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Bestaan ​​bakterieë wat uitsluitlik van nie-organiese materiaal leef?

Bestaan ​​bakterieë wat uitsluitlik van nie-organiese materiaal leef?


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Is daar bakterieë wat uitsluitlik nie-organiese materiaal verbruik? Beteken dit dat hulle nie organiese materiaal van ander organismes benodig om aan die lewe te bly en voort te plant nie? ’n Heeltemal pasifistiese bakterie.

Of anders geformuleer, is daar bakterieë wat aan die lewe kan bly en onbepaald kan voortplant met slegs nie-organiese materiaal teenwoordig (plus sonlig of termiese vents ens.)?

Ek vra spesifiek, om een ​​of meer bakterieë spesies te noem wat dit kan doen.


Sulfaatverminderende bakterieë kry hul energie om sulfaat na waterstofsulfied om te skakel. Hulle is relatief algemeen en was dalk die bron om sommige olie/gasneerslae "suur" te maak. Besonderhede in Wikipedia.


Organiese materiaal

Organiese materiaal, organiese materiaal, of natuurlike organiese materiaal verwys na die groot bron van koolstofgebaseerde verbindings wat in natuurlike en gemanipuleerde, terrestriële en akwatiese omgewings voorkom. Dit is materie wat bestaan ​​uit organiese verbindings wat afkomstig is van die oorblyfsels van organismes soos plante en diere en hul afvalprodukte in die omgewing. [1] Organiese molekules kan ook gemaak word deur chemiese reaksies wat nie lewe behels nie. [2] Basiese strukture word geskep uit sellulose, tannien, kutien en lignien, saam met ander verskeie proteïene, lipiede en koolhidrate. Organiese materiaal is baie belangrik in die beweging van voedingstowwe in die omgewing en speel 'n rol in waterretensie op die oppervlak van die planeet. [3]


Inhoud

R. pachyptila is in 1977 op 'n ekspedisie van die Amerikaanse badjas DSV ontdek Alvin na die Galápagos-skeur gelei deur geoloog Jack Corliss. [4] Die ontdekking was onverwags, aangesien die span hidrotermiese openinge bestudeer het en geen bioloë by die ekspedisie ingesluit is nie. Baie van die spesies wat tydens hierdie ekspedisie naby hidrotermiese vents gebly het, is nog nooit vantevore gesien nie.

Destyds was die teenwoordigheid van termiese fonteine ​​naby die midoseaniese rante bekend. Verdere navorsing het waterlewe in die gebied ontdek, ondanks die hoë temperatuur (ongeveer 350 – 380 °C). [5] [6]

Baie monsters is versamel, byvoorbeeld tweekleppige, polchaete, groot krappe, en R. pachyptila. [7] [8] Dit was die eerste keer dat spesies waargeneem is.

R. pachyptila ontwikkel uit 'n vryswemmende, pelagiese, nie-simbiotiese trochofoorlarwe, wat jeugdige (metatrochofore) ontwikkeling binnegaan, sessiel word en daarna simbiotiese bakterieë opdoen. [9] [10] Die simbiotiese bakterieë, waarvan volwasse wurms afhanklik is vir voedsel, kom nie in die gamete voor nie, maar word uit die omgewing deur die vel verkry in 'n proses wat soortgelyk is aan 'n infeksie. Die spysverteringskanaal verbind tydelik van 'n mond aan die punt van die ventrale mediale proses na 'n voorderm, middelderm, agterderm en anus en is voorheen gedink dat dit die metode was waarmee die bakterieë in volwassenes ingebring word. Nadat simbiote in die middelderm gevestig is, ondergaan hulle aansienlike hermodellering en vergroting om die trofosoom te word, terwyl die res van die spysverteringskanaal nie in volwasse monsters opgespoor is nie. [11]

Deur die vermiforme liggaam van wit chitoniese buis te isoleer, bestaan ​​'n klein verskil van die klassieke drie onderafdelings tipies van filum Pogonophora: [12] die prosoma, die mesosom en die metasoma.

Die eerste liggaamsgebied is die vaskulêre vertakkingspluim, wat helderrooi is as gevolg van die teenwoordigheid van hemoglobien wat tot 144 globienkettings bevat (elkeen sluit vermoedelik geassosieerde heemstrukture in). Hierdie buiswurmhemoglobiene is merkwaardig om suurstof in die teenwoordigheid van sulfied te dra, sonder om deur hierdie molekule geïnhibeer te word, soos hemoglobiene in die meeste ander spesies is. [13] [14] Die pluim verskaf noodsaaklike voedingstowwe aan bakterieë wat in die trofosoom woon. As die dier 'n bedreiging waarneem of aangeraak word, trek dit die pluim terug en die buis word gesluit as gevolg van die obturaculum, 'n spesifieke operculum wat die dier van die eksterne omgewing beskerm en isoleer. [15]

Die tweede liggaamsgebied is die vestimentum, gevorm deur spierbande, met 'n gevleuelde vorm, en dit bied die twee geslagsopeninge aan die einde. [16] [17] Die hart, verlengde gedeelte van dorsale vat, omsluit die vestimentum. [18]

In die middelste deel, die stam of derde liggaamsgebied, is vol vaskulêre vaste weefsel, en sluit liggaamswand, gonades en die seëlomiese holte in. Hier is ook die trofosoom, sponsagtige weefsel waar 'n biljoen simbiotiese, tiooutotrofiese bakterieë en swaelkorrels gevind word. [19] [20] Aangesien die mond, spysverteringstelsel en anus ontbreek, is die oorlewing van R. pachyptila is afhanklik van hierdie mutualistiese simbiose. [21] Hierdie proses, bekend as chemosintese, is binne die trofosoom herken deur Colleen Cavanaugh. [21]

Die oplosbare hemoglobiene wat in die tentakels teenwoordig is, is in staat om O te bind2 en H2S, wat nodig is vir chemosintetiese bakterieë. As gevolg van die kapillêre, word hierdie verbindings deur bakterieë geabsorbeer. [22] Tydens die chemosintese kataliseer die mitochondriale ensiem rhodanase die disproporsioneringsreaksie van die tiosulfaat anioon S2O3 2- tot swael S en sulfiet SO3 2- . [23] [24] Die R. pachyptilase bloedstroom is verantwoordelik vir die absorpsie van die O2 en voedingstowwe soos koolhidrate.

