021. [DOI: 10.3390/pr9081333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microalgae cultivation is a promising alternative to traditional agriculture in arid—semi-arid areas. The aim of this study is to assess the viability of long-term cultivation of native Arthrospira platensis in Gran Canaria. Maximum culture productivity (0.08 g/L/day) and optimal concentration range (0.6–0.9 g/L) were firstly determined in 8000 L raceway under a greenhouse. Afterwards, a stable productivity of 0.06 g/L/day (6.0 g/m2/day) was obtained by reusing the culture medium during 26 days of cultivation, with consistent biomass biochemical composition. Outdoor temperature and daily solar irradiation ranged between 17.9–30.7 °C and 79.2–274.8 W/m2, while culture pH and salinity were in the range 9.42–10.77 and 11.2–14.9 g/L, respectively. Protein (>60%), potassium (1.8 g/100 g) and C-phycocyanin (7.2%) content is in the high-range of commercial Spirulina, which makes BEA 1257B promising for food and extraction of natural pigments/antioxidants. The dried biomass complies with international standards for human consumption, because of low heavy metal content and no pathogens presence. Product quality can be improved by reducing ash (≃12%) and sodium (1.5%) content through biomass washing optimization and/or further dewatering step. Other microorganisms can be prevented by high alkaline conditions and mild chemical treatments. These results pave the way for a sustainable microalgae-based blue bioeconomy in the Canary Islands.
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Moukarzel R, Ridgway HJ, Guerin-Laguette A, Jones EE. Grapevine rootstocks drive the community structure of arbuscular mycorrhizal fungi in New Zealand vineyards. J Appl Microbiol 2021; 131:2941-2956. [PMID: 34028142 DOI: 10.1111/jam.15160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
AIM Arbuscular mycorrhizal fungi (AMF) are often regarded as non-specific symbionts, but some AMF communities show host preference in various ecosystems including vineyards. Grapevine plants are very responsive to AMF colonization. Although these fungi have potentially significant applications for sustainable agricultural ecosystems, there is a gap in knowledge regarding AMF-grapevine interactions worldwide and especially in New Zealand. This study focused on identifying AMF taxa colonizing grapevines in New Zealand vineyards and investigated the effect of grapevine rootstocks on AMF community diversity and composition. METHODS AND RESULTS Denaturing gradient gel electrophoresis (DGGE) and trap cultures were used to characterize the AMF communities. Grapevine roots from three vineyards and nine rootstocks were analysed by DGGE and used in trap cultures for AMF recovery. Trap cultures allowed the recovery of six AMF spore morphotypes that belonged to Ambispora sp., Claroideoglomus sp., Funneliformis sp. and Glomus sp. Bands excised, reamplified and sequenced from the DGGE were assigned to Glomus sp., Rhizophagus sp. and Claroideoglomus sp. The AMF community analyses demonstrated that rootstock significantly (P < 0·05) influenced the AMF community composition in all sites. CONCLUSIONS The study showed that for a comprehensive identification of AMF, both results from trap culture and molecular work were needed and that the rootstock cultivar was the main driver of the arbuscular mycorrhizal community colonizing the roots. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides a firm foundation for future research exploring the beneficial use of AMF in enhancing grapevine production and sustainability.
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Affiliation(s)
- R Moukarzel
- Lincoln University, Lincoln, Canterbury, New Zealand
| | - H J Ridgway
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 4704, Christchurch, New Zealand
| | - A Guerin-Laguette
- Mycotree C/-Southern Woods Nursery, Christchurch, Canterbury, New Zealand
| | - E E Jones
- Lincoln University, Lincoln, Canterbury, New Zealand
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Role of Phylogenetic Structure in the Dynamics of Coastal Viral Assemblages. Appl Environ Microbiol 2021; 87:AEM.02704-20. [PMID: 33741635 DOI: 10.1128/aem.02704-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Marine microbes, including viruses, are an essential part of the marine ecosystem, forming the base of the food web and driving biogeochemical cycles. Within this system, the composition of viral assemblages changes markedly with time, and some of these changes are repeatable through time; however, the extent to which these dynamics are reflected within versus among evolutionarily related groups of viruses is largely unexplored. To examine these dynamics, changes in the composition of two groups of ecologically important viruses and communities of their potential hosts were sampled every 2 weeks for 13 months at a coastal site in British Columbia, Canada. We sequenced two marker genes for viruses-the gene encoding the major capsid protein of T4-like phages and their relatives (gp23) and the RNA-dependent RNA polymerase (RdRp) gene of marnavirus-like RNA viruses-as well as marker genes for their bacterial and eukaryotic host communities, the genes encoding 16S rRNA and 18S rRNA. There were strong lagged correlations between viral diversity and community similarity of putative hosts, implying that the viruses influenced the composition of the host communities. The results showed that for both viral assemblages, the dominant clusters of phylogenetically related viruses shifted over time, and this was correlated with environmental changes. Viral clusters contained many ephemeral taxa and few persistent taxa, but within a viral assemblage, the ephemeral and persistent taxa were closely related, implying ecological dynamics within these clusters. Furthermore, these dynamics occurred in both the RNA and DNA viral assemblages surveyed, implying that this structure is common in natural viral assemblages.IMPORTANCE Viruses are major agents of microbial mortality in marine systems, yet little is known about changes in the composition of viral assemblages in relation to those of the microbial communities that they infect. Here, we sampled coastal seawater every 2 weeks for 1 year and used high-throughput sequencing of marker genes to follow changes in the composition of two groups of ecologically important viruses, as well as the communities of bacteria and protists that serve as their respective hosts. Different subsets of genetically related viruses dominated at different times. These results demonstrate that although the genetic composition of viral assemblages is highly dynamic temporally, for the most part the shuffling of genotypes occurs within a few clusters of phylogenetically related viruses. Thus, it appears that even in temperate coastal waters with large seasonal changes, the highly dynamic shuffling of viral genotypes occurs largely within a few subsets of related individuals.
