1. Boundless Lecture Slides Free to share, print, make copies and changes. Get yours at www.boundless.com Available on the Boundless Teaching Platform

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4. Detecting Uncultured Microorganisms Viral Genomes in Nature Environmental Genomics Microbial Genetics > Environmental Genomics Free to share, print, make copies and changes. Get yours at www.boundless.com www.boundless.com/microbiology?campaign_content=book_5777_section_96&campaign_term=Microbiology&utm_campaign=powerpoint&utm_ medium=direct&utm_source=boundless

5. Many organisms that can cause diseases are not culturable, so a unicellular culture cannot be obtained. Initial studies of microbial fauna showed that they are more diverse than expected and contained many microbes that were not culturable. Advances in molecular biological techniques allow the sequencing of all or at least many of the genomes of microbes found in a sample. Detecting Uncultured Microorganisms Free to share, print, make copies and changes. Get yours at www.boundless.com www.boundless.com/microbiology/textbooks/alternative-to-microbiology-principles-and-explorations-8th-jacquelyn-g-black-0470646217- 9780470646212/microbial-genetics-7/environmental-genomics-96/detecting-uncultured-microorganisms-510- 915?campaign_content=book_5777_section_96&campaign_term=Microbiology&utm_campaign=powerpoint&utm_medium=direct&utm_source=b oundless Environmental Shotgun Sequencing (ESS) View on Boundless.com Microbial Genetics > Environmental Genomics

6. Viruses infect all types of cellular life including animals, plants, bacteria, and fungi. Metagenomic sequencing has identified that there are an enormous number of species of virus in nature, showing that a a teaspoon of water has a million species of viruses. Viruses kill about 20% of the microbes that constitute the oceans microbial fauna, each day. This viral-driven biological turn over is needed for for life on earth to continue. Viruses can transfer genetic material from one species to another, and as such viruses may be a main driving force of evolution. Viral Genomes in Nature Free to share, print, make copies and changes. Get yours at www.boundless.com www.boundless.com/microbiology/textbooks/alternative-to-microbiology-principles-and-explorations-8th-jacquelyn-g-black-0470646217- 9780470646212/microbial-genetics-7/environmental-genomics-96/viral-genomes-in-nature-511- 7672?campaign_content=book_5777_section_96&campaign_term=Microbiology&utm_campaign=powerpoint&utm_medium=direct&utm_source= boundless Environmental Shotgun Sequencing (ESS) View on Boundless.com Microbial Genetics > Environmental Genomics

7. Free to share, print, make copies and changes. Get yours at www.boundless.com Appendix

8. Key terms culturable Able to be cultured (grown in a suitable environment). high-throughput sequencing Technologies that parallelize the sequencing process, producing thousands or millions of sequences at once. metagenomics The study of genomes recovered from environmental samples; especially the differentiation of genomes from multiple organisms or individuals, either in a symbiotic relationship, or at a crime scene. shotgun sequencing A DNA sequencing technique in which a large number of small fragments of a long DNA strand are generated at random, sequenced, and reassembled to form a sequence of the original strand. stool Feces; excrement. Free to share, print, make copies and changes. Get yours at www.boundless.com Microbial Genetics

9. Environmental Shotgun Sequencing (ESS) (A) sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds Free to share, print, make copies and changes. Get yours at www.boundless.com Wikimedia. "Environmental shotgun sequencing." CC BY http://commons.wikimedia.org/wiki/File%253AEnvironmental_shotgun_sequencing.png View on Boundless.comCC BYhttp://commons.wikimedia.org/wiki/File%253AEnvironmental_shotgun_sequencing.pngView on Boundless.com Microbial Genetics

10. Environmental Shotgun Sequencing (ESS) (A) sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds Free to share, print, make copies and changes. Get yours at www.boundless.com Wikimedia. "Environmental shotgun sequencing." CC BY http://commons.wikimedia.org/wiki/File%253AEnvironmental_shotgun_sequencing.png View on Boundless.comCC BYhttp://commons.wikimedia.org/wiki/File%253AEnvironmental_shotgun_sequencing.pngView on Boundless.com Microbial Genetics

