DOCSLIB.ORG

Temporal Changes in the Gut Microbiota in Farmed Atlantic Cod (Gadus Morhua) Outweigh 2 the Response to Diet Supplementation with Macroalgae

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Temporal Changes in the Gut Microbiota in Farmed Atlantic Cod (Gadus Morhua) Outweigh 2 the Response to Diet Supplementation with Macroalgae bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh 2 the response to diet supplementation with macroalgae. 3 4 C. Keating1,2 Y*, M. Bolton-Warberg3 Y, J. Hinchcliffe 5, R. Davies6, S. Whelan3, A.H.L. Wan7,8, 5 R. D. Fitzgerald3†, S. J. Davies9, U. Z. Ijaz2*, C. J. Smith1,2* 6 7 1Department of Microbiology, School of Natural Sciences, National University of Ireland 8 Galway, Ireland, H91 TK33. 9 2Water and Environment Group, Infrastructure and Environment Division, James Watt School of 10 Engineering, University of Glasgow, Glasgow, United Kingdom, G12 8LT. 11 3Carna Research Station, Ryan Institute, National University of Ireland Galway, Carna, Co. 12 Galway, Ireland, H91 V8Y1. 13 5Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 14 Sweden. 15 6AquaBioTech Group, Central Complex, Naggar Street, Targa Gap, Mosta, MST 1761, Malta 16 G.C. 17 7Irish Seaweed Research Group, Ryan Institute and School of Natural Sciences, National 18 University of Ireland Galway, Ireland, H91 TK33. 19 8Aquaculture Nutrition and Aquafeed Research Unit, Carna Research Station, Ryan Institute and 20 School of Natural Sciences, National University of Ireland Galway, Carna, Co. Galway, Ireland, 21 H91 V8Y1. 22 9 Department of Animal Production, Welfare and Veterinary Science, Harper Adams University, 23 Newport, Shropshire, UK, TF10 8NB. 24 25 YThese authors contributed equally. 26 * Correspondence: 27 Joint corresponding authors: [email protected]; [email protected]; 28 [email protected] 29 Keywords: Atlantic cod1, Hindgut microbiome2, Seaweed3, Macroalgae4, Ulva rigida5, 30 Ascophyllum nodosum6, 16S rRNA Amplicon sequencing7, Aquaculture8. bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 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. 31 Abstract 32 Background: Aquaculture successfully meets global food demands for many fish species. 33 However, aquaculture production of Atlantic cod (Gadus morhua) is modest in comparison to 34 market demand. For cod farming to be a viable economic venture specific challenges on how to 35 increase growth, health and farming productivity need to be addressed. Feed ingredients play a 36 key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with 37 both health and economic benefits for terrestrial farmed animals and fish. The impact of such 38 dietary supplements to cod gut integrity and microbiota, which contribute to overall fish 39 robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic 40 cod with macroalgae and determine the impacts on fish condition and growth, gut morphology 41 and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of 42 three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum 43 nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. 44 45 Results: The results demonstrated there was no significant difference in fish condition, gut 46 morphology or hindgut microbiota between the U. rigida supplemented fish group and the control 47 group at any time-point. This contrasts with the A. nodosum treatment. Fish within this group 48 were further categorised as either ‘Normal’ or ‘Lower Growth’. ‘Lower Growth’ individuals 49 found the diet unpalatable resulting in reduced weight and condition factor combined with an 50 altered gut morphology and microbiome relative to the other treatments. Excluding this group, 51 our results show that the hindgut microbiota was largely driven by temporal pressures with the 52 microbial communities becoming more similar over time irrespective of dietary treatment. The 53 core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and 54 Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales 55 (Lachnoclostridium). 56 57 Conclusions: Our study indicates that U. rigida macroalgae can be supplemented at 10% 58 inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition 59 or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. 