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Masry SHD, Taha TH, Botros WA, Mahfouz H, Al-Kahtani SN, Ansari MJ, Hafez EE. Antimicrobial activity of camphor tree silver nano-particles against foulbrood diseases and finding out new strain of Serratia marcescens via DGGE-PCR, as a secondary infection on honeybee larvae. Saudi J Biol Sci 2021; 28:2067-2075. [PMID: 33911922 PMCID: PMC8071921 DOI: 10.1016/j.sjbs.2021.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
American foulbrood (AFB) and European foulbrood (EFB) are the two major bacterial diseases affecting honeybees, leading to a decrease in viability of the hive, decreasing honey production, and resulting in significant economic losses to beekeepers. Due to the inefficiency and/or low efficacy of some antibiotics, researches with nanotechnology represent, possibly, new therapeutic strategies. Nanostructure drugs have presented some advantagesover the conventional medicines, such as slow, gradual and controlled release, increased bioavailability, and reduced side-effects. In this study, different infected larvae were collected from two apiaries; the combs that had symptoms of American and European foulbrood were isolated. In vitro antimicrobial activity of camphor tree silver nano-particles against foulbrood diseases were characterized using UV-Vis spectrophotometry and scanning electron microscope (SEM) that proves the formation of silver nanoparticles with size range 160-660 nm. The antimicrobial activity of the silver nanoparticles was tested using agar diffusion assay and proved their ability to effectively cease the pathogenic bacterial growth in both AFB and EFB. DGGE-PCR technique has been applied for the identification of un-common bacterial infections honeybees depending on 16S rRNA amplification from their total extracted DNA and has been identified as Serratia marcescens (TES), deposited in GenBank with a new accession number (MT240613). The results were confirmed strain has been detected by DGGE-PCR analysis causing uniquely infected brood that was attacked by the American Foulbrood It could be concluded that greenly synthesized silver nanoparticles is projected to be used as effective treatment for honeybee bacterial diseases. These material need more investigations under field conditions and study the possibility of its residues in honeybee products such as honey, and beeswax.
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Affiliation(s)
- Saad Hamdy Daif Masry
- Department of Plant Protection and Molecular Diagnosis, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Alexandria (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
- Abu Dhabi Agriculture and Food Safety Authority, Al Ain, United Arab Emirates
| | - Tarek Hosny Taha
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
| | - William A. Botros
- Nucleic Acids Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
| | - Hatem Mahfouz
- Department of Plant Production, Faculty of Environment Agricultural Science, Arish University, Egypt
| | - Saad Naser Al-Kahtani
- Arid Land Agriculture Department, College of Agricultural Sciences & Foods, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), India
| | - Elsayed Elsayed Hafez
- Department of Plant Protection and Molecular Diagnosis, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Alexandria (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
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Liu Q, Zhao Q, McMinn A, Yang EJ, Jiang Y. Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:94-102. [PMID: 37073396 PMCID: PMC10064379 DOI: 10.1007/s42995-020-00062-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles. Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity, revealing a huge, previously underestimated phylogenetic diversity with many new lineages. This technology has now become the most important tool to understand the ecological significance of this huge and novel diversity in polar oceans. In particular, high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments. Here, a brief overview of polar microbial eukaryote diversity, as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene, is presented. Using these 'omic' approaches, further attention still needs to be focused on differences between specific locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.
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Affiliation(s)
- Qian Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003 China
| | - Qiannan Zhao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003 China
| | - Andrew McMinn
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Eun Jin Yang
- Division of Polar Ocean Environment, Korea Polar Research Institute, 213-3 Songdo-dong, Yeonsu-gu, Incheon, 406-840 Korea
| | - Yong Jiang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003 China
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Romanis CS, Pearson LA, Neilan BA. Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies. J Microbiol Methods 2020; 180:106123. [PMID: 33316292 DOI: 10.1016/j.mimet.2020.106123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022]
Abstract
Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.
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Affiliation(s)
- Caitlin S Romanis
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia
| | - Leanne A Pearson
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia.
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Abstract
The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.
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Isolation of Microalgae from Mediterranean Seawater and Production of Lipids in the Cultivated Species. Foods 2020; 9:foods9111601. [PMID: 33158015 PMCID: PMC7692243 DOI: 10.3390/foods9111601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
Isolation and identification of novel microalgae strains with high lipid productivity is one of the most important research topics to have emerged recently. However, practical production processes will probably require the use of local strains adapted to commanding climatic conditions. The present manuscript describes the isolation of 96 microalgae strains from seawater located in Bay M’diq, Morocco. Four strains were identified using the 18S rDNA and morphological identification through microscopic examination. The biomass and lipid productivity were compared and showed good results for Nannochloris sp. (15.93 mg/L/day). The lipid content in the four species, namely Nannochloropsis gaditana, Nannochloris sp., Phaedactylum tricornutum and Tetraselmis suecica, was carried out by high performance liquid chromatography coupled to mass spectrometry (HPLC-MS ) highlighting the identification of up to 77 compounds.
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Sodré CS, Rodrigues PMG, Vieira MS, Marques Paes da Silva A, Gonçalves LS, Ribeiro MG, de Carvalho Ferreira D. Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients - a systematic review. J Oral Microbiol 2020; 12:1807179. [PMID: 32944157 PMCID: PMC7482892 DOI: 10.1080/20002297.2020.1807179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis. METHODS A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients. RESULTS 21 studies were included and the most identified species was Candida. The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21). CONCLUSIONS Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.
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Affiliation(s)
- Camila Stofella Sodré
- Faculty of Medicine, Department of Clinical Medicine, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Paulo Matheus Guerra Rodrigues
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
| | | | | | - Lucio Souza Gonçalves
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
| | - Marcia Gonçalves Ribeiro
- Medical Genetics Service, Martagão Gesteira Pediatric Institute (IPPMG- UFRJ), Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, Brazil
| | - Dennis de Carvalho Ferreira
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
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De Natale A, Mele BH, Cennamo P, Del Mondo A, Petraretti M, Pollio A. Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths. PLoS One 2020; 15:e0232512. [PMID: 32365130 PMCID: PMC7197799 DOI: 10.1371/journal.pone.0232512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
In this work, we want to investigate the impact of different substrates and different environmental condition on the biofilm communities growing on plaster, marble, and mortar substrates inside the Herculaneum Suburban Baths. To do so, we measured environmental conditions and sampled biofilm communities along the walls of the baths and used culture-dependent and -independent molecular techniques (DGGE) to identify the species at each sampling sites. We used the species pool to infer structure and richness of communities within each site in each substrate, and confocal light scanning microscopy to assess the three-dimensional structure of the sampled biofilms. To gather further insights, we built a meta-community network and used its local realizations to analyze co-occurrence patterns of species. We found that light is a limiting factor in the baths environment, that moving along sites equals moving along an irradiation gradient, and that such gradient shapes the community structure, de facto separating a dark community, rich in Bacteria, Fungi and cyanobacteria, from two dim communities, rich in Chlorophyta. Almost all sites are dominated by photoautotrophs, with Fungi and Bacteria relegated to the role of rare species., and structural properties of biofilms are not consistent within the same substrate. We conclude that the Herculaneum suburban baths are an environment-shaped community, where one dark community (plaster) and one dim community (mortar) provides species to a “midway” community (marble).
