Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2015 Microbial community diversity in freshwater sponges from Lake Baikal/Protein size in three domains of life and examples of unusually large proteins in Porifera: A review Katrina Agno Lutap Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons, and the Molecular Biology Commons Recommended Citation Lutap, Katrina Agno, "Microbial community diversity in freshwater sponges from Lake Baikal/Protein size in three domains of life and examples of unusually large proteins in Porifera: A review" (2015). Graduate Theses and Dissertations. 16627. https://lib.dr.iastate.edu/etd/16627 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. ! Microbial!community!diversity!in!freshwater!sponges!from!Lake!Baikal! ! Protein!size!in!three!domains!of!life!and!examples!of!unusually!large!proteins!in! Porifera:!A!review! ! by! ! Katrina!A.!Lutap!! ! ! ! A!thesis!submitted!to!the!graduate!faculty! ! in!partial!fulfillment!of!the!requirements!for!the!degree!of! ! MASTER!OF!SCIENCE! ! ! Major:!Molecular,!Cellular,!and!Developmental!Biology! ! Program!of!Study!Committee:! Dennis!Lavrov,!Major!Professor! Stephan!Schneider! Amy!Toth! Edward!Yu! ! ! ! ! ! ! Iowa!State!University! ! Ames,!Iowa! ! 2015! ! ! Copyright!©!Katrina!A.!Lutap,!2015.!All!rights!reserved. ii TABLE&OF&CONTENTS& & & & & & & & & & & &&&Page& & ABSTRACT&& & & & & & & & & & &&&&&&&&&&iv& CHAPTER&1.&GENERAL&INTRODUCTION&& & & & & & &&&&&&&&&&&1& & Introduction&& & & & & & & & & &&&&&&&&&&&1& & Thesis&Organization&& & & & & & & & &&&&&&&&&&&2& & References&& & & & & & & & & &&&&&&&&&&&6& & CHAPTER&2.&MICROBIAL&COMMUNITY&DIVERSITY&IN&FRESHWATER&SPONGES&FROM&& LAKE&BAIKAL&& & & & & & & & & & &&&&&&&&&&9& & Abstract&& & & & & & & & & &&&&&&&&&&9& & Introduction&& & & & & & & & & &&&&&&&&10& & Materials&and&Methods&& & & & & & & &&&&&&&&16& & Results&& & & & & & & & & &&&&&&&&18& & Discussion&& & & & & & & & & &&&&&&&&25& & References&& & & & & & & & & &&&&&&&&31&& & Tables&and&Figures&& & & & & & & & &&&&&&&&38& & CHAPTER&3.&PROTEIN&SIZE&IN&THREE&DOMAINS&OF&LIFE&AND&EXAMPLES&OF&& UNUSUALLY&LARGE&PROTEINS&IN&PORIFERA:&A&REVIEW&& & & & &&&&&&&&45& & Introduction&& & & & & & & & & &&&&&&&&45& & Average&protein&length&in&three&domains&of&life&& & & & &&&&&&&&46& & Mechanisms&for&maintaining&protein&size&or&ORF&length&& & & &&&&&&&&47& & Properties&associated&with&protein&length&& & & & & &&&&&&&&52& Long&open&reading&frames&across&taxa&& & & & & &&&&&&&&55& Long&open&reading&frames&in&Porifera&& & & & & &&&&&&&&57& Large&orphan&proteins&in&Porifera&& & & & & & &&&&&&&&59& Conclusions&& & & & & & & & & &&&&&&&&62& References&& & & & & & & & & &&&&&&&&63& Tables&and&Figures&& & & & & & & & &&&&&&&&70& & iii CHAPTER&4.&GENERAL&CONCLUSIONS&& & & & & & &&&&&&&&94& & Summary&and&Recommendations&& & & & & & &&&&&&&&94& & & ACKNOWLEDGMENTS&& & & & & & & & &&&&&&&&96& & iv ABSTRACT! ! Sponges! (phylum! Porifera)! are! sessile,! filterbfeeding! animals! that! are! found! in! both!marine!and!freshwater!environments.!They!are!known!to!be!assoCiated!with!highly! diverse!and!stable!miCrobial!Communities.!The!first!Component!of!this!thesis!presents!a! study!on!the!diversity!of!the!miCrobial!Communities!assoCiated!with!freshwater!sponges! ColleCted!from!Lake!Baikal,!Baikalospongia+intermedia+profundalis!(BIP)!and!Lubomirskia+ baicalensis+ (LB).! Based! on! previous! studies,! miCrobial! Communities! assoCiated! with! freshwater!sponges!are!not!as!diverse!as!those!from!marine!sponges.!However,!one!of! the!potential!reasons!for!this!observation!is!the!limitation!posed!by!Conventional!Cloning! and!sequenCing!methods!used!in!previous!studies!on!freshwater!sponges.!To!gain!better! insight!into!the!diversity!of!the!miCrobiome!in!freshwater!sponges,!we!performed!highb throughput!sequenCing!of!PCRbamplified!16S!rRNA!genes!and!of!metagenome!without! prior! amplifiCation! in! two! sponge! speCies! BIP! and! LB.! Using! teChniques! that! involve! greater!sequenCing!Coverage,!we!Can!observe!that!freshwater!sponge!miCrobiomes!Can! be! as! diverse! as! marine! sponge! miCrobiomes.! The! miCrobial! Communities! of! the! freshwater!sponges!were!also!Compared!using!diversity!indiCes!and!it!was!observed!that! the! host! sponge! and! ColleCtion! depth! Can! both! influenCe! the! diversity! of! miCrobial! assoCiations!in!Lake!Baikal!sponges.! The!availability!and!ease!of!acCess!to!CostbeffeCtive!deep!sequenCing!teChniques! yielded!an!inCrease!in!the!number!of!Completely!sequenCed!genomes!of!organisms!in! three!domains!of!life!ArChaea,!Bacteria,!and!Eukarya.!This!inCrease!in!publiCly!available! v datasets!led!to!an!improved!understanding!on!the!general!properties!of!proteins!as!well! as!their!length!distributions.!The!seCond!Component!of!this!thesis!presents!a!review!of! studies!on!protein!length!distribution!and!the!observed!differenCes!in!average!protein! length!across!all!three!domains!of!life.!The!review!also!discusses!proposed!explanations! for!why!organisms!maintain!their!protein!size!and!presents!some!examples!of!proteins! that! defy! Constraints! on! protein! size! from! literature! and! from! genomes! of! sponges! Amphimedon+queenslandica,!Oscarella+carmela,!and!Baikalospongia+intermedia.! ! 