60 nodosum is not a suitable feed supplement in a farmed cod diet. 61 62 Background 63 Sustainable food production is gaining increased attention from consumers, farmers, and 64 policymakers. This is spurred on by concerns on the impact of climate change, consumer 65 awareness, and the growing global food demand [1]–[3]. Currently, 151 million tonnes of fish are 66 produced annually for human consumption [4]. Wild fish stocks cannot sustain further increases 67 in demand. Several wild fish populations have collapsed or are in danger of critical decline from 68 over-fishing and habitat damage. A significant depletion in 4 European cod stocks (Kattegat, 69 North Sea, West of Scotland and Irish Sea) by the early 2000s led to wild stock enhancement 70 initiatives, such as the European Union’s Cod Recovery Plan (EC No 1342/2008; [5], and 71 ultimately included enforced catch quotas. However, despite their initial recovery, The 72 International Council for the Exploration of the Sea (ICES) have advised that the North Sea, 73 Celtic Sea, Irish Sea and West of Scotland cod stocks are in decline once more [6]–[9]. The cause 74 of this decline is unclear, with climate change, destruction of nearshore cod nurseries by trawling, bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 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. 75 grey seal predation and fisheries management being implicated [10]–[12]. The precarious 76 condition of these wild cod stocks means this is simply not a sustainable option to meet consumer 77 demand for this fish. 78 Commercial aquaculture has successfully met the market demand for a range of fish species, 79 including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), gilt-head 80 seabream (Sparus aurata), and seabass (Dicentrarchus labrax), thereby alleviating demand on 81 wild resources [4]. Despite the popularity of cod as a food fish, aquaculture production of farmed 82 cod is a business that has waxed and waned since the 1970’s. Currently, only 2.5% of the total 83 Atlantic cod produced for food is through aquaculture [3]-[4]. The economic viability of a 84 commercial cod farming operation presents a number of challenges including a consistent high- 85 quality broodstock, reducing high mortality, disease susceptibility, market pricing and high costs 86 associated with aquafeeds [13]–[15]. Developing novel feed ingredients and alternatives to 87 marine by-products in formulated diets not only could improve the economic viability of 88 commercial cod farming but could also have implications in the sustainability status of cod 89 farming and consumer perception of farmed cod. 90 One potential solution is to supplement the diet of farmed cod with high-quality functional 91 ingredients that provide health benefits, nutrition and are environmentally sustainable and low 92 cost. The use of macroalgae (also known as seaweeds) as a potential feed supplement could 93 further this sustainability agenda. The biomass can often be grown or sustainably harvested at 94 quantities that would meet commercial aquafeed demand. Dietary supplementation of macroalgae 95 has been trialled in many farmed fish species including Atlantic salmon (S. salar, [16], rainbow 96 trout (O. mykiss, [17], European seabass (D. labrax, [18], carp (C. carpio, [19]), and tilapia (O. 97 niloticus, [20]. Some studies have advocated that macroalgae could partially replace protein 98 constituents in formulated diets [21], [22]. However, the lower algal protein content (up to 27%) 99 in comparison to highly proteinaceous fishmeal (e.g. LT94 fish meal, ~ 67 %) and plant by- 100 products (e.g. soy protein concentrates, ~76%) typically used in formulated diets, indicate it 101 would be better to exploit algal meal as a functional feed supplement instead [23]. As a functional 102 feed supplement macroalgae can be used to supply trace metals, carotenoids, long-chain omega-3 103 polyunsaturated fatty acids, and vitamins that potentially benefit the growing farmed fish [24]. In 104 general, the inclusion of macroalgae into formulated fish diets without causing decreased growth 105 performance is approximately 10% [23]. However, the dietary macroalgae inclusion level that 106 fish can tolerate is dependent on the algal species and fish species, i.e. carnivorous versus 107 omnivorous fish, brown versus green macroalgae or indeed morphological differences in the fish 108 gastrointestinal tract [25]. 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.10.222604; this version posted August 10, 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. 109 There is a wealth of evidence outside of fish research showing that the gut microbiota is 110 intrinsically linked to digestive function, metabolism, immune support and general health as 111 shown in dogs [26] and rats [27] for example. For fish gut microbiota these links are less clearly 112 defined, though this is the focus of intensive research efforts in Atlantic salmon (S.