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Affiliation(s)
- Antonino De Natale
- Dipartimento di Biologia, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Bruno Hay Mele
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Paola Cennamo
- Facoltà di Lettere, University Suor Orsola Benincasa of Naples, Naples, Italy
| | - Angelo Del Mondo
- Dipartimento di Biologia, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
- * E-mail:
| | - Mariagioia Petraretti
- Dipartimento di Biologia, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Antonino Pollio
- Dipartimento di Biologia, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
- Metodologie Analitiche per la Salvaguardia dei Beni Culturali (Masbc), Task Force d’Ateneo Federico II di Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
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Paquette AJ, Sharp CE, Schnurr PJ, Allen DG, Short SM, Espie GS. Dynamic changes in community composition of Scenedesmus-seeded artificial, engineered microalgal biofilms. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mohapatra M, Behera P, Kim JY, Rastogi G. Seasonal and spatial dynamics of bacterioplankton communities in a brackish water coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:134729. [PMID: 31838414 DOI: 10.1016/j.scitotenv.2019.134729] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
Coastal ecosystems, one of the most productive ecosystems, are subjected to natural and anthropogenic stresses. Coastal bacterioplankton communities are highly dynamic due to spatiotemporal heterogeneity in the environmental parameters. We investigated the seasonal and spatial variation in bacterioplankton communities, their abundances and environmental drivers during one year period in Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes of bacterioplankton communities showed that they were dominated by heterotrophs namely α-Proteobacteria SAR11 and their sub-clades (SAR11_Ib, Chesapeake-Delaware_Bay, Candidatus_Pelagibacter, and SAR11_Surface_1), actinobacterial lineages (hgcI, CL500-29, and Candidatus_Aquiluna), β-Proteobacteria MWH-UniP1, β-Proteobacteria OM43, and verrucomicrobial clade Spartobacteria 'LD29'. Synechococcus was the dominant member within autotrophic cyanobacterial community. Response ratio derived from comparisons of taxon-specific absolute abundances and indicator analyses showed that SAR11_Surface_1 sub-clade occupied high-salinity environment especially during summer and winter and emerged as a strong indicator for mesohaline-polyhaline salinity regime. In contrast, Spartobacteria 'LD29', Actinobacteria hgcI, and CL500-29 preferred low-salinity freshwater environment and were strong indicators for oligohaline-mesohaline regimes. Spatiotemporal patterns were governed by 'distance-decay' and 'similarity-time' relationships. Bacterioplankton communities were mostly determined by salinity, dissolved oxygen, phosphate, and pH which resulted 'species sorting' leading to biogeographical patterns in the bacterioplankton communities. Modeling analysis revealed the characteristic shift in the indicator bacterioplankton taxa along with estuarine salinity gradient. This study has provided baseline information on the bacterioplankton communities and their environmental drivers within an anthropogenically impacted cyclone prone coastal lagoon which would be useful in assessing the impact of multiple stressors on this vulnerable ecosystem.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha 752030, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha 752030, India
| | - Ji Yoon Kim
- Center for Climate Change Adaptation, National Institute of Environmental Studies, Tsukuba 305-8506, Japan
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha 752030, India.
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Cai R, Kayal E, Alves-de-Souza C, Bigeard E, Corre E, Jeanthon C, Marie D, Porcel BM, Siano R, Szymczak J, Wolf M, Guillou L. Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Sci Rep 2020; 10:2531. [PMID: 32054950 PMCID: PMC7018713 DOI: 10.1038/s41598-020-59524-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/27/2020] [Indexed: 12/02/2022] Open
Abstract
As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.
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Affiliation(s)
- Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, US
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424 ABIMS, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Christian Jeanthon
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raffaele Siano
- Ifremer-Centre de Bretagne, Département/Unité/Laboratoire ODE/DYNECO/Pelagos, Z.I. Technopôle Brest-Iroise, Pointe du Diable BP70, 29280, Plouzané, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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El Sheikha AF. Tracing insect pests: is there new potential in molecular techniques? INSECT MOLECULAR BIOLOGY 2019; 28:759-772. [PMID: 31125162 DOI: 10.1111/imb.12601] [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: 04/25/2018] [Revised: 03/22/2019] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
Insects are amongst the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. Many kinds of insects are now resistant or cross-resistant to pesticides. Tracking studies have become very important for combatting insect pests and for better understanding their biology (eg insect population dynamics, movements, feeding behaviour and other ecological interactions). A wide variety of tracing approaches have been used including discriminative, tracer and molecular methods. The perfect technique for insect tracking is the technique that harmonizes with insects' 'normal' biology. Furthermore, the technique should be environmentally safe, cost-effective and easy to use. This paper reviews the current techniques used for insect traceability, documents the advantages and drawbacks of each method, and puts special focus on molecular techniques, including PCR-denaturing gradient gel electrophoresis as a new and promising traceability tool that could provide insects with a unique biological barcode and thus make it possible to trace their movements.
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Affiliation(s)
- A F El Sheikha
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, Nanchang, China
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, Shibin El Kom, Minufiya Government, Egypt
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Haoujar I, Cacciola F, Abrini J, Mangraviti D, Giuffrida D, Oulad El Majdoub Y, Kounnoun A, Miceli N, Fernanda Taviano M, Mondello L, Rigano F, Skali Senhaji N. The Contribution of Carotenoids, Phenolic Compounds, and Flavonoids to the Antioxidative Properties of Marine Microalgae Isolated from Mediterranean Morocco. Molecules 2019; 24:molecules24224037. [PMID: 31703456 PMCID: PMC6891583 DOI: 10.3390/molecules24224037] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
Abstract
This study aimed to investigate the potential of four sea water microalgae, isolated and cultivated at M′diq Bay in Morocco, as a new source of natural antioxidants. These microalgae belong to different classes, including Phaedactylium tricornitum (Bacillariophyceae), Nannochloropsis gaditana (Eustigmatophyceae), Nannochloris sp (Trebouxiophyceae), and Tetraselmis suecica (Chlorodendrophycea). The antioxidant properties were screened by the use of in vitro assays, namely 2,2-difenil-1-picrylhydrazyl, Ferric reducing antioxidant power, and Ferrous ions chelating activity, and compoundidentification was carried out in methanol and acetone extracts of both dried and fresh microalgae biomass by HPLC–PDA–MS analysis. Among the investigated microalgae, Phaedactylium tricornutum was the richest one regarding its carotenoid (especially all-E-fucoxanthin) and phenolic (especially protocatechuic acid) contents, as well as antioxidant activity (65.5%), followed by Nannochloris sp, Tetraselmis suicica, and Nannochloropsis gaditana, with antioxidant activity of 56.8%, 54.9%, and 51.1%, respectively.
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Affiliation(s)
- Imane Haoujar
- Laboratory of Microbiology and Applied Biotechnology, Department of Biology, Faculty of Sciences of Tetouan, Abd Al-Malek Essaadi University, Tetouan 93000, Morocco; (J.A.); (A.K.); (N.S.S.)
