DOCSLIB.ORG

Downloaded on 2017-02-12T13:45:47Z

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Downloaded on 2017-02-12T13:45:47Z Title Exploiting the diverse microbial ecology of marine sponges Author(s) Jackson, Stephen A. Publication date 2013 Original citation Jackson, S. A. 2013. Exploiting the diverse microbial ecology of marine sponges. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2013, Stephen A. Jackson http://creativecommons.org/licenses/by-nc-nd/3.0/ Embargo information Restricted to everyone for three years Item downloaded http://hdl.handle.net/10468/1037 from Downloaded on 2017-02-12T13:45:47Z Exploiting the Diverse Microbial Ecology of Marine Sponges A Thesis presented to the National University of Ireland for the Degree of Doctor of Philosophy Stephen Anthony Jackson, BSc. Department of Microbiology National University of Ireland Cork Head of Department: Dr Gerald Fitzgerald Research Supervisors: Prof. Alan Dobson & Dr John Morrissey 2013 1 For Daniel, My inspiration 2 Index 1 Abstract 7 Chapter 1: Literature Review 10 1.1 Marine sponges 11 1.1.1 Sponge anatomy and physiology 12 1.1.1.1 Sponge skeletons 12 1.1.1.2 Sponge cell types 13 1.1.1.3 Sponge physiology 14 1.2 Sponge associated microorganisms 15 1.2.1 Sponge associated bacteria 15 1.2.1.1 Culture dependent analyses 15 1.2.1.2 Culture independent analyses 16 1.2.1.2.1 Microscopy 16 1.2.1.2.2 16S rRNA clone libraries 18 1.2.1.2.3 Pyrosequencing 20 1.2.2 Sponge associated archaea 22 1.2.3 Sponge associated eukaryota 22 1.2.3.1 Sponge associated fungi 22 1.2.3.2 Sponge associated diatoms 23 1.2.3.3 Sponge associated dinoflagellates 23 1.2.3.4 Other sponge associated eukaryota 24 1.2.4 Sponge-specific microorganisms 24 1.3 Symbiotic functions of sponge associated microbes 27 1.3.1 Methods to elucidate sponge symbiont functions 27 1.3.2 Discrimination between food microbes and symbiotic microbes 28 1.3.3 Nutrient cycling in sponges 29 1.3.3.1 Carbon cycling 29 1.3.3.2 Nitrogen cycling 30 1.3.3.2.1 Nitrogen fixation 30 1.3.3.2.2 Nitrification 31 1.3.3.2.3 Denitrification 32 1.3.3.3 Sulphur cycling 33 1 1.3.4 Other putative symbiosis factors 36 1.4 Pharmacological potential of marine sponges 37 1.5 Exploiting the pharmacological potential of marine sponges 42 1.6 Metagenomic strategies for the discovery and production of novel industrial and pharmacological products 43 1.6.1 Problems associated with large insert metagenomic clone libraries 45 1.7 Summary 46 1.8 References 47 2.0 Chapter 2: Diverse and distinct sponge-specific bacterial communities in sponges from a single geographical location in Irish waters and antimicrobial activities of sponge isolates 103 2.1 Abstract 104 2.2 Introduction 105 2.3 Materials & Methods 107 2.3.1 Sponge sampling 107 2.3.2 Culture isolation 108 2.3.2.1 General isolation 108 2.3.2.2 Targeted isolation 108 2.3.3 Phylogenetic analysis of cultured isolates 110 2.3.4 Antimicrobial assays 111 2.3.5 Metagenomic DNA extraction from sponges 111 2.3.6 Metagenomic DNA extraction from seawater 111 2.3.7 PCR amplicon library preparation for pyrosequencing 112 2.3.8 Pyrosequencing data analysis 113 2.4 Results 114 2.4.1 Culture isolation 114 2.4.2 Antimicrobial assay 116 2.4.3 Pyrosequencing 119 2.5 Discussion 125 2.5.1 Isolated bacteria 125 2.5.2 Antimicrobial activities 126 2.5.3 Pyrosequencing 127 2 2.5.4 Community analysis 128 2.5.5 Sponge-specific phylotypes 130 2.5.6 Linking taxonomy to function 134 2.6 Conclusion 135 2.7 Acknowledgements 136 2.8 References 137 3.0 Chapter 3: Archaea dominate the microbial communities in the marine sponge Inflatella pellicula in the deep sea as revealed by pyrosequencing 147 3.1 Abstract 148 3.2 Introduction 148 3.3 Materials & Methods 150 3.3.1 Sampling 150 3.3.2 Metagenomic DNA extraction from sponges 151 3.3.3 Metagenomic DNA extraction from seawater 151 3.3.4 PCR amplicon library preparation for pyrosequencing 151 3.3.5 Pyrosequencing data analysis 152 3.4 Results 153 3.4.1 Sequencing 153 3.4.2 Sequence classification 154 3.4.3 Relative abundances of archaea and bacteria 154 3.4.4 Sponge and seawater from 780 m 155 3.4.5 Sponges and seawater from 2900 m 160 3.4.6 Phylogeny of clustered sponge sequences 162 3.5 Discussion 165 3.5.1 Context of this study 165 3.5.2 Archaeal relative abundance and diversity 166 3.5.3 Bacterial diversity 167 3.5.4 Functional capabilities of sponge symbionts 169 3.6 Conclusions 170 3.7 Acknowledgements 171 3.8 References 172 3 4.0 Chapter 4: ‘Mining’ the metagenomes of marine sponges 179 4.1 Abstract 180 4.2 Introduction 181 4.3 Materials & Methods 183 4.3.1 Sponge sampling 183 4.3.2 Metagenomic DNA extraction from sponges 183 