Nitraat en nitriet is giftig, maar word benodig vir biosintetiese prosesse. Die chemosintetiese bakterieë binne die trofosoom skakel nitraat om na ammoniumione, wat dan beskikbaar is vir die produksie van aminosure in die bakterieë, wat op hul beurt aan die buiswurm vrygestel word. Om nitraat na die bakterieë te vervoer, R. pachyptila konsentreer nitraat in sy bloed, tot 'n konsentrasie 100 keer meer gekonsentreerd as die omliggende water. Die presiese meganisme van R. pachyptilase vermoë om nitraat te weerstaan ​​en te konsentreer is nog onbekend. [14]

In die posterior deel, die vierde liggaamsgebied, is die opistosoom, wat die dier aan die buis anker en word gebruik vir die berging van afval van bakteriële reaksies. [25]

Die ontdekking van bakteriële ongewerwelde chemo-outotrofiese simbiose, veral in vestimentiferaan buiswurms R. pachyptila [21] en dan in vesikomiedmossels en mitielmossels het die chemo-outotrofiese potensiaal van die hidrotermiese uitlaatbuiswurm geopenbaar. [26] Wetenskaplikes het 'n merkwaardige bron van voeding ontdek wat help om die opvallende biomassa van ongewerwelde diere by vents te onderhou. [26] Baie studies wat op hierdie tipe simbiose gefokus het, het die teenwoordigheid van chemo-outotrofiese, endosimbiotiese, swaeloksiderende bakterieë hoofsaaklik in R. pachyptila, [27] wat uiterste omgewings bewoon en aangepas is vir die besondere samestelling van die gemengde vulkaniese en seewater. [28] Hierdie spesiale omgewing is gevul met anorganiese metaboliete, hoofsaaklik koolstof, stikstof, suurstof en swael. In sy volwasse fase, 'R. pachyptila gebrek aan 'n spysverteringstelsel. Om in sy energiebehoeftes te voorsien, behou dit daardie opgeloste anorganiese voedingstowwe (sulfied, koolstofdioksied, suurstof, stikstof) in sy pluim en vervoer dit deur 'n vaskulêre stelsel na die trofosoom, wat in gepaarde seëlomiese holtes gesuspendeer is en waar die intrasellulêre simbiotiese bakterieë is. word gevind. [20] [29] [30] Die trofosoom [31] is 'n sagte weefsel wat deur byna die hele lengte van die buis se seeloom loop. Dit behou 'n groot aantal bakterieë in die orde van 10 9 bakterieë per gram vars gewig. [32] Bakterieë in die trofosoom word in bakteriosiete behou, en het daardeur geen kontak met die eksterne omgewing nie. Dus maak hulle staat op R. pachyptila vir die assimilasie van voedingstowwe wat nodig is vir die verskeidenheid metaboliese reaksies wat hulle gebruik en vir die uitskeiding van afvalprodukte van koolstofbindingsweë. Terselfdertyd is die vestimentiferan heeltemal afhanklik van die mikro-organismes vir die neweprodukte van hul koolstofbindingsiklusse wat nodig is vir sy groei.

Aanvanklike bewyse vir 'n chemo-outotrofiese simbiose in R. pachyptila kom van mikroskopiese en biochemiese ontledings wat toon dat Gram-negatiewe bakterieë gepak is in 'n hoogs vaskulêre orgaan in die buiswurmstam wat die trofosoom genoem word. [21] Bykomende ontledings wat stabiele isotoop, [33] ensiematiese, [34] [26] en fisiologiese [35] karakteriserings behels het bevestig dat die eindsimbiote van R. pachyptila oksideer verminderde swaelverbindings om ATP te sintetiseer vir gebruik in outotrofiese koolstofbinding deur die Calvyn-siklus. Die gasheerbuiswurm maak die opname en vervoer moontlik van die substrate wat benodig word vir tiooutotrofie, wat HS − , O is2, en CO2, om 'n gedeelte van die organiese materiaal terug te ontvang wat deur die simbionbevolking gesintetiseer is. Die volwasse buiswurm, gegewe sy onvermoë om op deeltjies te voed en sy hele afhanklikheid van sy simbiote vir voeding, is die bakteriese bevolking dan die primêre bron van koolstofverkryging vir die simbiose. Die ontdekking van bakteriële-invertebrate chemo-outotrofiese simbiose, aanvanklik in vestimentiferaan-buiswurms [21] [26] en daarna in vesikomiedmossels en mitiliedmossels, [26] het gewys op 'n selfs meer merkwaardige bron van voeding wat die ongewerwelde diere by vents onderhou.

'n Wye verskeidenheid van bakteriese diversiteit word geassosieer met simbiotiese verhoudings met R. pachyptila. Baie bakterieë behoort aan die klas Epsilonproteobacteria [36] soos ondersteun deur die onlangse ontdekking in 2016 van die nuwe spesie Sulfurovum riftiae behoort aan die klas Epsilonproteobacteria, familie Helicobacteraceae geïsoleer uit R. pachyptila versamel van die East Pacific Rise. [37] Ander simbiote behoort aan die klas Delta-, Alfa- en Gamma-proteobakterieë. [36] Die Kandidaat Endoriftia persephone is 'n fakultatief R. pachyptila symbiont en is getoon dat dit 'n mixotroof is, en daardeur beide die Calvin Benson-siklus en omgekeerde TCA-siklus (met 'n ongewone ATP-sitraat liase) ontgin volgens beskikbaarheid van koolstofbronne en of dit vry in die omgewing of binne 'n eukariotiese gasheer leef. Die bakterieë verkies glo 'n heterotrofiese leefstyl wanneer koolstofbronne beskikbaar is. [31]

Bewyse gebaseer op 16S rRNA-analise bevestig dit R. pachyptilachemo-outotrofiese bakterieë behoort aan twee verskillende filums van Proteobacteria superphylum: Gammaproteobacteria phylum [38] [20] en Epsilonproteobacteria phylum (bv. Sulfurovum riftiae) [37] wat energie kry uit die oksidasie van anorganiese swaelverbindings soos waterstofsulfied (H2S, HS − , S 2- ) om ATP te sintetiseer vir koolstoffiksasie via die Calvyn-siklus. [20] Ongelukkig is die meeste van hierdie bakterieë steeds onkweekbaar. Simbiose werk so dat R. pachyptila verskaf voedingstowwe soos HS − , O2, CO2 aan bakterieë, en op sy beurt ontvang dit organiese materiaal van hulle. Dus, as gevolg van 'n gebrek aan 'n spysverteringstelsel, R. pachyptila hang geheel en al af van sy bakteriële simbione om te oorleef. [39] [40]

In die eerste stap van sulfiedoksidasie gaan gereduseerde swael (HS − ) van die eksterne omgewing na R. pachyptila bloed, waar, saam met O2, word dit deur hemoglobien gebind, wat die kompleks Hb-O vorm2-HS − en dan word dit na die trofosoom vervoer, waar bakteriese simbiote woon. Hier word HS − geoksideer na elementêre swael (S 0 ) of na sulfiet (SO3 2- ). [20]

In die tweede stap maak die simbiote sulfietoksidasie deur die "APS-pad", om ATP te kry. In hierdie biochemiese pad reageer AMP met sulfiet in die teenwoordigheid van die ensiem APS reduktase, wat APS (adenosien 5'-fosfosulfaat) gee. Dan reageer APS met die ensiem ATP-sulfurilase in die teenwoordigheid van pirofosfaat (PPi) wat ATP (substraatvlakfosforilering) en sulfaat (SO) gee4 2- ) as eindprodukte. [20] In formules:

Die elektrone wat tydens die hele sulfiedoksidasieproses vrygestel word, gaan in 'n elektronvervoerketting in, wat 'n protongradiënt lewer wat ATP (oksidatiewe fosforilering) produseer. Dus, ATP gegenereer uit oksidatiewe fosforilering en ATP geproduseer deur substraat-vlak fosforilering word beskikbaar vir CO2 fiksasie in Calvyn-siklus, waarvan die teenwoordigheid gedemonstreer is deur die teenwoordigheid van twee sleutelensieme van hierdie pad: fosforibulokinase en RubisCO. [26] [41]

Om hierdie ongewone metabolisme te ondersteun, R. pachyptila moet al die stowwe wat nodig is vir beide sulfiedoksidasie en koolstofbinding absorbeer, dit wil sê: HS − , O2 en CO2 en ander fundamentele bakteriële voedingstowwe soos N en P. Dit beteken dat die buiswurm toegang moet hê tot beide oksiese en anoksiese areas.

