DOCSLIB.ORG

Rebecca Olivia Maclennan Cowie a Thesis Submitted to Victoria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Rebecca Olivia Maclennan Cowie a Thesis Submitted to Victoria BACTERIAL COMMUNITY STRUCTURE, FUNCTION AND DIVERSITY IN ANTARCTIC SEA ICE Rebecca Olivia MacLennan Cowie A thesis submitted to Victoria University of Wellington in fulfillment of the requirement for the degree of Doctor of Philosophy in Ecology & Biodiversity Victoria University of Wellington Te Whare Wananga o te Upoko o te Ika a Maui 2011 “I make no apologies for putting microorganisms on a pedestal above all other living things. For if the last blue whale choked to death on the last panda, it would be disastrous but not the end of the world. But if we accidentally poisoned the last two species of ammonia-oxidisers, that would be another matter. It could be happening now and we wouldn’t even know...” Tom Curtis (July 2006) ACKNOWLEDGEMENTS I would first like to thank my supervisors, Ken Ryan and Els Maas, for without them this thesis would not have been possible. Ken, thank you for everything! Thanks for giving me the opportunity to carry out research as part of the K043 team in Antarctica. I am grateful for the wealth of time you had for me whenever I came knocking on your door. I appreciate for your support, time and effort throughout the last three years and especially during the write-up. Els, thank you for giving so much of your time and energy towards my research. Your knowledge and advice has been invaluable. To my friends, fellow students and office mates who helped me along the way both scientifically and recreationally I thank Bionda Morelissen, Alejandra Perea Blazquez, Charles Lee, David Weller, Abi Powell, Mareike Sudek, Ingrid Knapp and Jade Berman. For those who contributed in my research, I would like to thank the biotech group at NIWA for their guidance and interest in my research and to help pass the time in the laboratory. I would especially like to thank Matt Voyles for his time and patience. Thank you also to Kylie Price, Sarah Bury and Caoimhghin Ó Maolagáin. For the amazing Antarctica adventure, a once-in-a-lifetime experience I managed to do twice I thank Eileen Koh, Andrew Martin, Stuart Donachie, Mike Hudson, Schannel van Dijken, Marti Anderson, Russell Babcock, Mark Heath, Lisa Bryant, Ana Aguilar-Islas, Simon Davy and Chris Thorn. For funding, I thank the Foundation of Research Science and Technology, the Antarctic Research Center (VUW) Endowed Development Fund, the Faculty of Science Research Committee, the Royal Society of New Zealand and the Charles Flemming Fund. For logistical support I acknowledge Antarctica New Zealand, in particular Shulamit Gordon (LGP manager) and Brian Staite (LGP camp manager). Lastly, I would like to thank my family for their support. Thanks especially to my dad who sparked my interest in biology from a young age by spending hours with me at the beach looking in rock pools. Finally, to Gareth. I thank you for your unconditional love and support and your belief in me. Without you this PhD from start through to finish would not have been possible. ABSTRACT Antarctic sea ice is an important feature of the southern ocean where at its maximum it can cover 8 % of the Southern Hemisphere. It provides a stable environment for the colonisation of diverse and highly specialised microbes which play a central role in the assimilation and regulation of energy through the Antarctic food web. Polar environments are sensitive to changes in the environment. Small changes in temperature can have large effects on sea ice thickness and extent and Antarctic sea ice cover is expected to shrink by 25 % over the next century. It is unknown how the sea ice microbiota will respond. In order to understand the effects of climate change on the sea ice ecosystem it is necessary to obtain information about the community structure, function and diversity and their reactions with the environment. Studies have focused on algal diversity and physiology in Antarctic sea ice and in comparison studies on the prokaryotic community are few. Although prokaryotic diversity has been investigated using clone libraries and culture based methods, it is likely that certain species have still not been described. Almost nothing is known about the Antarctic sea ice bacterial community spatial and temporal dynamics under changing abiotic and biotic conditions or their role in biogeochemical cycles. This is the first study linking Antarctic bacterial communities to function by using statistics to investigate the relationships between environmental variables and community structure. Bacterial community structure was investigated by extracting both the DNA and RNA from the environment to understand both the metabolically active (RNA) and total (DNA) bacterial community. The thickness of the sea ice and nutrient concentrations were key factors