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • A Polysaccharide-Degrading Marine Bacterium Flammeovirga Sp. MY04 and Its Extracellular Agarase System
    中国科技论文在线 http://www.paper.edu.cn J. Ocean Univ. China (Oceanic and Coastal Sea Research) DOI 10.1007/s11802-012-1929-3 ISSN 1672-5182, 2012 11 (3): 375-382 http://www.ouc.edu.cn/xbywb/ E-mail:[email protected] A Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. MY04 and Its Extracellular Agarase System HAN Wenjun1), 2), 3), GU Jingyan1), 3), YAN Qiujie2), LI Jungang2), WU Zhihong3), *, GU Qianqun1), *, and LI Yuezhong3) 1) Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R . C hi n a 2) School of Life Science and Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China 3) State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, P. R. China (Received February 2, 2012; revised April 8, 2012; accepted May 29, 2012) © Ocean University of China, Science Press and Springer-Verlag Berlin Heidelberg 2012 Abstract Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported re- garding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and -1 -1 grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L ± 18.2 mg L liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These pro- -1 -1 teins have an activity of 310 U mg ± 9.6 U mg proteins.
    [Show full text]
  • Biodiversity of Psychrotrophic Microbes and Their Biotechnological Applications
    Journal of Applied Biology & Biotechnology Vol. 7(04), pp. 99-108, July-August, 2019 Available online at http://www.jabonline.in DOI: 10.7324/JABB.2019.70415 Biodiversity of psychrotrophic microbes and their biotechnological applications Ajar Nath Yadav1*, Neelam Yadav2, Shashwati Ghosh Sachan3, Anil Kumar Saxena4 1Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, Himachal Pradesh, India, 2Gopi Nath P. G. College, Veer Bahadur Singh Purvanchal University, Uttar Pradesh, India, 3Department of Bio-Engineering, Birla Institute of Technology, Ranchi, Jharkhand, India, 4ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India ARTICLE INFO ABSTRACT Article history: The extreme cold environments harbor novel psychrotrophic microbes. The psychrotrophic microbes have been reported Received on: December 02, 2018 Accepted on: January 16, 2019 as plant growth promoters and biocontrol agents for sustainable agriculture, in industry as cold-adapted hydrolytic enzymes and in medicine as secondary metabolites and pharmaceutical important bioactive compounds. Inoculation Available online: July 04, 2019 with psychrotrophic/psychrotolerant strains significantly enhanced root/shoot biomass and nutrients uptake as compared to non-bacterized control. The psychrotrophic microbes play important role in alleviation of cold stress in plant growing Key words: at high hill and low temperature and conditions. The psychrotrophic microbes have been reported from worldwide Adaptation, Biodiversity,
    [Show full text]
  • A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and Their Association with the Endangered, Endemic Snail Physella Johnsoni
    A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and their Association with the Endangered, Endemic Snail Physella johnsoni By Michael Bilyj A thesis submitted to the Faculty of Graduate Studies in partial fulfillment of the requirements for the degree of Master of Science Department of Microbiology Faculty of Science University of Manitoba Winnipeg, Manitoba October 2011 © Copyright 2011, Michael A. Bilyj 1 Abstract The seasonal population fluctuation of anoxygenic phototrophs and the diversity of cyanobacteria at the Sulphur Mountain thermal springs of Banff, Canada were investigated and compared to the drastic population changes of the endangered snail Physella johnsoni. A new species and two strains of Rhodomicrobium were taxonomically characterized in addition to new species of Rhodobacter and Erythromicrobium. Major mat-forming organisms included Thiothrix-like species, oxygenic phototrophs of genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised upwards of 9.6 x 104 CFU/cm2 of mat or 18.9% of total aerobic heterotrophic bacterial isolates at certain sites, while maximal purple nonsulfur and purple sulfur bacteria were quantified at 3.2 x 105 and 2.0 x 106 CFU/cm2 of mat, respectively. Photosynthetic activity measurements revealed incredibly productive carbon fixation rates averaging 40.5 mg C/cm2/24 h. A temporal mismatch was observed for mat area and prokaryote-based organics to P. johnsoni population flux in a ―tracking inertia‖ manner. 2 Acknowledgements It is difficult to express sufficient gratitude to my supervisor Dr. Vladimir Yurkov for his unfaltering patience, generosity and motivation throughout this entire degree.