Oksidasie van gereduseerde swaelverbindings vereis die teenwoordigheid van geoksideerde reagense soos suurstof en nitraat. Hidrotermiese vents word gekenmerk deur toestande van hoë hipoksie. In hipoksiese toestande begin swaelbergende organismes waterstofsulfied produseer. Daarom is die produksie van in H2S in anaërobiese toestande is algemeen onder tiotrofiese simbiose. H2S kan skadelik wees vir sommige fisiologiese prosesse aangesien dit die aktiwiteit van sitochroom c-oksidase inhibeer, wat gevolglik oksidatiewe fosforilasie benadeel. In R. pachyptila die produksie van waterstofsulfied begin na 24 uur se hipoksie. Ten einde fisiologiese skade te vermy sommige diere, insluitend Riftia pachyptila kan H bind2S na hemoglobien in die bloed om dit uiteindelik in die omliggende omgewing te verdryf.

Anders as metazoë, wat koolstofdioksied as 'n afvalproduk inasem, R. pachyptila-symbiontvereniging het 'n eis vir 'n netto opname van CO2 in plaas daarvan, as 'n cnidarian-symbion verenigings. [42] Omringende diepseewater bevat 'n oorvloedige hoeveelheid anorganiese koolstof in die vorm van bikarbonaat HCO3 − , maar dit is eintlik die ladinglose vorm van anorganiese koolstof, CO2, wat maklik oor membrane versprei kan word. Die lae gedeeltelike druk van CO2 in die diepsee-omgewing is te wyte aan die seewater alkaliese pH en die hoë oplosbaarheid van CO2, maar tog die pCO2 van die bloed van R. pachyptila kan soveel as twee grootteordes groter as die pCO wees2 van diepseewater. [42]

CO2 gedeeltelike drukke word na die omgewing van uitlaatvloeistowwe oorgedra as gevolg van die verrykte anorganiese koolstofinhoud van uitlaatvloeistowwe en hul laer pH. [20] CO2 opname in die wurm word versterk deur die hoër pH van sy bloed (7.3 – 7.4), wat die bikarbonaat-ioon bevoordeel en dus 'n steil gradiënt waaroor CO2 bevorder2 diffundeer in die vaskulêre bloed van die pluim. [43] [20] Die fasilitering van CO2 opname deur hoë omgewings-pCO2 is eers afgelei gebaseer op maatstawwe van verhoogde bloed en seëlomiese vloeistof pCO2 in buiswurms, en is daarna gedemonstreer deur inkubasies van ongeskonde diere onder verskeie pCO2 voorwaardes. [30]

Sodra CO2 deur die simbiote vasgestel word, moet dit deur die gasheerweefsel geassimileer word. Die toevoer van vaste koolstof aan die gasheer word via organiese molekules vanaf die trofosoom in die hemolimf vervoer, maar die relatiewe belangrikheid van translokasie en simbiotevertering is nog nie bekend nie. [30] [44] Studies het bewys dat die etiket binne 15 minute eers in simbionvrye gasheerweefsels verskyn, en dit dui op 'n aansienlike hoeveelheid vrystelling van organiese koolstof onmiddellik na fiksasie. Na 24 uur is gemerkte koolstof duidelik sigbaar in die epidermale weefsels van die liggaamswand. Resultate van die pols-jaag outoradiografiese eksperimente was ook duidelik met ultrastrukturele bewyse vir vertering van simbiote in die perifere streke van die trofosoom lobules. [44] [45]

In diepsee hidrotermiese openinge is sulfied en suurstof in verskillende gebiede teenwoordig. Inderdaad, die reduseervloeistof van hidrotermiese vents is ryk aan sulfied, maar arm aan suurstof, terwyl seewater ryker is aan opgeloste suurstof. Boonop word sulfied onmiddellik deur opgeloste suurstof geoksideer om gedeeltelik, of heeltemal, geoksideerde swaelverbindings soos tiosulfaat (S) te vorm2O3 2-) en uiteindelik sulfaat (SO4 2- ), onderskeidelik minder, of nie meer, bruikbaar vir mikrobiese oksidasiemetabolisme nie. [46] Dit veroorsaak dat die substrate minder beskikbaar is vir mikrobiese aktiwiteit, dus word bakterieë ingeperk om met suurstof te kompeteer om hul voedingstowwe te kry. Om hierdie probleem te vermy, het verskeie mikrobes ontwikkel om simbiose met eukariotiese gashere te maak. [47] [20] Trouens, R. pachyptila is in staat om die oksiese en anoksiese gebiede te bedek om beide sulfied en suurstof te kry. [48] ​​[49] [50] Danksy sy hemoglobien wat sulfied omkeerbaar en apart van suurstof kan bind deur middel van twee sisteïenreste, [51] [52] [53] en dit dan na die trofosoom kan vervoer, waar bakteriese metabolisme kan gebeur.

Die verkryging van 'n simbioet deur 'n gasheer kan op hierdie maniere plaasvind:

  • Omgewingsoordrag (simbione verkry van 'n vrylewende bevolking in die omgewing)
  • Vertikale oordrag (ouers dra symbionte oor na nageslag via eiers)
  • Horisontale oordrag (gashere wat dieselfde omgewing deel)

Bewyse dui daarop R. pachyptila verkry sy simbiote deur sy omgewing. Trouens, 16S rRNA geen-analise het getoon dat vestimentiferan buiswurms wat aan drie verskillende genera behoort: Riftia, Oasis, en Tevnia, deel dieselfde bakteriële simbiontfilotipe. [54] [55] [56] [57] [58]

Dit bewys dit R. pachyptila neem sy simbiote van 'n vrylewende bakteriese bevolking in die omgewing. Ander studies ondersteun ook hierdie tesis, want ontleding R. pachyptila eiers, is 16S rRNA wat aan die simbiont behoort nie gevind nie, wat wys dat die bakteriële simbiot nie deur vertikale oordrag oorgedra word nie. [59]

Nog 'n bewys om die omgewingsoordrag te ondersteun, kom uit verskeie studies wat in die laat 1990's uitgevoer is. [60] PCR is gebruik om a R. pachyptila simbiontgeen wie se volgorde baie ooreenstem met die fliC geen wat vir sekere primêre proteïensubeenhede (flagellien) kodeer wat benodig word vir flagellumsintese. Ontleding het dit getoon R. pachyptila symbiont het ten minste een geen wat nodig is vir flagellumsintese. Daarom het die vraag ontstaan ​​oor die doel van die flagellum. Vlagbeweeglikheid sou nutteloos wees vir 'n bakteriële simbiot wat vertikaal oorgedra word, maar as die simbiot uit die eksterne omgewing kom, sou 'n flagellum noodsaaklik wees om die gasheerorganisme te bereik en dit te koloniseer. Inderdaad, verskeie simbiote gebruik hierdie metode om eukariotiese gashere te koloniseer. [61] [62] [63] [64]

Hierdie resultate bevestig dus die omgewingsoordrag van R. pachyptila simbiose.