regulating bacterial community composition in Antarctic sea ice. Sea ice thickness is likely to have an effect on the physiological responses of algae leading to changes in photosynthate concentrations and composition of dissolved organic matter (DOM). Further investigations into the relationships between enzymatic activity and community structure revealed that the composition of the DOM drove variation between bacterial communities. i There was no relationship between bacterial abundance and chlorophyll-a (as a measure of algal biomass), suggesting a un-coupling of the microbial loop. However bacteria were actively involved in the hydrolysis of polymers throughout the sea ice core. Investigations using quantitative PCR (qPCR) found that the functional genes involved in denitrification and light energy utilisation were in low abundance therefore these processes are minor in Antarctic sea ice. These results confirm that sea ice bacteria are predominantly heterotrophs and have a major role in the cycling of carbon and nitrogen through the microbial loop. This is the first study to document archaea, one of the three domains of life, in Antarctic sea ice. Their diversity was investigated using clone library methods and the majority grouped with the recently described phylum Thaumarchaeota and the rest with the Euryarchaeota. One group closely clustered with the ammonia-oxidising “Candidatus Nitrosopumilus maritimus”. The abundance of archaea was investigated using qPCR and at most sites they comprised < 7 % of the total prokaryotic community. However, they were occasionally in high abundance which suggests that they may be able to utilise available ammonia via nitrification. The prokaryotic diversity was further investigated using culture-based methods and 454 sequencing. Bacterial OTUs were defined at 97% sequence identity and some were identified using both methods. However, many OTUs were identified using one or the other method suggesting that a greater amount of diversity could be gathered using both methods. This trend was also seen when comparing the 454 sequences from the DNA and RNA – based communities; therefore both the DNA and RNA should be extracted from the environment to investigate bacterial diversity. The rarefaction curves suggested that the community diversity had been fully sampled. However, the presence of some species in the culture-based database and not in the 454 sequences showed that some bacterial groups were not extracted from samples. These groups included Gram positive bacteria which have a thicker cell wall that is more difficult to rupture during extraction from the environment. The number of bacterial OTUs in Antarctic sea ice appears to be ~ 3 x 103, which is towards the lower end of species diversity estimates. Many of the abundant OTUs were cosmopolitan at all sites but in contrast, the rarer OTUs were endemic. Bacterial ii communities also showed a taxa-area relationship where communities that were collected closer together were more similar than those collected further apart. However, the environment rather than biogeography appeared to be controlling community change. These results suggest that the more abundant taxa may indeed be everywhere. These groups are likely to be more generalist species and able to survive dispersal. Rare taxa may be specialist species that become more abundant when the environment turns favourable. Bacterial groups belonging to the class Mollicutes and the phylum Planctomycetes were rare at the bottom of the sea ice core but became more dominant at the top of the ice core where DOM and nutrient concentrations are lower and irradiance is higher. These groups may be better adapted to a nutrient poor environment. My results show that although „everything is NOT everywhere‟ however, „the environment selects‟. Climate change leading to decreased ice thickness and extent will influence microbial community structure and function which will have an impact on the Antarctic sea ice ecosystem. This thesis provides baseline information that will be useful for further long term monitoring of these communities. iii TABLE OF CONTENTS ABSTRACT ............................................................................................................................ i TABLE OF CONTENTS .......................................................................................................... iv LIST OF FIGURES ................................................................................................................ vii LIST OF TABLES .................................................................................................................. xi ABBREVIATIONS ............................................................................................................... xiv CHAPTER 1: General Introduction ..............................................................................
