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Diversity II Notes Week 3

by: Jacob Erle

Diversity II Notes Week 3 211

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These are the lecture notes on The Human Microbiome and Introduction to Protists. The notes have been color coded to distinguish different things: Blue = common, general notes Green = interestin...
Diversity of Life II
Justine Weber
Class Notes




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This 6 page Class Notes was uploaded by Jacob Erle on Friday February 5, 2016. The Class Notes belongs to 211 at Syracuse University taught by Justine Weber in Spring 2016. Since its upload, it has received 41 views. For similar materials see Diversity of Life II in Foreign Language at Syracuse University.


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Date Created: 02/05/16
Diversity of Life II Notes Week 3 2/2/16 The Human Microbiome Evolution within a Microbial Context  unicellular microbes alone for ~3.5 billion years  early eukaryotes evolved in a prokaryotic context  adaptive immunity provides ‘memory’ of microbes o faster immune response o permits distinction of pathogenic vs. beneficial microbes Human Microbiome  bacteria have been in our guts for awhile  the human gut is:  very nutrient rich, (consistently) warm, moist, low O2 levels  until recently it has been hard to say what microbes do for us Research has been done in the Human Microbiome Project (HMP), American Gut, and  Metagenomics of the Human Intestinal Tract (MetaHIT)  HMP is the more traditional of the 3  American Gut allows people to send in samples to be sequenced and be compared to others  in the USA Goals of HMP 1.) Do individuals share a core human microbiome? 2.) Is there a correlation between microbial population structure and human genotype? 3.) Differences in human microbiome correlate with human health? 4.) Differences in relative abundance of bacteria? Gut Environment   Stomach has pH value of 2, but has plenty of bacteria living there (see Helicobacter) o Prior to 1982, stomach was thought to be sterile because of its high acidity  Largest diversity of bacteria seen in the Large intestine  neutral pH  The human gut is: o Diverse and has an abundance of nutrients o Moist and dark o Anaerobic o Very crowded and acidic There are several different lifestyle strategies for obtaining necessary nutrients.  The main  ones are: o Autotrophy – using elements/compounds found in the external environment  (sunlight) to energize materials into usable energy (Ex. Photosynthesis) o Heterotrophy – obtaining energy from usable materials and compounds present o *Lithotrophy – extracting energy from inorganic compounds (ammonium,  hydrogen sulfide) already found in the system  Heterotrophy is the strategy mainly used by the gut bacteria HMP Methods o HMP relied heavily on molecular methods o Unavailable until the 90’s o Based on sequencing and comparing DNA molecules o Doesn’t require cultivation  The majority of microbes cannot be cultivated (>99%) o Provides both taxonomic and functional information o Don’t provide direct evidence of function  Studies genes which can be potential, but not definite, indicators  o There are two main techniques used once total community DNA from a microbial  community has been extracted o Community Sampling Approach  Sequence and generate single­gene phylogenetic tree  Useful for identifying what is present in the community and ID’ing any novel  phenotypes  No understanding of how or why certain community members are present o Environmental Genomics Approach  ID gene categories present with partial to complete genomes  Able to link genes to phylotypes Diversity in Human Microbiome  4 most abundant phyla:  Skin, Nasal, Oral and Gastrointestinal o Skin and nasal communities close correlation o Gut and oral communities different from everything else o Urogenital somewhat different but does overlap somewhat with skin and nasal  Propionibacterium acnes live on skin and nose of most people  Bacteroides most abundant, and perhaps the most important, genus in the gut of (healthy)  people  E. coli – found in the gut of most (healthy) subjects, but has very low abundance Overview of Map Findings  Pathogens were found, but they were a small minority  Unexpected diversity found in most sites (thousands, not hundreds, of species)  Few generalists, and many specialists  Unrelated taxa often found in the same body site Prominant Bacterial Taxa Gut  A diversity of taxa within the Bacteroides genus widely prevalent and abundant in the gut.  Firmicutes (phylum) make up the largest portion of gut microbes Mouth  High degree of overlap between bacterial communities in tongue, cheek, and plaque.  Streptococcus species dominate oral cavity. Skin/Nose  Propionobacterium acnes widely prevalent across subjects.  Staphylococcus epidermidis widely prevalent on skin. Presence of core microbiome?  