R. pachyptila [65] is 'n tweehuisige vestimentiferaan. [66] Individue van hierdie spesie is sittend en word saamgegroepeer rondom diepsee hidrotermiese openinge van die Oos-Stille Oseaan-opgang en die Galapagos-skeur gevind. [67] Die grootte van 'n lappie individue wat 'n opening omring, is binne die skaal van tientalle meters. [68]

Die mannetjie se spermatosoa is draadvormig en bestaan ​​uit drie afsonderlike streke: die akrosoom (6 μm), die kern (26 μm) en die stert (98 μm). Dus, die enkele spermatosoa is oor die algemeen ongeveer 130 μm lank, met 'n deursnee van 0,7 μm, wat nouer word naby die stertarea en 0,2 μm bereik. Die sperm is gerangskik in 'n agglomerasie van ongeveer 340-350 individuele spermatozoa wat 'n fakkelagtige vorm skep. Die bekerdeel bestaan ​​uit akrosome en kern, terwyl die handvatsel deur die sterte bestaan. Die spermatozoa in die pakkie word deur fibrille bymekaar gehou. Fibrille bedek ook die verpakking self om kohesie te verseker. [ aanhaling nodig ]

Die groot eierstokke van wyfies loop binne die gonocoel oor die hele lengte van die stam en is ventraal na die trofosoom. Eiers in verskillende rypwordingsstadiums kan in die middelarea van die eierstokke gevind word, en afhangende van hul ontwikkelingstadium, word na verwys as: oögonia, oösiete en follikulêre selle. Wanneer die oösiete volwasse word, verkry hulle proteïen- en lipiedgeelkorrels. [ aanhaling nodig ]

Mannetjies laat hul sperm in seewater vry. Terwyl die vrygestelde agglomerasies van spermatozoa, waarna verwys word as spermatozeugmata, nie vir meer as 30 sekondes ongeskonde bly in laboratoriumtoestande nie, kan hulle integriteit vir langer tydperke in spesifieke hidrotermiese ventilasietoestande behou. Gewoonlik swem die spermatozeugmata die wyfie se buis in. Beweging van die tros word verleen deur die kollektiewe aksie van elke spermatozoon wat onafhanklik beweeg. Voortplanting is ook waargeneem waarby slegs 'n enkele spermatozoon die wyfie se buis bereik het. Oor die algemeen, bevrugting in R. pachyptila word as intern beskou. Sommige redeneer egter dat, aangesien die sperm in seewater vrygestel word en eers daarna die eiers in die ovidukte bereik, dit as intern-ekstern gedefinieer moet word. [ aanhaling nodig ]

R. pachyptila is heeltemal afhanklik van die produksie van vulkaniese gasse en die teenwoordigheid van sulfiedoksiderende bakterieë. Daarom is sy metabevolkingsverspreiding ten diepste gekoppel aan vulkaniese en tektoniese aktiwiteit wat aktiewe hidrotermiese ventilasieplekke skep met 'n lappende en efemere verspreiding. Die afstand tussen aktiewe terreine langs 'n skeur of aangrensende segmente kan baie hoog wees en honderde km bereik. [67] Dit laat die vraag ontstaan ​​oor larweverspreiding. R. pachytpila is in staat om larwes oor afstande van 100 tot 200 km te versprei [67] en gekweekte larwes toon lewensvatbaar vir 38 dae. [69] Alhoewel verspreiding as doeltreffend beskou word, is die genetiese variasie waargeneem in R. pachyptila metapopulasie is laag in vergelyking met ander vent spesies. Dit kan wees as gevolg van hoë uitsterwing gebeure en kolonisasie gebeure, as R. pachyptila is een van die eerste spesies wat 'n nuwe aktiewe terrein gekoloniseer het. [67]

Die endosimbionte van R. pachyptila word nie tydens paai na die bevrugte eiers oorgedra nie, maar word later tydens die larwale stadium van die vestimentiferaanwurm verkry. R. pachyptila planktoniese larwes wat deur seebodemstrome vervoer word totdat hulle aktiewe hidrotermiese ventilasieplekke bereik, word trofocores genoem. Die trofokernstadium het nie endosimbionte nie, wat verkry word sodra larwes in 'n geskikte omgewing en substraat vestig. Vrylewende bakterieë wat in die waterkolom voorkom, word lukraak ingeneem en gaan die wurm binne deur 'n gesilieerde opening van die vertakkingspluim. Hierdie opening is aan die trofosoom verbind deur 'n kanaal wat deur die brein gaan. Sodra die bakterieë in die ingewande is, word die wat voordelig vir die individu is, naamlik sulfiedoksiderende stamme, gepagositiseer deur epiteelselle wat in die middelderm gevind word, dan behou. Bakterieë wat nie moontlike endosimbionte verteenwoordig nie, word verteer. Dit laat vrae ontstaan ​​oor hoe R. pachyptila slaag daarin om te onderskei tussen noodsaaklike en nie-noodsaaklike bakteriese stamme. Die wurm se vermoë om 'n voordelige stam te herken, sowel as voorkeurgasheerspesifieke infeksie deur bakterieë is albei voorgestel as die drywers van hierdie verskynsel. [70]

R. pachyptila het die vinnigste groeitempo van enige bekende mariene ongewerwelde dier. Dit is bekend dat hierdie organismes 'n nuwe terrein koloniseer, tot seksuele volwassenheid groei en in minder as twee jaar in lengte tot 4,9 voet (1,5 m) toeneem. [71]


Sommige voordele van saprofitiese bakterieë

As 'n primêre organisme wat nodig is vir ontbinding, het saprofitiese bakterieë die ooglopende voordeel om voedingstowwe soos yster, fosfor en kalsium terug te keer na die Aarde, waar plante hulle absorbeer om lewensonderhoudende waterstof, stikstof, koolstof en ander vitamiene en minerale te produseer. Baie voordelige tipes bakterieë leef in die menslike liggaam om mense gesond te hou. Honderde organismes werk om die nie-lewende organismes af te breek wat mense eet. Sonder hulle sou kos nooit behoorlik verteer nie, en skadelike bakterieë sou vinnig vermeerder.

Plante bevat sellulose, 'n komponent wat mense nie eintlik kan verteer nie. Die bakterieë Spirochaeta cytophaga gebruik absorberende voeding om die sellulose af te breek, wat die krag van plantvoeding vir mense ontsluit. Nog 'n voorbeeld, Lactobacillus, breek melk af om jogurt te maak, terwyl ander soorte bakterieë dit afbreek om al die verskillende soorte kase te maak.

Beide aërobiese bakterieë en anaërobiese bakterieë is kritieke komponente in die afbreek van gifstowwe in riool, wat van kritieke belang is vir die voortdurende veiligheid van ons omgewing. Daarbenewens word die metaangas wat tydens die proses geproduseer word, soms as 'n goedkoop biogas in die plek van brandstof gebruik. Die biobrandstof-etanol kom ook van 'n proses wat ontwikkel is deur biotegnologie-kundiges wat anaërobiese bakterieë gebruik om rietsuiker en mielies af te breek.


Hoe bakterieë menslike voedsel afbreek

Verlede weke se plasing oor die veranderende samestelling van bakterieë in die vagina het baie belangstelling gegenereer, en aangesien daar op die oomblik baie gepraat is oor die menslike mikrobioom (al die bakterieë wat op die menslike liggaam leef) het ek gedink ek sal vashou met die tema. Hierdie week se plasing handel oor hoe bakterieë die voedingstowwe wat mense eet afbreek en dit gebruik om hul eie kos te skep.