Load more

Recommended publications
  • Genomic Insight Into the Host–Endosymbiont Relationship of Endozoicomonas Montiporae CL-33T with Its Coral Host
    ORIGINAL RESEARCH published: 08 March 2016 doi: 10.3389/fmicb.2016.00251 Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host Jiun-Yan Ding 1, Jia-Ho Shiu 1, Wen-Ming Chen 2, Yin-Ru Chiang 1 and Sen-Lin Tang 1* 1 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, 2 Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, Kaohsiung, Taiwan The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T. Its genome had potential sign of ongoing genome erosion and gene exchange with its Edited by: Rekha Seshadri, host. Testosterone degradation and type III secretion system are commonly present in Department of Energy Joint Genome Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Institute, USA Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, Reviewed by: this bacterium could move into coral cells via endocytosis after binding to coral’s Eph Kathleen M. Morrow, University of New Hampshire, USA receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase Jean-Baptiste Raina, are possible type III secretion effectors that might help coral to prevent mitochondrial University of Technology Sydney, Australia dysfunction and promote gluconeogenesis, especially under stress conditions.
    [Show full text]
  • Deciphering a Marine Bone Degrading Microbiome Reveals a Complex Community Effort
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 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 4.0 International license. 1 Deciphering a marine bone degrading microbiome reveals a complex community effort 2 3 Erik Borcherta,#, Antonio García-Moyanob, Sergio Sanchez-Carrilloc, Thomas G. Dahlgrenb,d, 4 Beate M. Slabya, Gro Elin Kjæreng Bjergab, Manuel Ferrerc, Sören Franzenburge and Ute 5 Hentschela,f 6 7 aGEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, 8 Kiel, Germany 9 bNORCE Norwegian Research Centre, Bergen, Norway 10 cCSIC, Institute of Catalysis, Madrid, Spain 11 dDepartment of Marine Sciences, University of Gothenburg, Gothenburg, Sweden 12 eIKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany 13 fChristian-Albrechts University of Kiel, Kiel, Germany 14 15 Running Head: Marine bone degrading microbiome 16 #Address correspondence to Erik Borchert, [email protected] 17 Abstract word count: 229 18 Text word count: 4908 (excluding Abstract, Importance, Materials and Methods) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.13.093005; this version posted November 18, 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 4.0 International license. 19 Abstract 20 The marine bone biome is a complex assemblage of macro- and microorganisms, however the 21 enzymatic repertoire to access bone-derived nutrients remains unknown.
    [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]
  • Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
    Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen.
    [Show full text]
  • Oil Type and Temperature Dependent Biodegradation Dynamics
    Ribicic et al. BMC Microbiology (2018) 18:83 https://doi.org/10.1186/s12866-018-1221-9 RESEARCH ARTICLE Open Access Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis Deni Ribicic1,2* , Kelly Marie McFarlin1, Roman Netzer1, Odd Gunnar Brakstad1, Anika Winkler3, Mimmi Throne-Holst1 and Trond Røvik Størseth1 Abstract Background: This study investigates a comparative multivariate approach for studying the biodegradation of chemically dispersed oil. The rationale for this approach lies in the inherent complexity of the data and challenges associated with comparing multiple experiments with inconsistent sampling points, with respect to inferring correlations and visualizing multiple datasets with numerous variables. We aim to identify novel correlations among microbial community composition, the chemical change of individual petroleum hydrocarbons, oil type and temperature by creating modelled datasets from inconsistent sampling time points. Four different incubation experiments were conducted with freshly collected Norwegian seawater and either Grane and Troll oil dispersed with Corexit 9500. Incubations were conducted at two different temperatures (5 °C and 13 °C) over a period of 64 days. Results: PCA analysis of modelled chemical datasets and calculated half-lives revealed differences in the biodegradation of individual hydrocarbons among temperatures and oil types. At 5 °C, most n-alkanes biodegraded faster in heavy Grane oil compared to light Troll oil. PCA analysis of modelled microbial community datasets reveal differences between temperature and oil type, especially at low temperature. For both oils, Colwelliaceae and Oceanospirillaceae were more prominent in the colder incubation (5 °C) than the warmer (13 °C). Overall, Colwelliaceae, Oceanospirillaceae, Flavobacteriaceae, Rhodobacteraceae, Alteromonadaceae and Piscirickettsiaceae consistently dominated the microbial community at both temperatures and in both oil types.
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?
    Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals? Amy Apprill1*, Jooke Robbins2, A. Murat Eren3, Adam A. Pack4,5, Julie Reveillaud3, David Mattila6, Michael Moore1, Misty Niemeyer7, Kathleen M. T. Moore7, Tracy J. Mincer1* 1 Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America, 2 Center for Coastal Studies, Provincetown, Massachusetts, United States of America, 3 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America, 4 University of Hawaii at Hilo, Hilo, Hawaii, United States of America, 5 The Dolphin Institute, Honolulu, Hawaii, United States of America, 6 Hawaiian Islands Humpback Whale National Marine Sanctuary, Kihei, Hawaii, United States of America, 7 International Fund for Animal Welfare, Yarmouth Port, Massachusetts, United States of America Abstract Microbes are now well regarded for their important role in mammalian health. The microbiology of skin – a unique interface between the host and environment - is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations.
    [Show full text]
  • Degrading Bacteria in Deep‐
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberdeen University Research Archive Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel) E. Gontikaki1 , L.D. Potts1, J.A. Anderson2 and U. Witte1 1 School of Biological Sciences, University of Aberdeen, Aberdeen, UK 2 Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK Keywords Abstract clone libraries, Faroe-Shetland Channel, hydrocarbon degradation, isolates, marine Aims: The aim of this study was the baseline description of oil-degrading bacteria, oil spill, Oleispira, sediment. sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination Correspondence in FSC sediments. Evangelia Gontikaki and Ursula Witte, School Methods and Results: Oil-degrading sediment bacteria from 135, 500 and of Biological Sciences, University of Aberdeen, 1000 m were enriched in cultures with crude oil as the sole carbon source (at Aberdeen, UK. ° E-mails: [email protected] and 12, 5 and 0 C respectively). The enriched communities were studied using [email protected] culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. 2017/2412: received 8 December 2017, Bacterial isolates included well-known oil-degrading taxa and several that are revised 16 May 2018 and accepted 18 June reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, 2018 Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at doi:10.1111/jam.14030 genus level particularly between the shallow and the deep, cold-water stations.
    [Show full text]
  • Aliagarivorans Marinus Gen. Nov., Sp. Nov. and Aliagarivorans Taiwanensis Sp
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1880–1887 DOI 10.1099/ijs.0.008235-0 Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation Wen Dar Jean,1 Ssu-Po Huang,2 Tung Yen Liu,2 Jwo-Sheng Chen3 and Wung Yang Shieh2 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Rd, Tainan, Wung Yang Shieh Taiwan, ROC [email protected] 2Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan, ROC 3College of Health Care, China Medical University, No. 91, Shyue-Shyh Rd, Taichung, Taiwan, ROC Two agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25–30 6C, in 2–4 % NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8–92.0 %) and the major cellular fatty acids were summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH; 26.4–35.6 %), C18 : 1v7c (27.1–31.4 %) and C16 : 0 (14.8–16.3 %) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively.
    [Show full text]
  • Colwellia and Marinobacter Metapangenomes Reveal Species
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317438; this version posted September 28, 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. 1 Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil 2 and dispersant exposure in deepsea microbial communities 3 4 Tito David Peña-Montenegro1,2,3, Sara Kleindienst4, Andrew E. Allen5,6, A. Murat 5 Eren7,8, John P. McCrow5, Juan David Sánchez-Calderón3, Jonathan Arnold2,9, Samantha 6 B. Joye1,* 7 8 Running title: Metapangenomes reveal species-specific responses 9 10 1 Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, 11 Georgia 30602-3636, USA 12 13 2 Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, Georgia 14 30602-7229, USA 15 16 3 Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de 17 Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional 18 Barranquilla, Colombia 19 20 4 Microbial Ecology, Center for Applied Geosciences, University of Tübingen, 21 Schnarrenbergstrasse 94-96, 72076 Tübingen, Germany 22 23 5 Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, 24 USA 25 26 6 Integrative Oceanography Division, Scripps Institution of Oceanography, UC San 27 Diego, La Jolla, CA 92037, USA 28 29 7 Department of Medicine, University of Chicago, Chicago, IL, USA 30 31 8 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA 32 33 9Department of Genetics, University of Georgia, 120 Green St., Athens, Georgia 30602- 34 7223, USA 35 36 *Correspondence: Samantha B.
    [Show full text]