Determination of the distribution, taxonomy and diversity of micro-organisms from DHABs, and isolation of strains with biotechnological potential BIODEEP-WP4.

Slides:

Advertisements

Similar presentations

Week 10W New This Week: Last week: Gram (+) Bacteria ID

Advertisements

Bacteria Classification

Bacterial Cells How is bacteria a part of recycling and biodegrading? It breaks down organic material for plant roots to use Draw the basic appearance.

Welcome to Who Wants to be a Millionaire

Latest from Essex Milano May 2004

Density, Viscosity, and Buoyancy

Anaerobic Culture Techniques

NITROGEN CYCLE. Nitro Composes about four-fifths (78.03 percent) by volume of the atmosphere an essential part of the amino acids. It is a basic element.

Characterization of Cellulolytic and Fermentative Communities in Everglades Soils Ilker Uz Soil and Water Science Department University of Florida.

Chapter 6 Microbial growth. Microbial growth – increase in the number of cells Depends on environmental factor such as temperature. Divided into groups.

1 Prokaryotic Microbial Diversity Early attempts at taxonomy: all plants and animals Whitaker scheme (late 20th century): Five kingdoms –Animalia, Plantae,

Mechanisms of U(VI) Reduction and Sediment Growth in Desulfovibrio Lee Krumholz Department of Botany and Microbiology.

Halophiles By Aubrey McDonald.

General Microbiology (MICR300) Lecture 8 Microbial Diversity: Archaea (Text Chapters: )

Methane CH4 Greenhouse gas (~20x more powerful than CO2)

Prokaryotic Microbial Diversity

Red Layer Microbial Observatory Biology In-Lab Workshop Photosynthetic Microbes from Local Rivers & Beyond.

Lab 6 Goals and Objectives: Exercise 18: Motility Determination – presence of flagella Exercise 27: Effect of Oxygen on Growth Exercise 37: Morphological.

Lecture 19 Redox Environments in the Oceans. Multi-colored sediments! What’s going on here???

Methods in Microbial Ecology

Bacterial Growth By Dr. Marwa Salah. Learning objectives Definition of bacterial growth. Requirements of bacterial growth. Types of respiration in bacteria.

Microbiology Microbiology lab. Skills Bacteriology 1 & Dr. Ibrahim Hassan, Microbiology PhD.

Selected and Differential Media. Define Selective Media Differential Media Enriched Media.

Haloferax sulfurifontis sp. nov., a Halophilic Archaeon Isolated from a Low Salt Sulfide-rich Spring K. N. Savage 1, M. S. Elshahed 1, A. Oren 2, L. R.

University of Essex BIODEEP-WP3 Analysis of species diversity, community structures and phylogeny of microorganisms and meiofauna in the Mediterranean.

Review Remember from earlier this year that there are two broad categories of organisms: *Prokaryotes – have No membrane bound organelle *Eukaryotes –

Archaebacteria and Eubacteria Important Features -all are prokaryotes -all have plasmids (small circular packages of DNA) -most have peptidoglycan in.

22.1 Enrichment Isolation –The separation of individual organisms from the mixed community Enrichment Cultures –Select for desired organisms through manipulation.

Chapter 6 – Microbial Growth $100 $200 $300 $400 $500 $100$100$100 $200 $300 $400 $500 Physical Requirements Chemical Requirements Growth of Bacterial.

Biodeep May 12-14, 2003 “Nature has more imagination than our dreams”

Bacterial communities in the seawater-brine chemocline in deep anoxic hypersaline basins (DHABs) in the eastern Mediterranean Sea Borin S., Daffonchio.

Isolation of Mn(II)-oxidizing Bacteria HMC 2010 short presentation Maren Emmerich.

19.1 Phylogenetic and Metabolic Diversity of Archaea Archaea share many characteristics with both Bacteria and Eukarya Archaea are split into two major.

Archaeal extreme halophiles (halobacteria, haloarchaea) require high concentration of NaCl for growth found in Great Salt Lake, Dead Sea, evaporation ponds.

CoNISMa, Consorzio Nazionale Interuniversitario Scienze del Mare Partner 1c DISTAM Università degli Studi di Milano Daniele Daffonchio Tullio Brusa Sara.

Aerobic Respiration. Anaerobic Respiration Chemolithotrophic respiration.

CoNISMa, Consorzio Nazionale Interuniversitario Scienze del Mare Partner 1c DISTAM Università degli Studi di Milano Daniele Daffonchio Tullio Brusa Sara.

BioDeep Meeting V: Marseilles, th April 2002 (1 st report) Workpackage 5 : Microbial metabolic activities Armand Bianchi, Jean Garcin, Christian.

Viable halophilic microorganisms in deep ancient salt deposits Helga Stan-Lotter 1, Sergiu Fendrihan 2 1 University of Salzburg, Austria; 2 Romanian Bioresource.

WP5 - MICROBIAL METABOLIC ACTIVITIES CNRS DR 12 - LMM BACTERIAL ACTIVITIES * STRICT ANAEROBIC ACTIVITIES * Methane Production (MP) * Sulfate Reduction.