Die referaat (verwysing 1 hieronder) van PLoS One fokus op koolhidrate. Begin met 'n bietjie biochemie-agtergrond: koolhidrate is molekules wat uitsluitlik van koolstof, waterstof en suurstof gemaak word (vandaar die naam). Hierdie drie molekules is gerangskik in 'n ringstruktuur vir die eenvoudige koolhidrate soos glukose, en daardie ringe word saamgevoeg in lang komplekse vertakkingskettings vir die komplekse koolhidrate soos stysel en sellulose.

Eenvoudige koolhidrate, soos die glukose wat in die prent hierbo getoon word, is redelik maklik om te metaboliseer en kan gebruik word om ATP (die molekules wat die sel vir energie gebruik) of in die sintese van proteïene aan te wakker. Meer komplekse koolhidrate soos stysel of sellulose (hieronder getoon) verg 'n bietjie meer moeite, aangesien dit in hul eenvoudige suikers afgebreek moet word voordat dit verwerk kan word. Om dit af te breek, gebruik bakterieë 'n spesifieke groep ensieme genaamd CAZymes wat staan ​​vir "Koolhidraat-aktiewe ensieme". Aangesien ensieme baie gespesialiseerd is in die molekules wat hulle afbreek, bestaan ​​verskillende CAZymes vir verskillende komplekse koolhidrate.

Verskillende bakterieë sal verskillende CAZymes hê, maar 'n intrige vraag wat die PLoS-vraestel uiteengesit het om i te beantwoords hoe die patroon van CAZymes deur die liggaam verander. Daar is nie net een bakteriese spesie in jou nie, maar baie, elke spesie is anders verwant aan dié wat dit omring. Dit is minder 'n gemeenskap van bakterieë binne jou en meer soos 'n swak georganiseerde safaripark, met verskillende spesies wat almal naby mekaar rond maal, wat staatmaak op die hulpbronne wat beskikbaar is in watter deel van die liggaam hulle ook al woon.

Die navorsers het die koolhidraatverterende vermoëns van 493 bakteriese genome vergelyk, wat verband hou met vyf verskillende plekke aan die buitekant en binnekant van die menslike liggaam. Toe hulle probeer om die aantal en verspreiding van CAZymes per spesie uit te werk, het hulle baie vinnig probleme ondervind. Sommige bakteriese families, soos Bacillaceae, het 'n gemiddeld van getal van 25 suikersplitsende ensieme gehad, met 'n respektabele standaardafwyking van 3,3 (vir die oningewydes meet die standaardafwyking hoe waarskynlik elke individu naby die gemiddelde is). Die bakteriese familie Clostridiaceae aan die ander kant het 'n gemiddeld van 56 suikersplitsende ensieme gehad maar met 'n standaardafwyking van 79! Benewens die groot variasie tussen spesies, maak dit dit ook moeilik om verwantskap tussen bakterieë te voorspel op grond van hul koolhidraatverterende vermoëns.

Aangesien die vergelyking van spesies blykbaar nie besonder bondige resultate opgelewer het nie, het die navorsers daarna oorgegaan om CAZymes volgens bakteriese habitat te vergelyk. Anders as mense, en eintlik byna alle eukariote, gee bakterieë nie net gene deur na hul nageslag nie, hulle kan ook gene oordra na 'n nabygeleë vriend. Dit is nie verbasend dat bakterieë wat op dieselfde plek op die liggaam woon, geneig was om meer soortgelyke koolhidraatverterende ensieme te hê as bakterieë wat meer verwant was deur spesies. Oor die algemeen het die navorsers vier hoofpatrone van koolhidraatgebruik gevind:

1) Bakterieë in die neus en neusholtes - Dit is nie verbasend dat hierdie bakterieë geneig was om baie min koolhidraatmetaboliseringsvermoë te hê (baie min mense inasem stysel)

2) Bakterieë in die vagina - Hierdie bakterieë was geneig om meer eenvoudige suikers af te breek, en het ook koolhidrate gehad forming ensieme om biofilms op te bou

3) Bakterieë in die mond - hierdie bakterieë het 'n wye reeks koolhidraatverterende ensieme om die stukkies kos wat in jou tande vasgevang word, af te breek. Die navorsers het ook drie ensieme geïdentifiseer wat gebruik word vir die metabolisering van dektraan, wat uniek vir mondbakterieë kan wees en blykbaar 'n merker vir plaakvorming was.

4) Bakterieë in die ingewande - dit is waar die groot koolhidraat-verterende spier lê! Nie net het dermbakterieë baie CAZymes vir menslike koolhidrate nie, hulle het ook reeks wat handel oor plantkoolhidrate. Baie van hierdie bakterieë het die vermoë om 'n sellulosoom te vorm - 'n groot kompleks van selluloseverterende ensieme wat almal bymekaar gehou word deur steierproteïene.

Dit mag dalk effens vreemd wees om te dink aan bakterieë wat in soveel dele van jou liggaam woon - wat jou ruimtes koloniseer en jou kos eet - maar regtig, dit sou baie meer van 'n verrassing gewees het om uit te vind dat hulle dit nie was nie. Byna elke oppervlak op aarde het bakterieë wat daarop woon, en mense is so 'n warm, klam, voedingryke oppervlak dat hulle 'n wonderlike leefomgewing vir 'n groot aantal bakteriese spesies bied.

Cantarel BL, Lombard V en Henrissat B (2012). Komplekse koolhidraatbenutting deur die gesonde menslike mikrobioom. PloS een, 7 (6) PMID: 22719820

Die menings wat uitgespreek word, is dié van die skrywer(s) en is nie noodwendig dié van Scientific American nie.

OOR DIE OUTEUR(S)

'n Biochemikus met 'n liefde vir mikrobiologie, die Lab Rat geniet dit om bakterieë te verken, te lees en daaroor te skryf. Nadat sy uiteindelik daarin geslaag het om haarself van die universiteit af te skeur, werk sy nou vir 'n klein maatskappy in Cambridge waar sy data in hanteerbare woorde en ongelooflike grafieke omskep.


Mikrobiese prosesse

Anaërobiese respirasie

As gevolg van 'n gebrek aan suurstof in die diep ondergrond, is die enigste manier vir lewe om voort te gaan deur anaërobiese asemhaling. Anaërobiese respirasie word gekenmerk deur die gebruik van alternatiewe verbindings as terminale elektronaannemers,

Litotrofie

Mikrobes gebruik verminderde anorganiese stowwe, soos yster, swael of magnesium om die chemiese energie te verkry wat nodig is om biosintese uit te voer. H2 gas is die primêre elektronskenker, hoewel ander verbindings soos SO3 2- S4O62 − , S 0 , Fe 2+ , en Mn(II) word ook gebruik [2].

Metanogenese

Metanogenese is die produksie van metaan deur mikrobes via anaërobiese respirasie. Metanogene soos hulle effektief genoem word, is slegs binne die domein Archaea geïdentifiseer. Diep ondergrondse archaea is bekend daarvoor dat hulle beskikbare organiese koolstofbronne metaboliseer en is verantwoordelik vir die produksie van groot sakke metaan wat in die aardkors vasgevang is.

Koolwaterstofafbraak

Metaboliese aktiwiteit in gebiede wat ryk is aan koolwaterstofstowwe ondersteun groot getalle anaërobiese heterotrofiese mikroörganismes. Hierdie mikrobes metaboliseer die koolwaterstowwe as beide 'n energiebron sowel as vir 'n koolstofbron. Hierdie organismes het spesiale relevansie in vandag se dag en ouderdom, aangesien petroleumprodukte toenemend meer en meer voorkom. Hierdie organismes fasiliteer die afbreek van hierdie stowwe, en is gebruik om oliestortings op te ruim en om ander petroleumdistillate te help afbreek [4].