4.3.3 Polymerase chain reaction 184 4.3.3.1 Polyketide synthase PCR 184 4.3.3.2 Non-ribosomal peptide synthetase PCR 184 4.3.3.3 Laccase PCR 184 4.3.4 Cloning and sequencing of PCR amplicons 185 4.3.4.1 Cloning PCR products 185 4.3.4.2 M13 PCR 185 4.3.4.3 Sequencing and analysis of cloned PCR products 186 4.3.5 Large insert metagenomic clone library construction 186 4.3.5.1 Insert preparation – DNA fractionation 186 4.3.5.2 Insert preparation 187 4.3.5.3 Vector preparation 187 4.3.5.4 Ligation, phage packaging & transfection 188 4.3.6 Clone library functional screening 189 4.3.6.1 Antimicrobial activity screening 189 4.3.6.2 Laccase activity screening 190 4.3.6.3 Lipase activity screening 190 4.3.7 Fosmid analysis 191 4.4 Results 192 4.4.1 Polyketide synthase genes 192 4.4.2 Non-ribosomal synthetase genes 194 4.4.3 Laccase genes 196 4.4.4 Functional screening of clone library 198 4.4.5 Fosmid end-sequencing 201 4.5 Discussion 202 4.5.1 PKS and NRPS 202 4.5.2 Laccase genes and clone library screening 203 4 4.6 Acknowledgements 206 4.7 References 207 5.0 Chapter 5: Maribacter spongiicola sp. nov., and Maribacter vaceletii sp. nov., isolated from marine sponges and emended description of the genus Maribacter 216 5.1 Abstract 217 5.2 Introduction 217 5.3 Materials & Methods 218 5.3.1 Sampling & culture isolation 218 5.3.2 Phylogenetic analysis 219 5.3.3 Phenotypic & biochemical characterisation 220 5.4 Results 222 5.4.1 Phylogenetic analysis 222 5.4.2 Biochemical characterisation 224 5.4.3 Phenotypic characterisation 226 5.5 Description of novel Maribacter spp. sponge isolates and emended description of the genus Maribacter 228 5.5.1 Emended description of the genus Maribacter Nedashkovskaya et al ., 2004 emend. Nedashkovskaya et al ., 2010 228 5.5.2 Description of Maribacter spongiicola sp. nov. 228 5.5.3 Description of Maribacter vaceletii sp. nov. 230 5.6 Acknowledgements 231 5.7 References 232 6.0 General discussion 239 6.1 References 250 7.0 Appendix 259 Supplementary Table S2.1 260 Supplementary Table S3.1 274 8.0 Acknowledgements 288 5 Declaration: I, the undersigned, hereby declare that the work herein is my own and that it has not been submitted for any other degree, either at University College Cork, or elsewhere. _____________________ Stephen Jackson 6 Abstract 7 Marine sponges (phylum Porifera ) are the oldest extant metazoan animals on earth today and they host large populations of symbiotic microbes: Bacteria , Archaea and unicellular Eukaryota . Those microbes play various ecological functions which are essential to the health of the host. Their functions include carbon, nitrogen and sulfur cycling as well as defence of the host through the production of bioactive secondary metabolites which protect against infection and predation. The diversity of sponge- associated microbes is remarkable with thousands of OTUs reported from individual sponge species. Amongst those populations are sponge-specific microbes which may be specific to sponges or specific to sponge species. Sponges are a source of a vast array of chemical entities with many bioactive properties of interest to industry and pharmacology. While marine natural product discovery concerns many animal phyla, Porifera account for the largest proportion of novel compounds. Evidence suggests that many of these compounds of interest are the products of symbiotic microbes. Descriptions of sponge-associated microbial community structures has been greatly advanced by the development of next-generation sequencing technologies while the discovery and exploitation of sponge derived biocatalysts and bioactive compounds has increased due to developments in sequence-based and function-based metagenomics. Here we use pyrosequencing to describe the bacterial communities associated with two shallow, temperate water sponges namely Raspailia ramosa and Stelligera stuposa from Irish coastal waters and to describe the bacterial and archaeal communities from three individuals of a single sponge species ( Inflatella pellicula ) from two different depths in cold, deep waters in the Atlantic Ocean in Irish waters, including at a depth of 2900 m, a depth far greater than that of any previous sequence-based sponge-microbe investigation. We identified diverse microbial communities in all sponges and the presence of sponge-specific taxa recruiting to previously described sponge-specific clusters and also to novel sponge-specific clusters. We also identified archaeal communities which dominated sponge-microbe communities. We demonstrate that sponge-associated microbial communities differ from ambient seawater communities indicating host selection processes.