11. Phocine distermper encephalitis This is a section from a harbor seal cerebral cortex. The white areas are tissue lesions caused a phocine distermper viral infection. Free to share, print, make copies and changes. Get yours at www.boundless.com Wikimedia. "Phocine distemper encephalitis." Public domain http://commons.wikimedia.org/wiki/File%253APhocine_distemper_encephalitis.jpg View on Boundless.comPublic domainhttp://commons.wikimedia.org/wiki/File%253APhocine_distemper_encephalitis.jpgView on Boundless.com Microbial Genetics

12. Free to share, print, make copies and changes. Get yours at www.boundless.com Microbial Genetics Prior to recent advances in __________ detecting and identifying microorganisms from a non-uniform (uncultured) sample was difficult. A) All of these answers B) DNA amplification C) computational power D) bioinformatics

13. Free to share, print, make copies and changes. Get yours at www.boundless.comwww.boundless.com Boundless - LO. "Boundless." CC BY-SA 3.0 http://www.boundless.com/CC BY-SA 3.0http://www.boundless.com/ Microbial Genetics Prior to recent advances in __________ detecting and identifying microorganisms from a non-uniform (uncultured) sample was difficult. A) All of these answers B) DNA amplification C) computational power D) bioinformatics

14. Free to share, print, make copies and changes. Get yours at www.boundless.com Microbial Genetics Viruses are often viewed as harmful, however viruses account for most of the __________ in the marine environment. A) carbon recycling B) oxygen recycling C) mammal deaths D) algal blooms

15. Free to share, print, make copies and changes. Get yours at www.boundless.comwww.boundless.com Boundless - LO. "Boundless." CC BY-SA 3.0 http://www.boundless.com/CC BY-SA 3.0http://www.boundless.com/ Microbial Genetics Viruses are often viewed as harmful, however viruses account for most of the __________ in the marine environment. A) carbon recycling B) oxygen recycling C) mammal deaths D) algal blooms

16. Attribution Wiktionary. "culturable." CC BY-SA 3.0 http://en.wiktionary.org/wiki/culturableCC BY-SA 3.0http://en.wiktionary.org/wiki/culturable Wiktionary. "shotgun sequencing." CC BY-SA 3.0 http://en.wiktionary.org/wiki/shotgun+sequencingCC BY-SA 3.0http://en.wiktionary.org/wiki/shotgun+sequencing Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//microbiology/definition/high-throughput- sequencingCC BY-SA 3.0http://www.boundless.com//microbiology/definition/high-throughput- sequencing Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metagenomics#SequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics#Sequencing Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metagenomics#SequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics#Sequencing Wikipedia. "DNA sequencing." CC BY-SA 3.0 http://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_sequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_sequencing Wikipedia. "Bacteria." CC BY-SA 3.0 http://en.wikipedia.org/wiki/BacteriaCC BY-SA 3.0http://en.wikipedia.org/wiki/Bacteria Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metagenomics#SequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics#Sequencing Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metagenomics#SequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics#Sequencing Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metagenomics#SequencingCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics#Sequencing Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/MetagenomicsCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics Wikipedia. "Metagenomics." CC BY-SA 3.0 http://en.wikipedia.org/wiki/MetagenomicsCC BY-SA 3.0http://en.wikipedia.org/wiki/Metagenomics Wikipedia. "Virus." CC BY-SA 3.0 http://en.wikipedia.org/wiki/VirusCC BY-SA 3.0http://en.wikipedia.org/wiki/Virus Wikipedia. "Virus." CC BY-SA 3.0 http://en.wikipedia.org/wiki/VirusCC BY-SA 3.0http://en.wikipedia.org/wiki/Virus Wikipedia. "Virus." CC BY-SA 3.0 http://en.wikipedia.org/wiki/VirusCC BY-SA 3.0http://en.wikipedia.org/wiki/Virus Wiktionary. "stool." CC BY-SA 3.0 http://en.wiktionary.org/wiki/stoolCC BY-SA 3.0http://en.wiktionary.org/wiki/stool Boundless Learning. "Boundless." CC BY-SA 3.0 http://www.boundless.com//biology/definition/metagenomicsCC BY-SA 3.0http://www.boundless.com//biology/definition/metagenomics Free to share, print, make copies and changes. Get yours at www.boundless.com Microbial Genetics