DOCSLIB.ORG

BACTERIAL DIVERSITY ASSOCIATED with RED SEAWEEDS, Gracilaria Manilaensis & Laurencia Sp., FOUND in PENINSULAR MALAYSIA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
BACTERIAL DIVERSITY ASSOCIATED with RED SEAWEEDS, Gracilaria Manilaensis & Laurencia Sp., FOUND in PENINSULAR MALAYSIA BACTERIAL DIVERSITY ASSOCIATED WITH RED SEAWEEDS, Gracilaria manilaensis & Laurencia sp., FOUND IN PENINSULAR MALAYSIA BY NAJATUL SU AD BINTI ABDULLAH INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA 2020 BACTERIAL DIVERSITY ASSOCIATED WITH RED SEAWEEDS, Gracilaria manilaensis & Laurencia sp., FOUND IN PENINSULAR MALAYSIA BY NAJATUL SU AD BINTI ABDULLAH A thesis submitted in fulfilment of the requirement for the degree of Doctor of Philosophy (Biosciences) Kulliyyah of Science International Islamic University Malaysia NOVEMBER 2020 ABSTRACT Red seaweeds, Rhodophyta, are very beneficial as a good source of nutrients, collagen, and bioactive metabolites. Thus, seaweeds are consumed or harvested for various industries, including processed food and nutraceuticals. It has been debated that metabolic compounds of the seaweeds could be due to the interactions between the seaweeds and its holobiont environment which hosts microorganisms such as bacteria, protists, algal virus, fungi, and diatoms. It was the interest of this research to investigate the bacterial community profile of edible red seaweed, Gracilaria manilaensis, often found in coastal villages of peninsular Malaysia, and compare it against Laurencia sp., which is a genus prolific for the discovery and extraction of bioactive metabolic compounds. Studies of bacterial diversity associated to other Rhodophyta species have been conducted worldwide, but not extensively in Malaysia. Isolation of bacteria from marine environment is primarily done for identification of bacterial species and exploring the value of bacteria or its bioactive compounds in biotechnological application. Eight selective enrichment media were used and the bacteria isolated was also compared to the bacteria profile identified through amplicon sequencing. For the seaweed, G. manilaensis, there was a total colony count of 1022 on 8 media with 3 replicates, which 80 isolates were selected for 16S rRNA identification and 43 OTUs were identified. Dominant bacteria phylum was Proteobacteria, and other isolated phyla were Firmicutes, Bacteroidetes, and Actinobacteria. The phyla profile was similar to that of the amplicon sequencing sample with 88 OTUs identified. For the red seaweed, Laurencia sp., 8 OTUs were isolated by bacteria culture-dependent approach and 41 OTUs were discovered by amplicon sequencing molecular approach. From the 8 culture OTUs, 3 were positive from bromoperoxidase gene. Sequences data analysis indicated that members of the Alphaproteobacteria and the Bacteroidetes which are predominant were likely to have an important role in the function of this marine bacterial community as the bacterial phyla observed are ubiquitous in seawater with some OTUs and isolates were homologous to bacteria in marine host cluster. Further investigation on these bacteria is hoped to reveal how the identified bacteria can be beneficial in a seaweed environment or for other biodiscoveries. ii خﻻصة البحث إن الطحالب احلمراء، أو رودوفيتا، مفيدة للغاية كمصدر جيد للعناصر الغذ ،ائية والكوﻻجني، املستقلبات النشطة احليوي . ةوابلتايل، أن اﻷعشاب البحرية تستهلك أو حتصد يف صناعات خمتلفة، مبا يف ذلك اﻷغذية املصنعة واملكمﻻت الغذائية. وجرت مناقشة إمكانية املركبات املستقلبات لﻷعشاب البحرية انجتة عن التفاعﻻت بني اﻷعشاب البحرية وبيئتها اليت تضم الكائنات اجملهرية مثل البكتياي والطﻻئعيات والفيوس الطحليب والفطرايت والدايتومات. وأمهية هذا البحث هي دراسة خصائص اجملتمع البكتيي للطحالب احلمراء الصاحلة لﻷكل، وهي إغراسيﻻراي مانيلينسيس اليت وجدت كثيا يف القرى الساحلية لشبه جزيرة ماليزاي، ومقارنتها مع لورينسيا إسيب، وهي مادة غز يرة اﻹنتاج ﻻكتشاف املستقلبات النشطة احليوية واستخﻻصها. وقد أجريت دراسات على التنوع ال يبكتي املرتبطة أبنواع رودوفيتا اﻷخرى يف مجيع أحناء العامل، ولكن ليست على نطاق واسع يف ماليزاي. ويتم عزل البكتياي عن البيئة البحرية أساسا لتحديد اﻷنواع البكتيية واستكشاف قيمة البكتياي أو ا مركباهتاحليوية يف تطبيقات التكنولوجيا احليوية. كما مت استخدام مثانية وسائط للتخصيب اﻻنتقائي ومتت أيضا مقارنة البكتياي املعزولة خبصائص البكتياي اليت مت حتديدها من خﻻل تسلسل اﻷمبليكون. وابلنسبة ﻷعشاب البحر، إغراسيﻻراي مانيلينسيس، كان هناك تعداد كلي من املستعمرات قدره ١٠٢٢ يف ٨ وسائط مع ٣ ِّ ِّ rRNA حاﻻت تكرار، أختيت ٨٠ حالة عزلية لتحديد هوية ١٦ رمز الَّران ال ريباس ي ( ) وحددت ٤٣ وحدة التصنيف التشغيلية (OTU). وشعبة البكتياي املهيمنة كانت بكتياي بروتينية، وغيها من الشعب املعزولة كانت متينات اجلدار، العصوانيات، والشعاوايت. وكان ملف تعريف الشعب شبيها مبثال عينة تسلسل اﻷمبليكون مع حتديد ٨٨ OTU. أما ابلنسبة للطحالب احلمراء، لورينسيا إسيب.