- Correspondence: (I.H.); (F.C.); Tel.: +21-262-422-8056 (I.H.); +39-090-676-6570 (F.C.)
| | - Francesco Cacciola
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98166 Messina, Italy;
- Correspondence: (I.H.); (F.C.); Tel.: +21-262-422-8056 (I.H.); +39-090-676-6570 (F.C.)
| | - Jamal Abrini
- Laboratory of Microbiology and Applied Biotechnology, Department of Biology, Faculty of Sciences of Tetouan, Abd Al-Malek Essaadi University, Tetouan 93000, Morocco; (J.A.); (A.K.); (N.S.S.)
| | - Domenica Mangraviti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (D.M.); (Y.O.E.M.); (M.F.T.); (L.M.)
| | - Daniele Giuffrida
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98166 Messina, Italy;
| | - Yassine Oulad El Majdoub
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (D.M.); (Y.O.E.M.); (M.F.T.); (L.M.)
- Laboratory of Plant Biotechnologies and Molecular Biology, Department of Biology, Faculty of Sciences of Meknes, Moulay Ismail University, Meknes 50000, Morocco
| | - Ayoub Kounnoun
- Laboratory of Microbiology and Applied Biotechnology, Department of Biology, Faculty of Sciences of Tetouan, Abd Al-Malek Essaadi University, Tetouan 93000, Morocco; (J.A.); (A.K.); (N.S.S.)
| | - Natalizia Miceli
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (D.M.); (Y.O.E.M.); (M.F.T.); (L.M.)
| | - Maria Fernanda Taviano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (D.M.); (Y.O.E.M.); (M.F.T.); (L.M.)
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy; (D.M.); (Y.O.E.M.); (M.F.T.); (L.M.)
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy;
- Unit of Food Science and Nutrition, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
- BeSeps.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy
| | - Francesca Rigano
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy;
| | - Nadia Skali Senhaji
- Laboratory of Microbiology and Applied Biotechnology, Department of Biology, Faculty of Sciences of Tetouan, Abd Al-Malek Essaadi University, Tetouan 93000, Morocco; (J.A.); (A.K.); (N.S.S.)
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Eland LE, Davenport RJ, Santos ABD, Mota Filho CR. Molecular evaluation of microalgal communities in full-scale waste stabilisation ponds. ENVIRONMENTAL TECHNOLOGY 2019; 40:1969-1976. [PMID: 29400147 DOI: 10.1080/09593330.2018.1435730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/25/2018] [Indexed: 06/07/2023]
Abstract
Waste stabilisation ponds (WSPs) are widely used across the world as a passive wastewater treatment for domestic wastewaters, but little is known about their ecology, especially their phototrophic communities. This study uses molecular methods and flow cytometry to assess the cyanobacterial and eukaryotic communities longitudinally throughout two systems, one treating domestic wastewater and the other mixed industrial/domestic wastewaters. More variation was seen between the systems than between different stages in the treatment processes for both eukaryotic and cyanobacterial communities. Chlorella species and Planktophrix cyanobacteria dominated both treatment systems. Arthrospira cyanobacteria were detected only in the industrial/domestic system. The balance between non-photosynthetic and photosynthetic organisms is rarely considered, though both play vital roles in WSP functioning. Flow cytometry showed that the facultative and first maturation pond in the industrial system contained a lower proportion of photosynthetic organisms compared to the domestic system. This is reflected in the species richness data and low dissolved oxygen levels detected. All data indicated that both systems are significantly different from one another and that variation longitudinally throughout the systems is lower. A more systematic study is needed to determine if it is the wastewater source rather than the initial inoculum that drives community composition.
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Affiliation(s)
- Lucy E Eland
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
| | - Russell J Davenport
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
| | - Andre Bezerra Dos Santos
- b Departamento de Engenharia Hidráulica e Ambiental , Universidade Federal do Ceará , Fortaleza , Brazil
| | - Cesar R Mota Filho
- a School of Civil Engineering and Geosciences, Newcastle University , Newcastle-upon-Tyne , UK
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30
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Duan S, Zhou X, Xiao H, Miao J, Zhao L. Characterization of Bacterial Microbiota in Tilapia Fillets Under Different Storage Temperatures. J Food Sci 2019; 84:1487-1493. [PMID: 31066925 DOI: 10.1111/1750-3841.14630] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 11/30/2022]
Abstract
This paper investigates the bacterial microbiota in tilapia fillets under cold (4 °C), iced (0 °C), and superchilled (-3 °C) storage conditions. At 4 °C, at least seven species/strains of Pseudomonas were detected in the fillets, five of which were dominant either at a certain stage or throughout the entire storage period. Shewanella was less dominant than Pseudomonas at 4 °C, while Serratia became dominant after 6 days storage at 4 °C. The microbiota in fillets stored at 0 and -3 °C were very similar and rarely changed during storage, yet differed greatly from the microbiota at 4 °C. Only two Pseudomonas species/strains grew at 0 and -3 °C, one of which was the most dominant. A Vibrionimonas sp. not found at 4 °C was found to be the second most dominant species at 0 and -3 °C. Shewanella and Psychrobacter were also present at 0 and -3 °C but were the minor genera. The most dominant strains at -3, 0, and 4 °C were separately isolated and subjected to full length 16S rDNA sequencing, which demonstrated that they were identical and were Pseudomonas fluorescens. The changes of the total bacterial count and TVBN value of the fillets inoculated with the isolated P. fluorescens were very similar to those of fillets with natural microbiota. This implies that P. fluorescens is the most important spoiler of tilapia fillets at -3, 0, or 4 °C. PRACTICAL APPLICATION: This research shows that fewer species of bacteria survive at 0 and -3 °C than those at 4 °C, while among these bacteria, the most important spoiler is P. fluorescens. This may provide some clues to extend the shelf life of tilapia fillets by taking some inhibitory measures targeted at P. fluorescens in the future.
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Affiliation(s)
- Shan Duan
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
| | - Xingzhi Zhou
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,CapitalBio Genomics Co., Ltd. Building 11, Dongguan-Taiwan Bio-Tech Collaboration Incubation Center, Dongguan, 523808, China
| | - Hang Xiao
- Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
| | - Jianyin Miao
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China
| | - Lei Zhao
- College of Food Science, South China Agricultural Univ., Guangzhou, 510642, China.,Dept. of Food Science, Univ. of Massachusetts, Amherst, MA, 01003, U.S.A
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31
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Yu H, Kim J, Lee C. Potential of mixed-culture microalgae enriched from aerobic and anaerobic sludges for nutrient removal and biomass production from anaerobic effluents. BIORESOURCE TECHNOLOGY 2019; 280:325-336. [PMID: 30780092 DOI: 10.1016/j.biortech.2019.02.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
This study examines the potential of the mixed-culture microalgal consortia enriched from aerobic sludge (AeS) and anaerobic sludge (AnS) with regard to nutrient removal and biomass production from four different anaerobic digestion (AD) effluents. Both the inocula achieved the complete removal of the NH4+-N (initial concentration of 40 mg/L) within 14 days from all the effluents. The AeS cultures showed faster and greater microalgal growth, although the NH4+-N removal rate was comparable or higher in the case of the AnS cultures. Further, the AeS and AnS cultures showed significantly different lipid production characteristics in terms of the fatty acid composition and the response to nitrogen deficiency. Nitrogen starvation caused changes in the microbial community structures in all the experimental cultures, which may have influenced the lipid metabolism and the microalgal growth. The overall results suggest that both the inocula exhibit good potential with regard to the treatment of AD effluents.