Sampling of tongue and feces to evaluate phyla and function results o Very inconsistent taxa seen  o Functions are constant across all taxa Functions are stable, required o Enormous variability in microbial taxa across individuals Functions of Microbiome have really expanded over the years  Pathogen resistance o Niche filling o Some microbes even synthesize antibiotics  Train and develop Immune System o Collect birth canal bacteria samples to inject in C­section infants, who lack bacteria  Synthesize many essential Amino Acids Applications to Water Quality  Water quality indications  pollution, presence of pathogens o Better to look for those easier to detect  Current indicator is E.coli but Bacteroides is easier to look for, more abundant and  prevalent 2/4/16 Protists – Part I Protists are:  non monophyletic; formerly their own Kingdom  all eukaryotes   many terrestrial and aquatic ecosystems could not function without protists  unicellular or in colonies without differentiation into tissues Why study Protists?  Ubiquitous – found everywhere that has water   variety of forms and functional types  many species undescribed  Underestimated Diversity  o small fraction of diversity in total number of described species, but protists have the  greatest genetic diversity of all eukaryotes  phytoplankton – base of aquatic food webs o responsible for ~50% of all photosynthesis on Earth  ½ of all O2 in atmosphere  microconsumers in decomposing dead matter in soil and water  Biofuel and nutritional supplements Old terms and groupings of protists  originally classified by nutritional modes: o photosynthetic protists o protozoa – heterotrophic protists  Protozoa often were separated by mode of locomotion o Mastigophora – flagellates o Ciliophora – ciliates  o Sacrodina – pseudopodia o Sporozoa – parasites, with no obvious locomotive structures o ………..NULL AND VOID  Modern biochemical, ultrastructure, and genetic analytic techniques have shown the ‘classic’  groupings don’t reflect correct phylogenetic relationships Endosymbiotic Theory – responsible for generating diversity of protists?   1 bacterium engulfs another, but doesn’t digest the engulfed o 1 gets enhanced chemical processes taken care of, and the other gets predator  protection and/or less energy expenditures  Origin of Mitochondria and Chloroplasts Many eukaryotes diversified as the result of many endosymbiotic interactions  Cyanobacteria were the original photosynthetic on Earth, ~3.5BYA  Scientists now able to study phylogeny by looking at mtDNA and/or membrane  structures (comparative morphology)  Alveolate Protists – 10,000 described species  System of membranous sacs beneath the plasma membrane (alveoli)  Similar cell surface pores and extrusive organelles – trichocysts  Similar mitochondrial structure – tubular cristae  Mostly single­celled, colonial is less common  Diverse nutritional modes in different groups Dinoflagellates (‘dinos’ = ‘whirling’, ‘flagellum’ = ‘whip’)  Habitat – mostly aquatic:  freshwater, estuarine, and more than 90% are found in  marine habitats o Found in all kinds of aquatic habitats in NY  Morphology o Amphiesma – complex cell covering and the Alveoli – flattened vesicles o Theca – armored cellulose plates supported by vesicles  ‘Naked’ – no cellulose plates o Typically 2 flagella – 1 equatorial, 1 perpendicular that are in grooves o Typically large cells (from 2micrometers to 2 millimeters)  o Some have spines  protect against predators that would otherwise  swallow them whole  More prominent spines can be induced to based on responses to  predation in their environment  o Unique nuclear structure o 5­10 times the DNA of most eukaryotic cells; chromosomes are  continuously condensed o When they have chloroplasts they have unique pigments; these have  diverged from a unique endosymbiotic event  Different pigments travel at different wavelengths, particularly  underwater  chlorophylls a and c2, peridinin (unique carotenoid), βcarotene,  diadinoxanthin and dinoxanthin (xanthophylls)    Store extra photosynthate as starch and oils  Ecology o often very motile; can travel to the surface to depths of 100m below and  back with no trouble  most single­celled organisms are fine at these depths  fewer air  spaces  move vertically in order to get at different nutrients available  during different times of the year  photosynthetic and non­photo species are about 50­50   some photosynthetic species are also mixotrophic – heterotrophic  and autotrophic  characteristic is common in protists, less common in plants  non­photosynthetic dinoflagellates (and mixotrophs) can take up  dissolved material or are predatory  most are free­living, but some are parasites/symbiotes on seaweeds or marine animals  Ex. zooxanthellae (non­motile stage) in corals –  endosymbiotes of coral tissues o Endosymbiotic interactions responsible for the  huge amount of coral diversity we see in oceans  today o Some are toxic, especially in estuaries and oceans  “Red tides” – harmful algal blooms that kill  fish, and others higher up on the food chain  by producing   Pfisteria outbreaks in  estuaries  Life cycle and reproduction o Asexual by binary fission o Some are sexual with 2 divisions, one after gametes fuse and one after cell dormancy o Can overwinter or make cysts  Examples:  Ceratium, Peridinium o Freshwater, seasonally abundant locally, photosynthetic and/or  mixotrophic See lecture slides for bioluminescence


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