Dusty Berggren Dissimilatory Sulfate Reducers (SRBs)

University of Essex BIODEEP-WP3 Analysis of species diversity, community structures and phylogeny of microorganisms and meiofauna in the Mediterranean.

Department of Microbiology, University of Oklahoma

CRISPR Direct Repeat Sequences Olivia Ho-Shing 22 November 2009.

Prochlorococcus : probes; distribution; Chile dot blots; Indian Ocean cruise Synechococcus cultures : status; multilocus sequencing approach 13 C/ 14 C.

BIODEEP MEETING - Marseille, April 2002 Workpackages 4 and 5 - Fabienne MOREL, Sam DUKAN Objectives : isolation of new strains from DHABs Interface.

The Classification Of Genus Bacillus

Chapter 6 Microbial Nutrition and Growth. Microbial Growth Microorganisms are found in the harshest of environments – Deep ocean – Volcanic vents – Polar.

Microbiology Colony Morphology. Key Organisms for study  Gram negative organisms  PA - Pseudomonas aeruginosa  PV- Proteus vulgaris  EC- Escherichia.

Influence of Chemical and Physical Factors in Environment

University of Essex BIODEEP-WP3 Analysis of species diversity, community structures and phylogeny of microorganisms and meiofauna in the Mediterranean.

Halophilic Archaea at Zodletone Spring

Chemical Properties of Seawater. I. The water molecule 1.Made of two hydrogen atoms and one oxygen atom.

- It is nutritive ingredient needed by a particular m.o to enhance it growth under laboratory condition. -Different type of media: 1- Growth media(general.

NAS Lecturer: Mr. M. Zivuku LECTURE 4 1 Objectives By the end of this unit, you should be able to ; Explain the cultivation of bacteria in terms of in.

PHT382 Lab. No. 3.

Biological adaptation to DHABs

Partner 1c CoNISMa, Consorzio Nazionale Interuniversitario Scienze del Mare DISTAM Università degli Studi di Milano Daniele Daffonchio Tullio Brusa Sara.

WP5 - MICROBIAL METABOLIC ACTIVITIES CNRS DR 12 - LMGEM

BIODEEP-WP4 BIODEEP-WP5 Andrea Sass , Terry McGenity

Biolog identification

Kingdom Archaebacteria

Flow diagrams (i) (ii) (iii) x – Example

3. Old Brain I III II V IV VII VI VIII IX X XII XI

Terry’s Code of Ethics for Bus Service Contractors

LECTURE 7. DOMAIN Archaea

Sequence of chemical compounds being reduced in soil after submergence

Aquatic microbial groups

Volume 22, Issue 9, Pages (September 2015)

Presentation transcript:

Determination of the distribution, taxonomy and diversity of micro-organisms from DHABs, and isolation of strains with biotechnological potential BIODEEP-WP4 University of Essex Andrea Sass, Terry McGenity, Boyd McKew

cultivation experiments with a suite of oxic and anoxic media variations in: Salt concentration Oxygen regime Organic substrate, electron acceptors identification of isolates

total Number of isolates on agar plates Summary of previously presented results: Oxic media

Isolates originating from liquid oxic enrichment cultures

new isolates from oxic media (samples cruise 2002): emphasis on highly saline media, all liquid growing organisms screened for unique morphology and ability to grow on sea water four strains isolated Idiomarina sp. (UI, extremely halotolerant, aerotactic) Bacillus halophilus (BS, halotolerant) -Proteobacterium (AS, halotolerant) Halorhabdus utahensis (AS,extremely halophilic)

Almost all isolates from sediments are related to Bacillus sp. found in marine or other saline environmens or e.g. glacial ice Almost all isolates from interfaces are related to organisms commonly found in marine plankton

AS6 BS6 NRRLB14851 (Marine) HTA437 (Mariana Trench) BS12 G550K (glacial Ice, 500,000 yr old) MK03 KASA34 (alkalaphilic, cold desert) B.macroides DS9 PL16 (marine sediments) DS5 MB-5 (marine sediments) YKJ-10 (fermented seafood) US7 BS29 LMG20241 (mural painting) AS28 B. pumilus BS3 YY (Paper mill) AS7 MB9 (marine sediments) US13 AS2 AS3 BS18 Virgib. pantothenticus (salt crystal, 293– 250 million yr old) Gracilib. halotolerans Marinococcus halophilus BS17 Halob. salinus (salt lake) Halob. litoralis Halob. trueperi US16 B. halophilus Marinococcus albus Halob. halophilus Halob. (salt lake) OS-5 (coastal marsh) AS5 KSM-S237 (alkaliphilic) DS16 BS25 DSM 8724 (alkaliphilic) B. alcalophilus MN-003 (oil contaminated marine sediments) DS1 AS12 US2 B. licheniformis US4 B. licheniformis DSK25 (deep-sea) US1 G200-T16 (Glacial ice) KSM-KP43 (alkaliphilic) G200-N5 (glacial ice, 200 yr old) DS Jukes-Cantor Fitch-Margoliash Halobacillus, Gracilibacillus Virgibacillus, Salibacillus RNA-group