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Affiliation(s)
- Hyeonjung Yu
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Jaai Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea.
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Paches M, Aguado D, Martínez-Guijarro R, Romero I. Long-term study of seasonal changes in phytoplankton community structure in the western Mediterranean (Valencian Community). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:14266-14276. [PMID: 30864033 DOI: 10.1007/s11356-019-04660-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Ecosystem-based management is one of the strategies to protect the coastal areas. One of the key elements is phytoplankton community composition since it represents a good indicator of anthropogenic pressures. This identifies the seasonal patterns of phytoplankton, and its alterations by the stress factors induced by human activities are highly valuable. This research represents the first attempt to study that 476 km of western Mediterranean coastal belongs to the Valencian Community (Spain) based on the phytoplankton composition approach. The water samples during a 5-year period (6757 water samples) were taken to determine its phytoplankton group's dynamics and its relationship with anthropogenic stressors by means of a series of plots and statistical analyses. Diatoms are the group that most contribute to the whole community composition with two periods of maximum abundance. The Prasinophyceae and Cryptophyceae show unimodal patterns varying its maximum values depending on the season. The picocyanobacteria group exhibited the clearest and best-defined pattern. Other groups have no clear seasonal pattern and become abundant in areas of higher anthropogenic pressure. Graphical abstract Figure A contains poor quality of text in image. Otherwise, please provide replacement figure file.A new graphical abstract, with higher quality is attached.
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Affiliation(s)
- Maria Paches
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain.
| | - Daniel Aguado
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
| | | | - Inmaculada Romero
- IIAMA, Universitat Politècnica de València, Camí de Vera s/n, 46022, Valencia, Spain
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Jeon BS, Park MG. Tuberlatum coatsi gen. n., sp. n. (Alveolata, Perkinsozoa), a New Parasitoid with Short Germ Tubes Infecting Marine Dinoflagellates. Protist 2019; 170:82-103. [DOI: 10.1016/j.protis.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/15/2018] [Indexed: 11/28/2022]
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Cennamo P, Pasquino N, Guarino V, Morra V, Giorgio A, Caputo P, Moretti A. Use of high-strength electromagnetic radiation to remove phototrophic biofilms from terracotta artifacts. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29654-29662. [PMID: 30144008 DOI: 10.1007/s11356-018-2946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
A novel technique, effective in eliminating biodeteriogens from biofilms encrusting terracotta artifacts, is presented here. This method is based on the use of high-strength electromagnetic radiation (EMR) in the radiofrequency band. Shards of terracotta from historical pots at the Botanical Garden of Naples, Italy, were used. The shards, after sterilization, were inoculated with several phototrophic microorganisms previously isolated from whole terracotta pots. The newly formed biofilms were exposed to EMR amplitude modulated by a train of rectangular pulses with Tr = 200 ns repetition time and 10% duty cycle. The exposure protocol consisted of three applications of 2 h each, every other day. Denaturing gradient gel electrophoresis analyses conducted on the newly formed biofilms showed that, after the first exposure to EMR, all species in the biofilms but one were still alive. The second exposure resulted in the disappearance of 9 out of 13 species that were initially present on the samples. After the third exposure, all species disappeared. Superficial layers of terracotta from the exposed samples, transferred to a culture medium at 24 °C for 72 h, did not show any re-growing of organisms. Petrographic analyses of the sampleswere carried out before and after the treatments; they showed that exposure to EMR did not cause structural alterations in the treated substrates. Moreover, the amplitude of the EMR that samples were exposed to was not high enough to cause any significant increase in the temperature of the substrates; that is, no thermal effect, which is the most relevant effect when matter or organisms containing water are exposed to EMR, was observed. Finally, the field strength of the EMR showed to be non-invasive for the artifacts and non-dangerous for operators and the environment as compared to other techniques adopted in the field of conservation of cultural heritage.
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Affiliation(s)
- Paola Cennamo
- Facoltà di Lettere, Università Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy.
| | - Nicola Pasquino
- Dipartimento di Ingegneria Elettrica e delle Tecnologie dell'Informazione, Università di Napoli Federico II, Via Claudio 21, 80125, Naples, Italy
| | - Vincenza Guarino
- Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Ed. L, Via Cinthia 26, 80126, Naples, Italy
| | - Vincenzo Morra
- Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Ed. L, Via Cinthia 26, 80126, Naples, Italy
| | - Antonella Giorgio
- Dipartimento di Biologia, Università di Napoli Federico II, Via Foria 223, 80139, Naples, Italy
| | - Paolo Caputo
- Dipartimento di Biologia and Orto Botanico di Napoli, Università di Napoli Federico II, Via Foria 223, 80139, Naples, Italy
| | - Aldo Moretti
- Dipartimento di Biologia, Università di Napoli Federico II, Via Foria 223, 80139, Naples, Italy
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Mucko M, Bosak S, Casotti R, Balestra C, Ljubešić Z. Winter picoplankton diversity in an oligotrophic marginal sea. Mar Genomics 2018; 42:14-24. [PMID: 30249373 DOI: 10.1016/j.margen.2018.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 01/01/2023]
Abstract
Marine picoplankton, unicellular organisms with cell sizes up to 3 μm in diameter, numerically dominate marine ecosystems, encompassing Archaea, Bacteria, Eukarya (protists and fungi) as well as viruses. Autotrophic and heterotrophic picoplankton abundance and community composition with a focus on picoeukaryotes (PEs) were investigated in the winter of 2016 at three stations along a coast-to-offshore transect in the southern Adriatic Sea. Abundances were estimated by flow cytometry, while community composition by Illumina High-Throughput Sequencing (HTS) of 16S and 18S rRNA genes. The photosynthetic picoplankton diversity was also investigated by High-Performance Liquid Chromatography (HPLC) of liposoluble pigments. Heterotrophic bacteria and cyanobacteria (Prochlorococcus and Synechococcus) accounted for up to 7 × 105; 2.3 × 104 and 2.5 × 104 cells mL-1, respectively, while photosynthetic picoeukaryotes peaked with 3 × 103 cells mL-1. Prokaryotes, as revealed by HTS were dominated by Alphaproteobacteria (mainly SAR11, 44.91% of total 16S sequence reads), followed by Gammaproteobacteria (Oceanospirillales and Pseudomonadales, 14.96%), Bacteroidetes (mainly Flavobacteriales, 13%), Cyanobacteria (Prochlorococcus and Synechococcus, 9.52%), Marinimicrobia (SAR406, 7.97%), Deltaproteobacteria (SAR324, 3.83%), Actinobacteria (2.24%) and Chloroflexi (SAR202, 1.90%). Photosynthetic pigment concentrations were very low (12.12 μgL-1 at the most) and taxonomic pigments could be attributed to Prochlorococcus, Synechococcus, Prymnesiophyceae, Bacillariophyceae, Chrysophyceae, and Prasinophyceae. HTS data revealed that PEs were dominated by heterotrophs, such as Syndiniophyceae, parasitic dinoflagellates (79.67% of total 18S sequence reads), Dinophyceae (8.7%) and the radiolarians Collodaria belonging to Sphaerozoidae (22.1%) and Spumellaria (5.0%). On the other hand, photoautotrophs, including Chlorophyta (Mamiellophyceae, Prasinophyceae, Trebouxiophyceae, and Ulvophyceae), Stramenopiles (Bacillariophyta, Chrysophyceae, Dictyochophyceae, Pelagophyceae), photoautotrophic Cryptophyta and some Haptophyta (Prymnesiophyceae), did not exceed 5% of total sequence reads. This study provides the first snapshot of the PEs diversity in oligotrophic euphotic waters of the southern Adriatic Sea, hence setting the stage for large-scale surveying and characterization of the eukaryotic diversity in the entire basin.