1 CHAPTER(1( GENERAL(INTRODUCTION( ( Sponges((phylum(Porifera)(are(sessile,(filterEfeeding(animals(that(can(be(found(in( both(marine(and(freshwater(environments((Bergquist,(1978,(Penney,(1986).(They(harbor( numerous(microorganisms(that(can(range(from(archaeA(and(bacteriA(to(fungi,(diatoms,( dinoflagellates,( and( viruses( ( (Taylor( et( al.,( 2007).( The( first( component( of( this( thesis( presents( A( study( on( the( diversity( of( the( microbial( communities( associated( with( freshwater( sponges( collected( from( Lake( Baikal,( Baikalospongia+intermedia+profundalis( and(Lubomirskia+baicalensis.( The(availability(and(ease(of(access(to(costEeffective(deep(sequencing(techniques( yielded(an(increase(in(the(number(of(completely(sequenced(genomes(of(organisms(in(all( three( domains( of( life.( This( increase( in( publicly( available( datasets( led( to( An( improved( understanding(on(the(general(properties(of(proteins(as(well(as(their(length(distributions.( The( second( component( of( this( thesis( presents( A( review( of( studies( on( protein( length( distribution( and( the( observed( differences( in( average( protein( length( across( all( three( domains( of( life.( The( review( also( discusses( proposed( explanations( for( why( organisms( maintain( their( protein( size( and( presents( some( examples( of( proteins( that( defy( constraints(on(protein(size(from(literature(and(from(genomes(of(sponges(Amphimedon+ queenslandica,(Oscarella+carmela,(and(Baikalospongia+intermedia.( ( ( 2 Thesis!Organization! This! thesis! Contains! a! general! introduCtion! that! gives! an! overview! of! the! two! studies! (Chapter! 1),! a! study! on! the! diversity! of! miCrobial! Communities! in! Lake! Baikal! sponges! (Chapter! 2),! a! review! of! studies! on! protein! size! and! unusually! large! proteins!! (Chapter! 3),! and! a! general! ConClusion! that! summarizes! the! findings! and! reCommendations! (Chapter! 4).! Chapter! 2! presents! a! perspeCtive! on! the! diversity! of! miCrobiomes!in!freshwater!sponges!via!highbthroughput!sequenCing!of!metagenomes!of! Baikalospongia+ intermedia+ profundalis! and! Lubomirskia+ baicalensis.! Chapter! 3! is! a! review! of! studies! on! protein! length! in! ArChaea,! Bacteria,! and! Eukarya,! and! presents! some!examples!of!unusually!large!proteins!from!sponges!Amphimedon+queenslandica,! Oscarella+carmela,!and!Baikalospongia+intermedia.! ! Overview!1.!MiCrobial!Community!diversity!in!freshwater!sponges!from!Lake!Baikal! Sponges! form! Close! assoCiations! with! miCrobial! Communities! that! are! highly! diverse! and! stable! (HentsChel! et! al.,! 2002,! Taylor! et! al.,! 2007).! In! marine! sponges,! at! least! 28! bacterial! phyla! have! been! isolated! (HentsChel! et! al.,! 2012).! However,! information!about!miCroorganisms!assoCiated!with!sponges!in!freshwater!environments! is! limited.! Previous! studies! on! freshwater! sponges! Spongilla+ lacustris,! Lubomirskia+ baicalensis,! Ephydatia+ fluviatilis,! and! Baikalospongia+ intermedia! reported! 14! bacterial! phyla!(Gernert!et!al.,!2005,!Kaluzhnaya!et!al.,!2012,!Costa!et!al.,!2013,!Kaluzhnaya!and! ItskoviCh,! 2014),! of! whiCh! the! abundant! isolates! belong! to! groups! ACtinobacteria! and! Proteobacteria.!Based!on!these!studies,!it!is!presumed!that!freshwater!sponges!host!less! 3 diverse!miCrobial!Communities.!One!of!the!potential!reasons!for!this!observation!is!the! limitations!posed!by!Conventional!methods!(i.e.!denaturing!gradient!gel!eleCtrophoresis,! restriCtion! fragment! length! polymorphism,! 16S! rRNA! gene! amplifiCation,! cloning,! and! sequencing)!used!in!previous!studies!on!freshwater!sponges.!The!use!of!high!throughput! sequenCing!Can!reveal!a!better!perspeCtive!of!the!diversity!and!test!the!previous!notion! of!pauCity!of!assoCiated!miCroorganisms!in!freshwater!sponges.!! To!gain!better!insight!into!the!diversity!of!the!miCrobiome!in!freshwater!sponges,! we! performed!