Anoxic media Number of isolates from anoxic enrichments Summary of previuosly presented results:

Affiliation of anaerobic isolates

Clostridium barkeri (XV) Clostridium propionicum DSM 1682 T (XIVb) Clostridium oroticum (XIVa) Clostridium aerotolerans (XIVa) Clostridium indolis (XIVa) Peptostreptococcus micros (XIII) Sporoanaerobacter acetigenes (XII) Clostridium acidiurici (XII) Clostridium paradoxum (XI) Clostridium sp. FL4 Clostridium oceanicum (I) AN-AS4B AN-AS17 AN-AS4C AN-AS3B AN-BS1C AN-AS6E AN-AS6C AN-AS8 AN-US3 Clostridium proteolyticum (II) Clostridium pfennigii Clostridium cellulolyticum (III) Clostridium sporosphaeroides (IV) Clostridium thermoautotrophicum (VI) Thermoanaerobacterium thermosulfurigenes (VII) Sporomusa sphaeroides (IX) Thermoanaerobacter ethanolicus (V) Bacillus subtilis Clostridium spiroforme (XVIII) Actinomyces bovis 0.1 Thermohalobacter berrensis (XII) Tepidibacter thalassicus Maximum likelihood

Flexibacter aggregans ssp. catalaticus AN-BI4 AN-BI3A Desulfovibrio vulgaris Wolinella succinogenes Helicobacter pylori Thiomicrospira denitrificans Arcobacter nitrofrigilis Campylobacter jejuni Sulfurospirillum arcachonense Chlorobium limicola Sulfurospirillum barnesii Sulfurospirillum deleyianum Sulfurospirillum sp. strain 18.1 Uncultured hydrothermal vent bacterium Cytophaga fermentans Marinilabilia salmonicolor Anaerophaga thermohalophila Rikenella microfusus Empedobacter brevis Chryseobacterium gleum Tenacibaculum maritimum Flavobacterium aquatile Cytophaga marinoflava Bacteroides fragilis Porphyromoas asaccharolytica Sporocytophaga myxococcoides 0.1 Maximum likelihood -Proteobacteria CFB-Group

10 m A B

Actinomyces bovis AN-BI5B Megasphaera elsdenii Clostridium butyricum Bacillus subtilis Acetohalobium arabaticum Orenia marismortui Orenia salinaria Halanaerobacter lacunarum Halanaerobacter chitinivorans Halobacteroides halobius AN-AI1A AN-DS1 AN-UI1A Halanaerobium praevalens Halanaerobium sp. KT-2/3-3 (Kebrit Deep, Red Sea) Halanaerobium congolense Halanaerobium saccharolyticum Halothermothrix orenii 0.1 Maximum likelihood

54R Atalante-A Atalante B Atalante B T36 T31 clMT17 T42 AN-AI3 Methanospirillum hungatei Halogeometricum borinquense Halobaculum gomorrense Halococcus salifodinae Halococcus morrhuae Halobacterium salinarum Halorubrum saccharovorum Halorubrum sodomense Halorubrum vacuolatum Natrialba asiatica Natrialba magadii Natrinema pellirubrum Natronorubrum bangense Natronococcus occultus Natronobacterium gregoryi Haloarcula marismortui rrnA Haloarcula marismortui rrnB Haloarcula sinaiiensis major Haloarcula sinaiiensis minor Halomicrobium mukohataei Haloferax volcanii Haloterrigena thermotolerans Natronomonas pharaonis Halosimplex carlsbadense ATCC BAA-75 gene A Halosimplex carlsbadense ATCC BAA-75 gene B Halosimplex carlsbadense ATCC BAA-75 gene C Halorhabdus utahensis Halobiforma haloterrestris 10 nuc substitutions per 100 bases Jukes-Cantor distance calculation Fitch-Margoliash treeing algorithm 550 nucleotides of 16S rRNA compared Haloarchaea have been isolated from LAtalante Basin

new enrichment approaches with media (samples cruise 2002): emphasis on: methane-oxidizing bacteria sulfate-reducing bacteria no methane consumption detectable no growth of sulfate-reducing bacteria no more anaerobic isolates

Isolates with reference to affiliation and environment sampled

Anaerobic bacteria: Anaerobic extremely halophilic bacteria from every basin, different from each basin From sediments predominantly marine anaerobic sporeformers were obtained Most strains from lAtalante basin Archaebacteria from lAtalante interface and sediment No SRB

from BI, AS and BS all moderately halophilic predominantly Gram negative -Proteobacteria obtained from BI predominantly Gram-positive Sporeformers obtained from AS and BS (matches results from isolation on agar plates) Halobacillus sp. were often isolated anaerobically in high-salt media Aerobic isolates from anoxic enrichments:

Bannock interface: High number of isolates, mostly aerobic LAtalante and Urania interface: Fewer isolates, mostly anaerobic Quality of interface sample critical for cultivation success sample taken for cultivation with higher proportion of low salinity (oxic) waters? samples for cultivation with higher proportion of brine?