، فقد مت اكتشاف ٨ OTU عن طريق املزرعة ةالبكتيي املنعزلة واكتشاف ٤١ OTU عن طريق هنج جزيئي متسلسل اﻷمبليكون. ومن مثانية مستفردات OTU، كانت ثﻻثة منها إجيابية من جني بروموبروكسيديز. وقد أشار حتليل بياانت التسلسل إىل أن أفراد متقلبات ألفا والعصوانيات كانت سائدة مرجحة وهلا دور مهم يف وظيفة هذا اجملتمع البكتيي البحري حيث أهنا شوهدت يف كل مكان يف مياه البحر مع بعض OTU والشعب كانت متماثلة مع البكتياي يف اجملموعة البحرية املضيفة. ومن املأمول إجراء مزيد من الدراسة بشأن هذه البكتياي لكشف كيفية استفادهتا يف بيئة اﻷعشاب البحرية أو يف اﻻكتشافات البيولوجية اﻷخرى. iii APPROVAL PAGE The thesis of Najatul Su Ad binti Abdullah has been approved by the following: _____________________________ Mohd Azrul Naim bin Mohammad Supervisor _____________________________ Zaima Azira Zainal Abidin Co-Supervisor ______ ________ Normawaty Mohammad Noor Co-Supervisor _____________________________ Zarina Zainuddin Internal Examiner _____________________________ Goh Kian Mau External Examiner _____________________________ I-Made Sudiana External Examiner _____________________________ Siti Aesah @ Naznin Muhammad Chairman iv DECLARATION I hereby declare that this thesis is the result of my own investigations, except where otherwise stated. I also declare that it has not been previously or concurrently submitted as a whole for any other degrees at IIUM or other institutions. Najatul Su Ad binti Abdullah Signature ........................................................... Date ......................................... v COPYRIGHT PAGE INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA DECLARATION OF COPYRIGHT AND AFFIRMATION OF FAIR USE OF UNPUBLISHED RESEARCH BACTERIAL DIVERSITY ASSOCIATED WITH RED SEAWEEDS, Gracilaria manilaensis & Laurencia sp., FOUND IN PENINSULAR MALAYSIA I declare that the copyright holders of this thesis are jointly owned by the student and IIUM. Copyright © 2020 Najatul Su Ad binti Abdullah and International Islamic University Malaysia. All rights reserved. No part of this unpublished research may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise without prior written permission of the copyright holder except as provided below 1. Any material contained in or derived from this unpublished research may be used by others in their writing with due acknowledgement. 2. IIUM or its library will have the right to make and transmit copies (print or electronic) for institutional and academic purposes. 3. The IIUM library will have the right to make, store in a retrieved system and supply copies of this unpublished research if requested by other universities and research libraries. By signing this form, I acknowledged that I have read and understand the IIUM Intellectual Property Right and Commercialization policy. Affirmed by Najatul Su Ad binti Abdullah ……..……..…………… ………………….. Signature Date HT PAGE vi ACKNOWLEDGEMENTS In the name of Allah, the Most Gracious and the Most Merciful. And of His signs is that He sends the winds as bringers of good tidings and to let you taste His mercy and so the ships may sail at His command and so you may seek of His bounty, and perhaps you will be grateful (Ar-Rum: 46). SubhannAllah and Alhamdulillah, for these bounties and may we always be thankful. Alhamdulillah, All Praise to Allah Al-Mighty for this wonderful journey. I would not have achieved this without His Guidance and Benevolence in every aspect in my life. I would like to convey my deepest gratitude to my primary supervisor, Dr. Mohd Azrul Naim Mohamad, chairman of my supervisory committee, Assoc. Prof. Dr. Normawaty Mohd Noor, and co-supervisor, Assoc. Prof. Dr. Zaima Azira Zainal Abidin, for their dedication to see me through this PhD journey. Their advices and help, academically and personally, had motivated me each time I struggled through problems during my study and personal life. May Allah reward all of you and the faculty of Kulliyyah of Science, who all become my mentors, for every effort done towards my study completion. I would like to acknowledge the Academic Trainee Scheme of International Islamic University Malaysia and the Ministry of Higher Education under SLAB, for the sponsorship of my studies. I would also like to thank the staff and my friends at KOS and in IIUM for their continuous support, help, laughter, and motivation that have made this journey memorable. It will be an endless list to name all of you, but I believe you all know who you are. To my family, mum dad, kids, and parents-in-law, your endless love and prayers have comforted me through my hardest times and struggles. You all celebrated my success no matter how small, and for that I am grateful. Lastly, to my husband who is my closest supporter, I can’t express enough how much I am in love and indebted to you for all your care and sacrifices over these years for me. This is for us for never giving up on our dreams vii TABLE OF CONTENTS Abstract ..................................................................................................................... ii Abstract in Arabic
Load more

Recommended publications
  • Genomics 98 (2011) 370–375
    Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc.