    [Show full text]
  • Validation of the Asaim Framework and Its Workflows on HMP Mock Community Samples
    Validation of the ASaiM framework and its workflows on HMP mock community samples The ASaiM framework and its workflows have been tested and validated on two mock metagenomic data of an artificial community (with 22 known microbial strains). The datasets are available on EBI metagenomics database (project accession number: SRP004311). First we checked that the targeted abundances (based on number of PCR product) from both mock datasets were similar to the effective abundance (by mapping reads on reference genomes). Second, taxonomic and functional results produced by the ASaiM framework have been extensively analyzed and compared to expectations and to results obtained with the EBI metagenomics pipeline (S. Hunter et al. 2014). For these datasets, the ASaiM framework produces accurate and precise taxonomic assignations, different functional results (gene families, pathways, GO slim terms) and results combining taxonomic and functional information. Despite almost 1.4 million of raw metagenomic sequences, these analyses were executed in less than 6h on a commodity computer. Hence, the ASaiM framework and its workflows are proven to be relevant for the analysis of microbiota datasets. 1Data On EBI metagenomics database, two mock community samples for Human Microbiome Project (HMP) are available. Both samples contain a genomic mixture of 22 known microbial strains. Relative abundance of each strain has been targeted using the number of PCR product of their respective 16S sequences (Table 1). In first sample (SRR072232), the targeted 16S copies of the strains vary by up to four orders of magnitude between the strains (Table 1), whereas in second sample (SRR072233) the same 16S copy number is targeted for each strain (Table 1).
    [Show full text]
  • Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
    Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family.
    [Show full text]
  • {Replace with the Title of Your Dissertation}
    The Mechanism of Foaming in Deep-Pit Swine Manure Storage A Dissertation SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Mi Yan IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Adviser: Bo Hu October, 2016 © Mi Yan 2016 i Acknowledgements There are many people that contribute to this PhD thesis with their work, advice or encouragement. First of all, I would like to thank my advisor Dr. Bo Hu, who gave me the opportunity and long term support to write this dissertation. He gave me the freedom to work on my idea and plans, and gave great suggestions when I need support. There are many difficult time during this research, but there is always great support provided from him, from technical discussion to mental encouragement. I am also grateful to my committee members Dr. Larry Jacobson, Dr. Steve Severtson and Dr. Gerald Shurson. They took time from their tight schedule to make critical remarks and helpful suggestions, as well as their confidence on me and my work. Thanks are also dedicated to several experts, particularly to Dr. Chuck Clanton and David Schmidt for their valuable inputs and inspiring discussions. Besides valuable discussions, Dr. Brian Hetchler and Dr. Neslihan Akdeniz provide a great amount of valuable samples for experiments. I am also grateful to Dr. Michael Sadowsky that provided great help in microbial sequencing analysis, to Dr. LeeAnn Higgins and Dr. Susan Viper that provided great help in proteomic analysis. My colleagues at Bioproducts and Biosystems Engineering played an important role towards the successful completion of this dissertation.
    [Show full text]
  • The Role of Charcoal and Dietary Crude Protein Supplemented with Probiotic Escherchia Coli Strains UM2 and UM7
    Gut microbiome analysis in piglet models infected with Escherchia coli K88: The role of charcoal and dietary crude protein supplemented with probiotic Escherchia coli strains UM2 and UM7. by Shahab Meshkibaf A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfillment of the requirements of the degree of MASTER OF SCIENCE Department of Medical Microbiology and Infectious Diseases University of Manitoba Winnipeg Copyright © 2011 by Shahab Meshkibaf ABSTRACT Entrotoxigenic Escherichia coli (ETEC) K88 is a causative agent of post-weaning diarrhea (PWD) in early-weaned pigs. This study investigated the efficacy of two alternative diets, charcoal (0.1, 0.5, 1, and 2%) and a low crude protein (CP) diet (17%) supplemented with probiotic E. coli strains (UM2 and UM7), against PWD infection in ETEC K88 challenged piglets. The present study found that charcoal had no effect on the challenged piglets’ performance, ileal and colonic microbiota or their fermentation end products. There was, however, a correlation between charcoal dosage and fecal consistency score. Charcoal reduced the ileal mucosal attached ETEC K88. Feeding a low-CP diet resulted in a lower ileal ammonia concentration. The low-CP diet reduced the E. coli populations in the ileal digesta as well as lowered mRNA expression of the IL-1ß. We concluded that the use of both 1-2% charcoal diet and a low-CP diet supplemented with probiotic E. coli strains were effective in reducing the incidence and severity of PWD infection. ACKNOWLEDGEMENTS I would like to thank all people who have helped and inspired me during my graduate study.