Figuur 4: Hierdie ligmikrograaf toon 'n 100× vergroting van rooibloedselle wat met P. falciparum (gesien as pers) besmet is. (krediet: wysiging van werk deur Michael Zahniser skaalstaafdata van Matt Russell)

Lede van die genus Plasmodium moet 'n muskiet en 'n gewerwelde dier besmet om hul lewensiklus te voltooi. In gewerwelde diere ontwikkel die parasiet in lewerselle en gaan voort om rooibloedselle te infekteer, en bars uit en vernietig die bloedselle met elke ongeslagtelike replikasiesiklus ([Figuur 4]). Van die vier Plasmodium spesies wat bekend is om mense te besmet, P. falciparum verantwoordelik vir 50 persent van alle malariagevalle en is die primêre oorsaak van siekteverwante sterftes in tropiese streke van die wêreld. In 2010, it was estimated that malaria caused between 0.5 and 1 million deaths, mostly in African children. Gedurende die verloop van malaria, P. falciparum kan meer as die helfte van 'n mens se sirkulerende bloedselle besmet en vernietig, wat lei tot ernstige bloedarmoede. In response to waste products released as the parasites burst from infected blood cells, the host immune system mounts a massive inflammatory response with delirium-inducing fever episodes, as parasites destroy red blood cells, spilling parasite waste into the blood stream. P. falciparum word deur die Afrika-malariamuskiet aan mense oorgedra, Anopheles gambiae. Tegnieke om blootstelling aan hierdie hoogs aggressiewe muskietspesie dood te maak, te steriliseer of te vermy, is noodsaaklik vir malariabeheer.

Hierdie fliek beeld die patogenese van Plasmodium falciparum, the causative agent of malaria.


Looking for LUCA, the last universal common ancestor

A hydrothermal vent in the north-east Pacific Ocean, similar to the kind of environment in which LUCA seems to have lived. Credit: NOAA

Around 4 billion years ago there lived a microbe called LUCA: the Last Universal Common Ancestor. There is evidence that it could have lived a somewhat 'alien' lifestyle, hidden away deep underground in iron-sulfur rich hydrothermal vents. Anaerobic and autotrophic, it didn't breathe air and made its own food from the dark, metal-rich environment around it. Its metabolism depended upon hydrogen, carbon dioxide and nitrogen, turning them into organic compounds such as ammonia. Most remarkable of all, this little microbe was the beginning of a long lineage that encapsulates all life on Earth.

If we trace the tree of life far enough back in time, we come to find that we're all related to LUCA. If the war cry for our exploration of Mars is 'follow the water', then in the search for LUCA it's 'follow the genes'. The study of the genetic tree of life, which reveals the genetic relationships and evolutionary history of organisms, is called phylogenetics. Over the last 20 years our technological ability to fully sequence genomes and build up vast genetic libraries has enabled phylogenetics to truly come of age and has taught us some profound lessons about life's early history.

For a long time it was thought that the tree of life formed three main branches, or domains, with LUCA at the base – eukarya, bacteria and archaea. The latter two – the prokaryotes – share similarities in being unicellular and lack a nucleus, and are differentiated from one another by subtle chemical and metabolic differences. Eukarya, on the other hand, are the complex, multicellular life forms comprised of membrane-encased cells, each incorporating a nucleus containing the genetic code as well as the mitochondria 'organelles' powering the cell's metabolism. The eukarya are considered so radically different from the other two branches as to necessarily occupy its own domain.

However, a new picture has emerged that places eukarya as an offshoot of bacteria and archaea. This "two-domain tree" was first hypothesized by evolutionary biologist Jim Lake at UCLA in 1984, but only got a foothold in the last decade, in particular due to the work of evolutionary molecular biologist Martin Embley and his lab at the University of Newcastle, UK, as well as evolutionary biologist William Martin at the Heinrich Heine University in Düsseldorf, Germany.

Bill Martin and six of his Düsseldorf colleagues (Madeline Weiss, Filipa Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger and Shijulal Nelson-Sathi) published a 2016 paper in the journal Natuur Mikrobiologie describing this new perspective on LUCA and the two-domain tree with phylogenetics.

Previous studies of LUCA looked for common, universal genes that are found in all genomes, based on the assumption that if all life has these genes, then these genes must have come from LUCA. This approach has identified about 30 genes that belonged to LUCA, but they're not enough to tell us how or where it lived. Another tactic involves searching for genes that are present in at least one member of each of the two prokaryote domains, archaea and bacteria. This method has identified 11,000 common genes that could potentially have belonged to LUCA, but it seems far-fetched that they all did: with so many genes LUCA would have been able to do more than any modern cell can.

Bill Martin and his team realized that a phenomenon known as lateral gene transfer (LGT) was muddying the waters by being responsible for the presence of most of these 11,000 genes. LGT involves the transfer of genes between species and even across domains via a variety of processes such as the spreading of viruses or homologous recombination that can take place when a cell is placed under some kind of stress.

A growing bacteria or archaea can take in genes from the environment around them by 'recombining' new genes into their DNA strand. Often this newly-adopted DNA is closely related to the DNA already there, but sometimes the new DNA can originate from a more distant relation. Over the course of 4 billion years, genes can move around quite a bit, overwriting much of LUCA's original genetic signal. Genes found in both archaea and bacteria could have been shared through LGT and hence would not necessarily have originated in LUCA.

The field of hydrothermal vents known as Loki’s Castle, in the North Atlantic Ocean, where scientists found archaea believed to be related to the archaea that created eukaryotes through endosymbiosis with bacteria. Credit: R B Pedersen/Centre for Geobiology

Knowing this, Martin's team searched for 'ancient' genes that have exceptionally long lineages but do not seem to have been shared around by LGT, on the assumption that these ancient genes should therefore come from LUCA. They laid out conditions for a gene to be considered as originating in LUCA. To make the cut, the ancient gene could not have been moved around by LGT and it had to be present in at least two groups of archaea and two groups of bacteria.

"While we were going through the data, we had goosebumps because it was all pointing in one very specific direction," says Martin.

Once they had finished their analysis, Bill Martin's team was left with just 355 genes from the original 11,000, and they argue that these 355 definitely belonged to LUCA and can tell us something about how LUCA lived.

Such a small number of genes, of course, would not support life as we know it, and critics immediately latched onto this apparent gene shortage, pointing out that essential components capable of nucleotide and amino acid biosynthesis, for example, were missing. "We didn't even have a complete ribosome," admits Martin.

However, their methodology required that they omit all genes that have undergone LGT, so had a ribosomal protein undergone LGT, it wouldn't be included in the list of LUCA's genes. They also speculated that LUCA could have gotten by using molecules in the environment to fill the functions of lacking genes, for example molecules that can synthesize amino acids. After all, says Martin, biochemistry at this early stage in life's evolution was still primitive and all the theories about the origin of life and the first cells incorporate chemical synthesis from their environment.

What those 355 genes do tell us is that LUCA lived in hydrothermal vents. The Düsseldorf team's analysis indicates that LUCA used molecular hydrogen as an energy source. Serpentinization within hydrothermal vents can produce copious amounts of molecular hydrogen. Plus, LUCA contained a gene for making an enzyme called 'reverse gyrase', which is found today in extremophiles existing in high-temperature environments including hydrothermal vents.