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Affiliation(s)
- Maja Mucko
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Sunčica Bosak
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Raffaella Casotti
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121 Naples, Italy
| | - Cecilia Balestra
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121 Naples, Italy
| | - Zrinka Ljubešić
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, 10000 Zagreb, Croatia.
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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Wang Y, Shi T, Huang G, Gong J. Molecular Detection of Eukaryotic Diets and Gut Mycobiomes in Two Marine Sediment-Dwelling Worms, Sipunculus nudus and Urechis unicinctus. Microbes Environ 2018; 33:290-300. [PMID: 30146540 PMCID: PMC6167119 DOI: 10.1264/jsme2.me18065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The present study aimed to reveal the eukaryotic diets of two economically important marine sediment-inhabiting worms, Sipunculus nudus (peanut worm) and Urechis unicinctus (spoon worm), using clone libraries and phylogenetic analyses of 18S rRNA genes. Fungal rDNA was also targeted and analyzed to reveal mycobiomes. Overall, we detected a wide range of eukaryotic phylotypes associated with the larvae of S. nudus and in the gut contents of both worms. These phylotypes included ciliates, diatoms, dinoflagellates, eustigmatophytes, placidids, oomycetes, fungi, nematodes, flatworms, seaweeds, and higher plants. Oomycetes were associated with the planktonic larvae of S. nudus. The composition of eukaryotic diets shifted greatly across the larval, juvenile, and adult stages of S. nudus, and among different gut sections in U. unicinctus, reflecting lifestyle changes during the ontogeny of the peanut worm and progressive digestion in the spoon worm. Malassezia-like fungi were prevalent in mycobiomes. Epicoccum and Trichosporon-related phylotypes dominated mycobiomes associated with larval individuals and in the gut contents of adults, respectively. The gut mycobiome of S. nudus was successively characterized through the midgut, aspiratory intestines, hindgut, and rectum as having a high proportion of Climacodon-Rhizochaete, Ceriporiopsis, Cladosporium-Pseudomicrostroma, and Malassezia-related species in the libraries. These results emphasize the dynamics of diets and gut mycobiomes in marine benthic animals.
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Affiliation(s)
- Yaping Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Tiantian Shi
- School of Life Sciences, South China Normal University
| | | | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences.,School of Marine Sciences, Sun Yat-sen University
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Segawa T, Matsuzaki R, Takeuchi N, Akiyoshi A, Navarro F, Sugiyama S, Yonezawa T, Mori H. Bipolar dispersal of red-snow algae. Nat Commun 2018; 9:3094. [PMID: 30082897 PMCID: PMC6079020 DOI: 10.1038/s41467-018-05521-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/19/2018] [Indexed: 11/25/2022] Open
Abstract
Red-snow algae are red-pigmented unicellular algae that appear seasonally on the surface of thawing snow worldwide. Here, we analyse the distribution patterns of snow algae sampled from glaciers and snow patches in the Arctic and Antarctica based on nuclear ITS2 sequences, which evolve rapidly. The number of phylotypes is limited in both polar regions, and most are specific to either the Arctic or Antarctica. However, the bipolar phylotypes account for the largest share (37.3%) of all sequences, suggesting that red-algal blooms in polar regions may comprise mainly cosmopolitan phylotypes but also include endemic organisms, which are distributed either in the Arctic or Antarctica. Red-snow algae are red-pigmented unicellular algae that appear seasonally on the surface of thawing snow worldwide. Here, Segawa et al. analyse nuclear ITS2 sequences from snow algae from the Arctic and Antarctica, identifying dominant phylotypes present in both poles as well as endemic organisms.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 409-3898, 1000 Shimokato, Chuo, Yamanashi, Japan. .,National Institute of Polar Research, 10-3 Midori-cho, Tachikawa, Tokyo, Japan.
| | - Ryo Matsuzaki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan
| | - Ayumi Akiyoshi
- National Institute of Polar Research, 10-3 Midori-cho, Tachikawa, Tokyo, Japan
| | - Francisco Navarro
- Departamento de Matemática Aplicada a las Tecnologías de la Información y las Comunicaciones, ETSI de Telecomunicación, Universidad Politécnica de Madrid, Av. Complutense, 30, 28040, Madrid, Spain
| | - Shin Sugiyama
- Institute of Low Temperature Science, Hokkaido University, Nishi8, Kita19, Sapporo, Japan
| | - Takahiro Yonezawa
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, Japan.,School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai, 200438, China
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
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Parladé E, Hom-Diaz A, Blánquez P, Martínez-Alonso M, Vicent T, Gaju N. Effect of cultivation conditions on β-estradiol removal in laboratory and pilot-plant photobioreactors by an algal-bacterial consortium treating urban wastewater. WATER RESEARCH 2018; 137:86-96. [PMID: 29544206 DOI: 10.1016/j.watres.2018.02.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/09/2018] [Accepted: 02/24/2018] [Indexed: 06/08/2023]
Abstract
The use of microalgal consortia for urban wastewater treatment is an increasing trend, as it allows simultaneous nutrient removal and biomass production. Emerging contaminants proposed for the list of priority substances such as the hormone 17β-estradiol are commonly found in urban wastewater, and their removal using algal monocultures has been accomplished. Due to the inherent potential of algae-based systems, this study aimed to assess the capability of native photobioreactor biomass to remove 17β-estradiol under indoor and outdoor conditions. At the same time, the microbial community changes in regular and bioaugmented operations with Scenedesmus were assessed. The results show that almost complete removal (>93.75%) of the hormone 17β-estradiol can be attained in the system under favourable seasonal conditions, although these conditions greatly influence biomass concentrations and microbial diversity. Even under the harsh conditions of low temperatures and solar irradiation, the established consortium removed more than 50% of the pollutant in 24 h. While species from genus Chlorella were stable during the entire operation, the microbial diversity analysis revealed that assorted and evenly distributed populations stimulate the removal rates. Bioaugmentation assays proved that the input of additional biomass results in higher overall removal and decreases the yield per mg of biomass.