    [Show full text]
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Cone-Forming Chloroflexi Mats As Analogs of Conical
    268 Appendix 2 CONE-FORMING CHLOROFLEXI MATS AS ANALOGS OF CONICAL STROMATOLITE FORMATION WITHOUT CYANOBACTERIA Lewis M. Ward, Woodward W. Fischer, Katsumi Matsuura, and Shawn E. McGlynn. In preparation. Abstract Modern microbial mats provide useful process analogs for understanding the mechanics behind the production of ancient stromatolites. However, studies to date have focused on mats composed predominantly of oxygenic Cyanobacteria (Oxyphotobacteria) and algae, which makes it difficult to assess a unique role of oxygenic photosynthesis in stromatolite morphogenesis, versus different mechanics such as phototaxis and filamentous growth. Here, we characterize Chloroflexi-rich hot spring microbial mats from Nakabusa Onsen, Nagano Prefecture, Japan. This spring supports cone-forming microbial mats in both upstream high-temperature, sulfidic regions dominated by filamentous anoxygenic phototrophic Chloroflexi, as well as downstream Cyanobacteria-dominated mats. These mats produce similar morphologies analogous to conical stromatolites despite metabolically and taxonomically divergent microbial communities as revealed by 16S and shotgun metagenomic sequencing and microscopy. These data illustrate that anoxygenic filamentous microorganisms appear to be capable of producing similar mat morphologies as those seen in Oxyphotobacteria-dominated systems and commonly associated with 269 conical Precambrian stromatolites, and that the processes leading to the development of these features is more closely related with characteristics such as hydrology and cell morphology and motility. Introduction Stromatolites are “attached, lithified sedimentary growth structures, accretionary away from a point or limited surface of initiation” (Grotzinger and Knoll 1999). Behind this description lies a wealth of sedimentary structures with a record dating back over 3.7 billion years that may be one of the earliest indicators of life on Earth (Awramik 1992, Nutman et al.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
    Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10).
    [Show full text]
  • Yu-Chen Ling and John W. Moreau
    Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig.
    [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]
  • Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergol
    applied sciences Article Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland Magdalena Dyda 1,2,* , Agnieszka Laudy 3, Przemyslaw Decewicz 4 , Krzysztof Romaniuk 4, Martyna Ciezkowska 4, Anna Szajewska 5 , Danuta Solecka 6, Lukasz Dziewit 4 , Lukasz Drewniak 4 and Aleksandra Skłodowska 1 1 Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] 2 Research and Development for Life Sciences Ltd. (RDLS Ltd.), Miecznikowa 1/5a, 02-096 Warsaw, Poland 3 Laboratory of Environmental Analysis, Museum of King John III’s Palace at Wilanow, Stanislawa Kostki Potockiego 10/16, 02-958 Warsaw, Poland; [email protected] 4 Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] (P.D.); [email protected] (K.R.); [email protected] (M.C.); [email protected] (L.D.); [email protected] (L.D.) 5 The Main School of Fire Service, Slowackiego 52/54, 01-629 Warsaw, Poland; [email protected] 6 Department of Plant Molecular Ecophysiology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +48-786-28-44-96 Citation: Dyda, M.; Laudy, A.; Abstract: The aim of the presented investigation was to describe seasonal changes of microbial com- Decewicz, P.; Romaniuk, K.; munity composition in situ in different biocenoses on historical sandstone of the Northern Pergola in Ciezkowska, M.; Szajewska, A.; the Museum of King John III’s Palace at Wilanow (Poland).