Martin Embley, who specializes in the study eukaryotic evolution, says the realization of the two-domain tree over the past decade, including William Martin's work to advance the theory, has been a "breakthrough" and has far-reaching implications on how we view the evolution of early life. "The two-domain tree of life, where the basal split is between the archaea and the bacteria, is now the best supported hypothesis," he says.

It is widely accepted that the first archaea and bacteria were likely clostridia (anaerobes intolerant of oxygen) and methanogens, because today's modern versions share many of the same properties as LUCA. These properties include a similar core physiology and a dependence on hydrogen, carbon dioxide, nitrogen and transition metals (the metals provide catalysis by hybridizing their unfilled electron shells with carbon and nitrogen). Yet, a major question remains: What were the first eukaryotes like and where do they fit into the tree of life?

A schematic of the two-domain tree, with eukaryotes evolving from endosymbiosis between members of the two original trunks of the tree, archaea and bacteria. Credit: Weiss et al/Nature Microbiology

Phylogenetics suggests that eukaryotes evolved through the process of endosymbiosis, wherein an archaeal host merged with a symbiont, in this case a bacteria belonging to the alphaproteobacteria group. In the particular symbiosis that spawned the development of eukarya, the bacteria somehow came to thrive within their archaeal host rather than be destroyed. Hence, bacteria came to not only exist within archaea but empowered their hosts to grow bigger and contain increasingly large amounts of DNA. After aeons of evolution, the symbiont bacteria evolved into what we know today as mitochondria, which are little battery-like organelles that provide energy for the vastly more complex eukaryotic cells. Consequently, eukaryotes are not one of the main branches of the tree-of-life, but merely a large offshoot.

A paper that appeared recently in Nature, written by a team led by Thijs Ettema at Uppsala University in Sweden, has shed more light on the evolution of eukaryotes. In hydrothermal vents located in the North Atlantic Ocean – centered between Greenland, Iceland and Norway, known collectively as Loki's Castle– they found a new phylum of archaea that they fittingly named the 'Asgard' super-phylum after the realm of the Norse gods. The individual microbial species within the super-phylum were then named after Norse gods: Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota. This super-phylum represents the closest living relatives to eukaryotes, and Ettema's hypothesis is that eukaryotes evolved from one of these archaea, or a currently undiscovered sibling to them, around 2 billion years ago.

If it's possible to date the advent of eukaryotes, and even pinpoint the species of archaea and bacteria they evolved from, can phylogenetics also date LUCA's beginning and its split into the two domains?

It must be noted that LUCA is not the origin of life. The earliest evidence of life dates to 3.7 billion years ago in the form of stromatolites, which are layers of sediment laid down by microbes. Presumably, life may have existed even before that. Yet, LUCA's arrival and its evolution into archaea and bacteria could have occurred at any point between 2 to 4 billion years ago.

Phylogenetics help narrow this down, but Martin Embley isn't sure our analytical tools are yet capable of such a feat. "The problem with phylogenetics is that the tools commonly used to do phylogenetic analysis are not really sophisticated enough to deal with the complexities of molecular evolution over such vast spans of evolutionary time," he says.

Embley believes this is why the three-domain tree hypothesis lasted so long – we just didn't have the tools required to disprove it. However, the realization of the two-domain tree suggests that better techniques are now being developed to handle these challenges.

These techniques include examining the ways biochemistry, as performed in origin-of-life experiments in the lab, can coincide with the realities of what actually happens in biology.

This is a concern for Nick Lane, an evolutionary biochemist at University College of London, UK. "What I think has been missing from the equation is a biological point of view," he says. "It seems trivially easy to make organic [compounds] but much more difficult to get them to spontaneously self-organize, so there are questions of structure that have largely been missing from the chemist's perspective."

Jupiter’s moon Europa has a subterranean ocean, a rocky seabed, and geothermal heat produced by Jupiter’s gravitational tides. Water, rock and heat were all that were required by LUCA, so could similar life also exist on Europa? Credit: NASA/JPL–Caltech/SETI Institute

For example, Lane highlights how lab experiments routinely construct the building blocks of life from chemicals like cyanide, or how ultraviolet light is utilized as an ad hoc energy source, yet no known life uses these things. Although Lane sees this as a disconnect between lab biochemistry and the realities of biology, he points out that William (Bill) Martin's work is helping to fill the void by corresponding to real-world biology and conditions found in real-life hydrothermal vents. "That's why Bill's reconstruction of LUCA is so exciting, because it produces this beautiful, independent link-up with real world biology," Lane says.

The biochemistry results in part from the geology and the materials that are available within it to build life, says Martin Embley. He sees phylogenetics as the correct tool to find the answer, citing the Wood–Ljungdahl carbon-fixing pathway as evidence for this.

Carbon-fixing involves taking non-organic carbon and turning it into organic carbon compounds that can be used by life. There are six known carbon-fixing pathways and work conducted over many decades by microbiologist Georg Fuchs at the University of Freiburg has shown that the Wood–Ljungdahl pathway is the most ancient of all the pathways and, therefore, the one most likely to have been used by LUCA. Indeed, this is corroborated by the findings of Bill Martin's team.

In simple terms the Wood–Ljundahl pathway, which is adopted by bacteria and archaea, starts with hydrogen and carbon dioxide and sees the latter reduced to carbon monoxide and formic acid that can be used by life. "The Wood–Ljungdahl pathway points to an alkaline hydrothermal environment, which provides all the things necessary for it – structure, natural proton gradients, hydrogen and carbon dioxide," says Martin. "It's marrying up a geological context with a biological scenario, and it has only been recently that phylogenetics has been able to support this."

Astrobiological implications

Understanding the origin of life and the identity of LUCA is vital not only to explaining the presence of life on Earth, but possibly that on other worlds, too. Hydrothermal vents that were home to LUCA turn out to be remarkably common within our solar system. All that's needed is rock, water and geochemical heat. "I think that if we find life elsewhere it's going to look, at least chemically, very much like modern life," says Martin.

Moons with cores of rock surrounded by vast global oceans of water, topped by a thick crust of water-ice, populate the Outer Solar System. Jupiter's moon Europa and Saturn's moon Enceladus are perhaps the most famous, but there is evidence that hints at subterranean oceans on Saturn's moons Titan and Rhea, as well as the dwarf planet Pluto and many other Solar System bodies. It's not difficult to imagine hydrothermal vents on the floors of some of these underground seas, with energy coming from gravitational tidal interactions with their parent planets. The fact that the Sun does not penetrate through the ice ceiling does not matter – the kind of LUCA that Martin describes had no need for sunlight either.

"Among the astrobiological implications of our LUCA paper is the fact that you do not need light," says Martin. "It's chemical energy that ran the origin of life, chemical energy that ran the first cells and chemical energy that is present today on bodies like Enceladus."

As such, the discoveries that are developing our picture of the origin of life and the existence of LUCA raise hopes that life could just as easily exist in a virtually identical environment on a distant locale such as Europa or Enceladus. Now that we know how LUCA lived, we know the signs of life to look out for during future missions to these icy moons.

Laura Eme et al. Archaea and the origin of eukaryotes, Nature Reviews Microbiology (2017). DOI: 10.1038/nrmicro.2017.133


Defining Life

What is life, exactly? This is a question that keeps biologists up at night. The science of biology is the study of life, yet scientists can’t agree on an absolute definition. Are the individual cells of your body, with all their complex machinery, “alive?” What about a computer program that learns and evolves? Can a wild fire – which feeds, grows, and reproduces – be considered a living entity?