Load more

Recommended publications
  • Taxonomy and Diversity of the Sponge Fauna from Walters Shoal, a Shallow Seamount in the Western Indian Ocean Region
    Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region By Robyn Pauline Payne A thesis submitted in partial fulfilment of the requirements for the degree of Magister Scientiae in the Department of Biodiversity and Conservation Biology, University of the Western Cape. Supervisors: Dr Toufiek Samaai Prof. Mark J. Gibbons Dr Wayne K. Florence The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed and conclusions arrived at, are those of the author and are not necessarily to be attributed to the NRF. December 2015 Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region Robyn Pauline Payne Keywords Indian Ocean Seamount Walters Shoal Sponges Taxonomy Systematics Diversity Biogeography ii Abstract Taxonomy and diversity of the sponge fauna from Walters Shoal, a shallow seamount in the Western Indian Ocean region R. P. Payne MSc Thesis, Department of Biodiversity and Conservation Biology, University of the Western Cape. Seamounts are poorly understood ubiquitous undersea features, with less than 4% sampled for scientific purposes globally. Consequently, the fauna associated with seamounts in the Indian Ocean remains largely unknown, with less than 300 species recorded. One such feature within this region is Walters Shoal, a shallow seamount located on the South Madagascar Ridge, which is situated approximately 400 nautical miles south of Madagascar and 600 nautical miles east of South Africa. Even though it penetrates the euphotic zone (summit is 15 m below the sea surface) and is protected by the Southern Indian Ocean Deep- Sea Fishers Association, there is a paucity of biodiversity and oceanographic data.
    [Show full text]
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
    [Show full text]
  • Proposal for a Revised Classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3*
    Morrow and Cárdenas Frontiers in Zoology (2015) 12:7 DOI 10.1186/s12983-015-0099-8 DEBATE Open Access Proposal for a revised classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3* Abstract Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today’s marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida).
    [Show full text]
  • Microbiome Exploration of Deep-Sea Carnivorous Cladorhizidae Sponges
    Microbiome exploration of deep-sea carnivorous Cladorhizidae sponges by Joost Theo Petra Verhoeven A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology Memorial University of Newfoundland March 2019 St. John’s, Newfoundland and Labrador ABSTRACT Members of the sponge family Cladorhizidae are unique in having replaced the typical filter-feeding strategy of sponges by a predatory lifestyle, capturing and digesting small prey. These carnivorous sponges are found in many different environments, but are particularly abundant in deep waters, where they constitute a substantial component of the benthos. Sponges are known to host a wide range of microbial associates (microbiome) important for host health, but the extent of the microbiome in carnivorous sponges has never been extensively investigated and their importance is poorly understood. In this thesis, the microbiome of two deep-sea carnivorous sponge species (Chondrocladia grandis and Cladorhiza oxeata) is investigated for the first time, leveraging recent advances in high-throughput sequencing and through custom developed bioinformatic and molecular methods. Microbiome analyses showed that the carnivorous sponges co-occur with microorganisms and large differences in the composition and type of associations were observed between sponge species. Tissues of C. grandis hosted diverse bacterial communities, similar in composition between individuals, in stark contrast to C. oxeata where low microbial diversity was found with a high host-to-host variability. In C. grandis the microbiome was not homogeneous throughout the host tissue, and significant shifts occured within community members across anatomical regions, with the enrichment of specific bacterial taxa in particular anatomical niches, indicating a potential symbiotic role of such taxa within processes like prey digestion and chemolithoautotrophy.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Identification and Characterization of a Halotolerant, Cold-Active Marine Endo–1,4-Glucanase by Using Functional Metagenomics
    Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota Marjolaine Martin, Sophie Biver, Sébastien Steels, Tristan Barbeyron, Murielle Jam, Daniel Portetelle, Gurvan Michel, Micheline Vandenbol To cite this version: Marjolaine Martin, Sophie Biver, Sébastien Steels, Tristan Barbeyron, Murielle Jam, et al.. Identi- fication and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota. Applied and Environmental Microbi- ology, American Society for Microbiology, 2014, 80 (16), pp.4958-4967. 10.1128/AEM.01194-14. hal-02138133 HAL Id: hal-02138133 https://hal.archives-ouvertes.fr/hal-02138133 Submitted on 23 May 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AEM Accepts, published online ahead of print on 6 June 2014 Appl. Environ. Microbiol. doi:10.1128/AEM.01194-14 Copyright © 2014, American Society for Microbiology. All Rights Reserved. 1 Functional screening
    [Show full text]
  • Distribution of Aerobic Anoxygenic Phototrophs in Freshwater Plateau Lakes
    Pol. J. Environ. Stud. Vol. 27, No. 2 (2018), 871-879 DOI: 10.15244/pjoes/76039 ONLINE PUBLICATION DATE: 2018-01-15 Original Research Distribution of Aerobic Anoxygenic Phototrophs in Freshwater Plateau Lakes Yingying Tian1, 2, Xingqiang Wu1*, Qichao Zhou3, Oscar Omondi Donde1, 2, 4, Cuicui Tian1, Chunbo Wang1, Bing Feng1, 2, Bangding Xiao1* 1Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, University of Chinese Academy of Sciences, Wuhan 430072, China 2University of Chinese Academy of Sciences, Beijing 100101, China 3Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Yunnan Institute of Environmental Science (Kunming China International Research Center for Plateau Lake), Kunming 650034, China 4Egerton University, Department of Environmental Science, P. O. Box 536-20115, Egerton-Kenya Received: 13 February 2017 Accepted: 23 July 2017 Abstract Aerobic anoxygenic phototrophic (AAP) bacteria are known functionally as photoheterotrophic microbes. Though numerously reported from ocean habitats, their distribution in freshwater lakes is far less documented. In the present study we investigated the dynamics of AAP bacteria in freshwater plateau lakes. Results revealed a high abundance of AAP bacteria in eutrophic lakes. Moreover, AAP bacteria were positively correlated with TN, TP, and Chl a, but the variations of AAP bacterial proportion to potential total bacteria (AAPB%). Alphaproteobacteria-related sequences dominated lakes Luguhu, Erhai, and Chenghai at ratios of 93.9, 85.4, and 70.6%, respectively, and in total comprised eight clearly defined subgroups. Sequences affiliated with Beta- and Grammaproteobacteria were found to be rare taxa. Additionally, Alkalibacterium-like sequences belonging to Firmutes were assigned.
    [Show full text]
  • Microbial Diversity in Long-Term Water-Flooded Oil Reservoirs with Different in Situ Temperatures in China
    Microbial diversity in long-term water-flooded oil reservoirs with different SUBJECT AREAS: BIODIVERSITY in situ temperatures in China MICROBIOLOGY Fan Zhang1, Yue-Hui She2,3, Lu-Jun Chai1, Ibrahim M. Banat4, Xiao-Tao Zhang1, Fu-Chang Shu2, ECOLOGY Zheng-Liang Wang2, Long-Jiang Yu3 & Du-Jie Hou1 ENVIRONMENTAL SCIENCES 1The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, China; Received School of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China, 2College of Chemistry and 1 August 2012 Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023, China, 3College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430079, China, 4School of Biomedical Sciences, University of Ulster, Accepted Coleraine, BT52 1SA, N. Ireland, UK. 27 September 2012 Published Water-flooded oil reservoirs have specific ecological environments due to continual water injection and oil 23 October 2012 production and water recycling. Using 16S rRNA gene clone library analysis, the microbial communities present in injected waters and produced waters from four typical water-flooded oil reservoirs with different in situ temperatures of 256C, 406C, 556C and 706C were examined. The results obtained showed that the Correspondence and higher the in situ temperatures of the oil reservoirs is, the less the effects of microorganisms in the injected requests for materials waters on microbial community compositions in the produced waters is. In addition, microbes inhabiting in the produced waters of the four water-flooded oil reservoirs were varied but all dominated by should be addressed to Proteobacteria. Moreover, most of the detected microbes were not identified as indigenous.