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Affiliation(s)
- Eloi Parladé
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Andrea Hom-Diaz
- Chemical, Biological and Environmental Engineering Department, Escola d'Enginyeria, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Chemical, Biological and Environmental Engineering Department, Escola d'Enginyeria, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain.
| | - Maira Martínez-Alonso
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Teresa Vicent
- Chemical, Biological and Environmental Engineering Department, Escola d'Enginyeria, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Nuria Gaju
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
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Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers. World J Microbiol Biotechnol 2018; 34:69. [DOI: 10.1007/s11274-018-2452-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 04/24/2018] [Indexed: 11/27/2022]
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Wang Y, Gong Y, Dai L, Sommerfeld M, Zhang C, Hu Q. Identification of harmful protozoa in outdoor cultivation of Chlorella and the use of ultrasonication to control contamination. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Karabey B, Eroglu D, Vural C, Ozdemir G, Yerlikaya O, Kinik O. Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2018; 55:956-963. [PMID: 29487437 DOI: 10.1007/s13197-017-3003-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/16/2017] [Accepted: 12/18/2017] [Indexed: 10/18/2022]
Abstract
In this study, it was aimed to determine microbial flora members in three traditional Tulum cheeses (C1, C2 and C3) produced in different villages and settlement areas in İzmir, Turkey. For this purpose, culture depended and 16S rRNA based culture independent methods were used. According to the results of culture depended method, Lactococcus spp., Enterococcus spp., Staphylococcus spp., Lactobacillus spp., Pediococcus spp. and yeast-mold were detected in all samples at different levels. In order to determine and identify both of the culturable and non-culturable microorganisms, denaturing gradient gel electrophoresis (DGGE) method was used. DGGE results have shown that there were eight different dominant microorganisms (Streptococcus thermophilus, Lactococcus lactis subs. lactis, Streptococcus infantarius subs. infantarius, Lactobacillus gallinarum, Streptococcus equinus, Enterococcus faecalis, Enterococcus faecium, Lactococcus garvieae) in three regionally cheese samples. Further more, total bacterial loads were monitored with real-time PCR (qPCR) method. According to the results, 3.5 × 108, 3.8 × 108, 8.4 × 108 copy number of DNA was detected in C1, C2 and C3 cheese samples, respectively. This study is the first description for the dynamics of microbial composition of Izmir Tulum cheese after the production and brining processes.
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Affiliation(s)
- Burcin Karabey
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Didem Eroglu
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Caner Vural
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Guven Ozdemir
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Oktay Yerlikaya
- 2Department of Dair Technology, Faculty of Agriculture, Ege University, Bornova, Izmir, Turkey
| | - Ozer Kinik
- 2Department of Dair Technology, Faculty of Agriculture, Ege University, Bornova, Izmir, Turkey
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Thongsripong P, Chandler JA, Green AB, Kittayapong P, Wilcox BA, Kapan DD, Bennett SN. Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases. Ecol Evol 2018; 8:1352-1368. [PMID: 29375803 PMCID: PMC5773340 DOI: 10.1002/ece3.3676] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/23/2017] [Accepted: 11/03/2017] [Indexed: 01/01/2023] Open
Abstract
Vector-borne diseases are a major health burden, yet factors affecting their spread are only partially understood. For example, microbial symbionts can impact mosquito reproduction, survival, and vectorial capacity, and hence affect disease transmission. Nonetheless, current knowledge of mosquito-associated microbial communities is limited. To characterize the bacterial and eukaryotic microbial communities of multiple vector species collected from different habitat types in disease endemic areas, we employed next-generation 454 pyrosequencing of 16S and 18S rRNA amplicon libraries, also known as metabarcoding. We investigated pooled whole adult mosquitoes of three medically important vectors, Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus, collected from different habitats across central Thailand where we previously characterized mosquito diversity. Our results indicate that diversity within the mosquito microbiota is low, with the majority of microbes assigned to one or a few taxa. Two of the most common eukaryotic and bacterial genera recovered (Ascogregarina and Wolbachia, respectively) are known mosquito endosymbionts with potentially parasitic and long evolutionary relationships with their hosts. Patterns of microbial composition and diversity appeared to differ by both vector species and habitat for a given species, although high variability between samples suggests a strong stochastic element to microbiota assembly. In general, our findings suggest that multiple factors, such as habitat condition and mosquito species identity, may influence overall microbial community composition, and thus provide a basis for further investigations into the interactions between vectors, their microbial communities, and human-impacted landscapes that may ultimately affect vector-borne disease risk.