    [Show full text]
  • Acetobacteroides Hydrogenigenes Gen. Nov., Sp. Nov., an Anaerobic Hydrogen-Producing Bacterium in the Family Rikenellaceae Isolated from a Reed Swamp
    %paper no. ije063917 charlesworth ref: ije063917& New Taxa - Bacteroidetes International Journal of Systematic and Evolutionary Microbiology (2014), 64, 000–000 DOI 10.1099/ijs.0.063917-0 Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp Xiao-Li Su,1,2 Qi Tian,1,3 Jie Zhang,1,2 Xian-Zheng Yuan,1 Xiao-Shuang Shi,1 Rong-Bo Guo1 and Yan-Ling Qiu1 Correspondence 1Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Yan-Ling Qiu Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China [email protected] 2University of Chinese Academy of Sciences, Beijing 100049, PR China 3Ocean University of China, Qingdao, 266101, PR China A strictly anaerobic, mesophilic, carbohydrate-fermenting, hydrogen-producing bacterium, designated strain RL-CT, was isolated from a reed swamp in China. Cells were Gram-stain- negative, catalase-negative, non-spore-forming, non-motile rods measuring 0.7–1.0 mm in width and 3.0–8.0 mm in length. The optimum temperature for growth of strain RL-CT was 37 6C (range 25–40 6C) and pH 7.0–7.5 (range pH 5.7–8.0). The strain could grow fermentatively on yeast extract, tryptone, arabinose, glucose, galactose, mannose, maltose, lactose, glycogen, pectin and starch. The main end products of glucose fermentation were acetate, H2 and CO2. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth; however, it stimulated growth slightly. Nitrate, sulfate, sulfite, thiosulfate, elemental sulfur and Fe(III) nitrilotriacetate were not reduced as terminal electron acceptors.
    [Show full text]
  • Comparative Analysis of the Composition Of
    Comparative Analysis of the Composition of Intestinal Bacterial Communities in Dastarcus helophoroides Fed Different Diets Author(s): Wei-Wei Wang, Cai He, Jun Cui, Hai-Dong Wang, and Meng-Lou Li Source: Journal of Insect Science, 14(111):1-13. 2014. Published By: Entomological Society of America DOI: http://dx.doi.org/10.1673/031.014.111 URL: http://www.bioone.org/doi/full/10.1673/031.014.111 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Journal of Insect Science: Vol. 14 | Article 111 Wang et al. Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets Wei-Wei Wang,1a Cai He,2b Jun Cui,1c Hai-Dong Wang,1d and Meng-Lou Li1e* 1Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, P.
    [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]
  • Supplemental Material S1.Pdf
    Phylogeny of Selenophosphate synthetases (SPS) Supplementary Material S1 ! SelD in prokaryotes! ! ! SelD gene finding in sequenced prokaryotes! We downloaded a total of 8263 prokaryotic genomes from NCBI (see Supplementary Material S7). We scanned them with the program selenoprofiles (Mariotti 2010, http:// big.crg.cat/services/selenoprofiles) using two SPS-family profiles, one prokaryotic (seld) and one mixed eukaryotic-prokaryotic (SPS). Selenoprofiles removes overlapping predictions from different profiles, keeping only the prediction from the profile that seems closer to the candidate sequence. As expected, the great majority of output predictions in prokaryotic genomes were from the seld profile. We will refer to the prokaryotic SPS/SelD !genes as SelD, following the most common nomenclature in literature.! To be able to inspect results by hand, and also to focus on good-quality genomes, we considered a reduced set of species. We took the prok_reference_genomes.txt list from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/, which NCBI claims to be a "small curated subset of really good and scientifically important prokaryotic genomes". We named this the prokaryotic reference set (223 species - see Supplementary Material S8). We manually curated most of the analysis in this set, while we kept automatized the !analysis on the full set.! We detected SelD proteins in 58 genomes (26.0%) in the prokaryotic reference set (figure 1 in main paper), which become 2805 (33.9%) when considering the prokaryotic full set (figure SM1.1). The difference in proportion between the two sets is due largely to the presence of genomes of very close strains in the full set, which we consider redundant.
    [Show full text]