    [Show full text]
  • Imperialibacter Roseus Gen. Nov., Sp. Nov., a Novel Bacterium of the Family Flammeovirgaceae Isolated from Permian Groundwater
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4136–4140 DOI 10.1099/ijs.0.052662-0 Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater Hui Wang,1,2,3 Junde Li,1 Tianling Zheng,2 Russell T. Hill3 and Xiaoke Hu1 Correspondence 1Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Xiaoke Hu 2Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, [email protected] Xiamen University, Xiamen 361005, China 3Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1v6c/C16 : 1v7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycoli- pids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T (5CICC 10659T5KCTC 32399T). Bacteria affiliated with the family Flammeovirgaceae of the staining was performed according to the method described phylum Bacteroidetes are widely distributed in various by Gerhardt et al.
    [Show full text]
  • Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
    RESEARCH ARTICLE Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Sonja Oberbeckmann1,2,3☯, A. Mark Osborn1,2,4, Melissa B. Duhaime5☯* 1 Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom, a11111 2 School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom, 3 Environmental Microbiology Working Group, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany, 4 School of Applied Sciences, Royal Melbourne Institute of Technology University, PO Box 77, Bundoora, VIC3083, Australia, 5 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Oberbeckmann S, Osborn AM, Duhaime MB (2016) Microbes on a Bottle: Substrate, Season Abstract and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris. PLoS Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem- ONE 11(8): e0159289. doi:10.1371/journal. level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize pone.0159289 aquatic plastic debris and members of these biofilm communities are speculated to include Editor: Dee A. Carter, University of Sydney, pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing AUSTRALIA microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in Received: May 11, 2015 selecting for unique microbial communities. This work aimed to characterize microbial bio- Accepted: April 26, 2016 film communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communi- Published: August 3, 2016 ties, and identify seasonal and geographical influences on the communities.
    [Show full text]
  • An Annotated Checklist of the Marine Macroinvertebrates of Alaska David T
    NOAA Professional Paper NMFS 19 An annotated checklist of the marine macroinvertebrates of Alaska David T. Drumm • Katherine P. Maslenikov Robert Van Syoc • James W. Orr • Robert R. Lauth Duane E. Stevenson • Theodore W. Pietsch November 2016 U.S. Department of Commerce NOAA Professional Penny Pritzker Secretary of Commerce National Oceanic Papers NMFS and Atmospheric Administration Kathryn D. Sullivan Scientific Editor* Administrator Richard Langton National Marine National Marine Fisheries Service Fisheries Service Northeast Fisheries Science Center Maine Field Station Eileen Sobeck 17 Godfrey Drive, Suite 1 Assistant Administrator Orono, Maine 04473 for Fisheries Associate Editor Kathryn Dennis National Marine Fisheries Service Office of Science and Technology Economics and Social Analysis Division 1845 Wasp Blvd., Bldg. 178 Honolulu, Hawaii 96818 Managing Editor Shelley Arenas National Marine Fisheries Service Scientific Publications Office 7600 Sand Point Way NE Seattle, Washington 98115 Editorial Committee Ann C. Matarese National Marine Fisheries Service James W. Orr National Marine Fisheries Service The NOAA Professional Paper NMFS (ISSN 1931-4590) series is pub- lished by the Scientific Publications Of- *Bruce Mundy (PIFSC) was Scientific Editor during the fice, National Marine Fisheries Service, scientific editing and preparation of this report. NOAA, 7600 Sand Point Way NE, Seattle, WA 98115. The Secretary of Commerce has The NOAA Professional Paper NMFS series carries peer-reviewed, lengthy original determined that the publication of research reports, taxonomic keys, species synopses, flora and fauna studies, and data- this series is necessary in the transac- intensive reports on investigations in fishery science, engineering, and economics. tion of the public business required by law of this Department.
    [Show full text]
  • Succession and Cazyme Expression of Marine Bacterial
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Sweet and magnetic: Succession and CAZyme expression of marine bacterial communities encountering a mix of alginate and pectin particles Carina Bunse1,2,*, Hanna Koch3,4,*, Sven Breider3, Meinhard Simon1,3 and Matthias Wietz2,3# 1Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Germany 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany 3Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany 4Department of Microbiology, Radboud University Nijmegen, The Netherlands *These authors contributed equally to this work. #Corresponding author HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Am Handelshafen 12 27570 Bremerhaven Germany Email: [email protected] Telephone +49-471-48311454 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT Polysaccharide particles are an important nutrient source and microhabitat for marine bacteria. However, substrate-specific bacterial dynamics in a mixture of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed.
    [Show full text]