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Affiliation(s)
- Panpim Thongsripong
- Department of MicrobiologyInstitute of Biodiversity Sciences and SustainabilityCalifornia Academy of SciencesSan FranciscoCAUSA
- Department of Tropical MedicineMedical Microbiology, and PharmacologyUniversity of Hawai'i at ManoaHonoluluHIUSA
- Present address:
Department of Tropical MedicineTulane UniversityNew OrleansLAUSA
| | - James Angus Chandler
- Department of MicrobiologyInstitute of Biodiversity Sciences and SustainabilityCalifornia Academy of SciencesSan FranciscoCAUSA
- Present address:
Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Amy B. Green
- Department of MicrobiologyUniversity of Hawai'i at ManoaHonoluluHIUSA
| | - Pattamaporn Kittayapong
- Center of Excellence for Vectors and Vector‐Borne Diseases and Department of BiologyFaculty of ScienceMahidol University at SalayaNakhon PathomThailand
| | - Bruce A. Wilcox
- Global Health Asia and Integrative Research and Education ProgramFaculty of Public HealthMahidol UniversityBangkokThailand
| | - Durrell D. Kapan
- Department of Entomology and Center for Comparative GenomicsInstitute of Biodiversity Sciences and SustainabilityCalifornia Academy of SciencesSan FranciscoCAUSA
- Center for Conservation and Research TrainingPacific Biosciences Research CenterUniversity of Hawai'i at ManoaHonoluluHIUSA
| | - Shannon N. Bennett
- Department of MicrobiologyInstitute of Biodiversity Sciences and SustainabilityCalifornia Academy of SciencesSan FranciscoCAUSA
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Milanez GD, Masangkay FR, Thomas RC, Ordona MOGO, Bernales GQ, Corpuz VCM, Fortes HSV, Garcia CMS, Nicolas LC, Nissapatorn V. Molecular identification of Vermamoeba vermiformis from freshwater fish in lake Taal, Philippines. Exp Parasitol 2017; 183:201-206. [DOI: 10.1016/j.exppara.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 11/28/2022]
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Tan S, Liu H. Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA. Appl Microbiol Biotechnol 2017; 102:389-401. [PMID: 29080999 DOI: 10.1007/s00253-017-8565-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 11/28/2022]
Abstract
Planktonic protists, including both autotroph and heterotroph, have been recognized as a major contributor to primary production and consumers of bacteria, archaea and picophytoplankton. However, the understanding of protistan diversity is typically impeded by the large amount of metazoans when employing universal primers to environmental samples. In this study, we developed 3 blocking primers to inhibit the amplification of metazoan DNA in PCR. First, we optimized the design and concentration of blocking primers by using 2 metazoans and 3 protists in quantitative PCR. No significant difference (q > 0.05) was found in protistan community structure at phylum, family or OTU levels and genetic diversity between samples amplified with and without adding blocking primers, indicating that the blocking primer does not alter the composition of protistan community. An application to samples with a high abundance of metazoans showed that the blocking primer can reduce 42.1-72.4% of metazoan sequences, resulting the retrieval of a higher protistan richness and diversity. The use of the blocking primer helped to identify protistan community composition from a large size fraction, which is usually dominated by metazoans. Protistan community from the small (0.2-10 μm) and large (> 10 μm) size fractions exhibited a low similarity of 36.6% and shared 14.7% OTUs. About 63.8% of the OTUs were unique to the large fraction. Species from groups, such as Lepidodinium, Warnowia, Kareniaceae, Torodiniales, Phaeocystis, Chrysochromulina and Chrysophyceae, were enriched in the large fraction, indicating that they could be largely underestimated in studies that exclude the large-sized cells. Blocking primers are a promising tool to increase the efficiency for the characterization of protistan diversity in aquatic planktonic ecosystems.
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Affiliation(s)
- Shangjin Tan
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China.
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Li WT, Lo C, Su CY, Kuo H, Lin SJH, Chang HW, Pang VF, Jeng CR. Locally extensive meningoencephalitis caused by Miamiensis avidus (syn. Philasterides dicentrarchi) in a zebra shark. DISEASES OF AQUATIC ORGANISMS 2017; 126:167-172. [PMID: 29044046 DOI: 10.3354/dao03166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Scuticociliatosis, caused by ciliated protozoa in the subclass Scuticociliatia of the phylum Ciliophora, can cause fatal disease in teleost fish species. However, information on scuticociliatosis in elasmobranchs is still scarce. In this report, we describe a case of locally extensive meningoencephalitis caused by Miamiensis avidus (syn. Philasterides dicentrarchi) in a 2 yr old captive zebra shark Stegostoma fasciatum. Granulocytic meningoencephalitis was observed through histological assessment. Inflammation was confined to the ventral aspect of the brain with a large number of ciliated protozoa, transforming into non-suppurative meningitis in the lateral aspect, and gradually vanished in the dorsal aspect. No histopathological and polymerase chain reaction (PCR) evidence of systemic dissemination of M. avidus was found. PCR targeting the gene coding the small-subunit ribosomal RNA (SSUrRNA) of M. avidus was performed on the brain, liver, and gill tissues, and only brain tissue yielded a positive result. The DNA sequences from amplicons of the protozoal SSUrRNA gene were completely matched to that of M. avidus. The distribution of protozoa in the current case was mainly located in the brain and suggests the possibility of a direct neural invasive pathway of M. avidus through the nasal cavity/ampullary system and/or a unique tissue tropism of M. avidus specific to the brain in zebra sharks. Further investigations on the pathogenesis of M. avidus in elasmobranchs, especially zebra sharks, are needed.
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Affiliation(s)
- Wen-Ta Li
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei 10617, Taiwan, ROC
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Mäki A, Salmi P, Mikkonen A, Kremp A, Tiirola M. Sample Preservation, DNA or RNA Extraction and Data Analysis for High-Throughput Phytoplankton Community Sequencing. Front Microbiol 2017; 8:1848. [PMID: 29018424 PMCID: PMC5622927 DOI: 10.3389/fmicb.2017.01848] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022] Open
Abstract
Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affected the results of the NGS analysis. A mock community was pooled from phytoplankton species with variation in nucleus size and cell wall hardness. Although the study showed potential for studying Lugol-preserved sample collections, it demonstrated critical challenges in the DNA-based phytoplankton analysis in overall. The 18S rRNA gene sequencing output was highly affected by the variation in the rRNA gene copy numbers per cell, while sample preservation and nucleic acid extraction methods formed another source of variation. At the top, sequence-specific variation in the data quality introduced unexpected bioinformatics bias when the sliding-window method was used for the quality trimming of the Ion Torrent data. While DNA-based analyses did not correlate with biomasses or cell numbers of the mock community, rRNA-based analyses were less affected by different RNA extraction procedures and had better match with the biomasses, dry weight and carbon contents, and are therefore recommended for quantitative phytoplankton analyses.
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Affiliation(s)
- Anita Mäki
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Pauliina Salmi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anu Mikkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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Granada‐Moreno C, Aburto‐Medina A, los Cobos Vasconcelos D, González‐Sánchez A. Microalgae community shifts during the biogas upgrading in an alkaline open photobioreactor. J Appl Microbiol 2017; 123:903-915. [DOI: 10.1111/jam.13552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/11/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022]
Affiliation(s)
- C.I. Granada‐Moreno
- Coordinación de Ingeniería Ambiental Instituto de Ingeniería UNAM Circuito Escolar Ciudad Universitaria Mexico City Mexico
| | - A. Aburto‐Medina
- Centre for Environmental Sustainability and Remediation School of Applied Sciences RMIT University Bundoora Vic. Australia
- Instituto Tecnológico y de Estudios Superiores de Monterrey Puebla México
| | - D. los Cobos Vasconcelos
- Coordinación de Ingeniería Ambiental Instituto de Ingeniería UNAM Circuito Escolar Ciudad Universitaria Mexico City Mexico
| | - A. González‐Sánchez
- Coordinación de Ingeniería Ambiental Instituto de Ingeniería UNAM Circuito Escolar Ciudad Universitaria Mexico City Mexico
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Changes of Scots Pine Phyllosphere and Soil Fungal Communities during Outbreaks of Defoliating Insects. FORESTS 2017. [DOI: 10.3390/f8090316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Lara E, Fernández LD, Schiaffino MR, Izaguirre I. First freshwater member ever reported for the family Bathycoccaceae (Chlorophyta; Archaeplastida) from Argentinean Patagonia revealed by environmental DNA survey. Eur J Protistol 2017; 60:45-49. [DOI: 10.1016/j.ejop.2017.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/31/2017] [Indexed: 01/08/2023]
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