    [Show full text]
  • Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production
    UC San Diego UC San Diego Previously Published Works Title Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production. Permalink https://escholarship.org/uc/item/6263h6gw Journal Chemistry & biology, 22(9) ISSN 1074-5521 Authors Choi, Eun Ju Nam, Sang-Jip Paul, Lauren et al. Publication Date 2015-09-01 DOI 10.1016/j.chembiol.2015.07.014 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Graphical Abstract Authors Eun Ju Choi, Sang-Jip Nam, Lauren Paul, ..., Christopher A. Kauffman, Paul R. Jensen, William Fenical Correspondence [email protected] In Brief Choi et al. illustrate that low-nutrient media and long incubation times lead to the isolation of rare, previously uncultured marine bacteria that produce new antibacterial metabolites. Their work demonstrates that unique marine bacteria are easier to cultivate than previously suggested. Highlights Accession Numbers d Simple methods allow the isolation of rare, previously JN703500 KJ572269 uncultured marine bacteria JN703501 KJ572270 JN703502 KJ572271 d Previously uncultured marine bacteria produce new JN703503 KJ572272 antibacterial metabolites JN368460 KJ572273 JN368461 KJ572274 KJ572262 KJ572275 KJ572263 KJ572264 KJ572265 KJ572266 KJ572267 KJ572268 Choi et al., 2015, Chemistry & Biology 22, 1–10 September 17, 2015 ª2015 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Please cite this article in press as: Choi et al., Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production, Chemistry & Biology (2015), http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Chemistry & Biology Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Eun Ju Choi,1,2,3 Sang-Jip Nam,1,2,4 Lauren Paul,1 Deanna Beatty,1 Christopher A.
    [Show full text]
  • Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
    Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota
    [Show full text]
  • Monitoring of Biofouling Communities in a Portuguese Port Using a Combined Morphological and Metabarcoding Approach Joana Azevedo 1,2,3, Jorge T
    www.nature.com/scientificreports OPEN Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach Joana Azevedo 1,2,3, Jorge T. Antunes1,2,3, André M. Machado 1, Vitor Vasconcelos1,2, Pedro N. Leão 1* & Elsa Froufe 1* Marine biofouling remains an unsolved problem with a serious economic impact on several marine associated industries and constitutes a major vector for the spread of non-indigenous species (NIS). The implementation of biofouling monitoring programs allows for better fouling management and also for the early identifcation of NIS. However, few monitoring studies have used recent methods, such as metabarcoding, that can signifcantly enhance the detection of those species. Here, we employed monthly monitoring of biofouling growth on stainless steel plates in the Atlantic Port of Leixões (Northern Portugal), over one year to test the efect of commercial anti-corrosion paint in the communities. Fouling organisms were identifed by combining morpho-taxonomy identifcation with community DNA metabarcoding using multiple markers (16S rRNA, 18S rRNA, 23S rRNA, and COI genes). The dominant colonizers found at this location were hard foulers, namely barnacles and mussels, while other groups of organisms such as cnidarians, bryozoans, and ascidians were also abundant. Regarding the temporal dynamics of the fouling communities, there was a progressive increase in the colonization of cyanobacteria, green algae, and red algae during the sampled period with the replacement of less abundant groups. The tested anticorrosion paint demonstrated to have a signifcant prevention efect against the biofouling community resulting in a biomass reduction. Our study also reports, for the frst time, 29 NIS in this port, substantiating the need for the implementation of recurring biofouling monitoring programs in ports and harbours.
    [Show full text]
  • Concerted Gene Recruitment in Early Plant Evolution Jinling Huang* and J Peter Gogarten†
    Open Access Research2008HuangVolume and 9, Issue Gogarten 7, Article R109 Concerted gene recruitment in early plant evolution Jinling Huang* and J Peter Gogarten† Addresses: *Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA. †Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA. Correspondence: Jinling Huang. Email: [email protected] Published: 8 July 2008 Received: 30 April 2008 Revised: 24 June 2008 Genome Biology 2008, 9:R109 (doi:10.1186/gb-2008-9-7-r109) Accepted: 8 July 2008 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2008/9/7/R109 © 2008 Huang and Gogarten; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Eukaryotic<p>Analysesto the split ofhorizontal ofred the algae red gene andalgal transfergreen <it>Cyanidioschyzon</it> plants.</p> genome identified 37 genes that were acquired from non-organellar sources prior Abstract Background: Horizontal gene transfer occurs frequently in prokaryotes and unicellular eukaryotes. Anciently acquired genes, if retained among descendants, might significantly affect the long-term evolution of the recipient lineage. However, no systematic studies on the scope of anciently acquired genes and their impact on macroevolution are currently available in eukaryotes. Results: Analyses of the genome of the red alga Cyanidioschyzon identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants.
    [Show full text]