Trying to define life is not just a philosophical exercise. We need to understand what separates living creatures from non-living matter before we can claim to find life elsewhere in the Universe.

In 1944, the physicist Erwin Shrodinger defined living matter as that which “avoids the decay into equilibrium.” This definition refers to the Second Law of Thermodynamics, which says that entropy always increases. Entropy is often referred to as chaos or disorder, but really it is the spreading out of energy towards a state of uniformity. This law can be seen in a cold glass of water that slowly grows warmer until it is the same temperature as the surrounding air. Because of this trend toward equilibrium, the Universe eventually will have a complete lack of structure, consisting of evenly spread atoms of equal warmth.

But living things, said Shrodinger, are able to postpone this trend. Consider: while you are alive your body maintains its structure, but once you die your body begins to break down through bacterial action and chemical processes. Eventually the atoms of your body are evenly spread out, recycled by the Earth. To die is to submit your body to the entropy of the Universe.

Living things resist entropy by taking in nutrients. This biochemical process of taking in energy for activities and expelling waste byproducts is known as a “metabolism.” If metabolism is a sign of life, scientists can look for the waste byproducts of a metabolism when searching for life on other worlds.

Image of the Viking Lander.
Credit: NSSDC Photo Gallery

At least, that was the idea behind the Viking Lander‘s Labeled Release Experiment, conducted on Mars in 1976. This experiment tested for metabolic clues to life by adding radioactively labeled liquid nutrients to a sample of Martian soil. If these nutrients were consumed by life forms, any gases released as waste byproducts would also be radioactively labeled.

After the nutrient was injected, there was a rapid increase in carbon dioxide (CO2) gas. Because this gas had the radioactive label, scientists at first concluded that organisms in the Martian soil were eating the nutrient and releasing the CO2 as a waste byproduct. However, the Martian soil turned out to have a unique soil chemistry that could produce a metabolic-like reaction. Although the test remains inconclusive, most scientists believe that non-living, chemical processes in the Martian soil caused the “metabolic” reaction. The Viking experiments showed that while metabolism may be a quality of life, it is not a narrow enough guideline to search for life elsewhere.

Another quality of all life on Earth is a dependence on water. Since water plays such a crucial role in all known life forms, many scientists believe that water-use will be a quality universal to all life. But Benton Clark, an astrobiologist with the University of Colorado and Lockheed Martin, says that water is really a side issue.

“Water doesn’t define life, it is just an aspect of our environment,” says Clark.

Life on Earth evolved with water, and so today life on Earth is dependent on that resource. But we cannot say that without water, life is impossible. On Earth, life has been able to adapt to the harshest environments, so it is possible that life may have found a way to survive on worlds that have no liquid water.

Steven Benner, an astrobiologist with the University of Florida, agrees that water is not necessarily a universal quality of life.

“We can conceive of chemistries that might occur in sulfuric acid as a solvent – as on Venus – or in methane-ammonia mixtures – as on Jupiter,” says Benner. “Discovering these would have a profound impact on our view of life, however, as well as the way that NASA looks for it.”

A recent definition of life (often created to Gerald Joyce of the Scripps Research Institute) doesn’t mention either metabolism or water. This definition says that life is “a self-sustaining system capable of Darwinian evolution.”

But Clark says most life forms technically are not self-sustaining. Animals feed on plants or other animals, plants need microorganisms at their roots to take up nutrients, and bacteria often live inside other organisms, relying on the internal environment of their host. He says the only truly self-sustaining organisms are chemolithotrophs and photolithotrophs, and they are relatively rare.

Clark says that Darwinian evolution is another problematic criteria. How could you tell if something has undergone Darwinian evolution? The time scales involved are enormous – scientists would need a complete understanding of an organism’s fossil history before being able to declare that the object is, indeed, alive.

According to Clark, living organisms exhibit at least 102 observable qualities. Adding all these qualities together into a single – if exceedingly long – definition still does not capture the essence of life. But Clark has picked out three qualities from this list that he considers universal, creating a new definition of life. This definition says that “life reproduces, and life uses energy. These functions follow a set of instructions embedded within the organism.”

The instructions are the DNA and RNA “letters” that make up the genetic code in all organisms on Earth. A wild fire, one might say, reproduces and uses energy. So do crystals and various chemical reactions. In fact, Benner says that, “every spontaneous chemical process must expend free energy, living or not.”

“Every spontaneous chemical process must expend free energy, living or not,” Benner says. The formation of these crystals is an example.
Credit: National Ignition Facility Programs

But Clark says none of these phenomena are “alive” because none of them have the embedded instructions of a genetic code. We know there are no instructions, because there has not been any mutation over the years. They follow the rules of physics rather than embedded instructions, and so they behave the same every time. Mutation, says Clark, is the key to understanding whether or not something has embedded instructions.

Not all living things are capable of reproduction, however. Mules are born sterile. Most honeybees do not reproduce: only the Queen bee has that honor. Many human beings live their entire lives without producing offspring, and no one would argue that such people were not therefore alive.

But Clark says that reproduction and energy-use need not both occur for life to exist. He divides life into two categories: “organisms” and “Lifeforms.” Organisms channel energy according to embedded instructions, and this energy allows the organism to perform certain activities. A Lifeform, says Clark, is a broader category that encompasses organisms and makes reproduction possible.

“What I am proposing is that the individual physical entities should be called ‘organisms,’ but it sometimes takes a collection of organisms, the ‘Lifeform,’ to achieve reproduction,” says Clark.

There have been many definitions of life created over the years, but there has yet to be a single definition accepted by all. Every definition has had to face down challenges to its validity. According to Carol Cleland of the University of Colorado, this is because definitions are concerned only with language and concepts they can’t expand our understanding of the world. We can only define things we already understand.

Cleland says that scientists in the seventeenth century had the same problem trying to define water. There are many descriptions of water – it’s wet, thirst-quenching, it freezes and turns into vapor – but other substances also have these qualities. Once scientists discovered molecular chemistry, they could define water to everyone’s satisfaction as one oxygen atom coupled with two hydrogen atoms (H2O). Perhaps we need a similar revolution in scientific thought in order to define life.

Image of a water molecule, 2 hydrogen atoms and 1 oxygen atom.
Credit: FTC

“Current attempts to answer the question, ‘What is life?’ by defining life in terms of features like metabolism or reproduction – features that we ordinarily use to recognize samples of terrestrial life – are unlikely to succeed,” says Cleland. “What we need to answer the question, ‘What is life?’ is a general theory of living systems.”

Could we use Clark’s definition to find life on other worlds? The Viking Lander already looked for energy-use in the form of a metabolism, and the results were inconclusive. To search for this criterion as a means for finding life, we would need to consider other ways life could use energy.

The problem with searching for life forms with embedded instructions, says Clark, is that the criteria may be too specific. The only instructions we know of are DNA and RNA – there may be other genetic systems possible in the Universe that do not resemble the system found here on Earth.


Lotus japonicus: A Model Plant for the Legume Family☆

The Model Plant Features

Many cultivated legumes such as pea and soybean have complex genomes or are, for other reasons, not amenable to modern molecular genetic methods. Its favorable biological properties made L. japonicus the model plant of choice for classical and molecular genetic analysis of legumes. The qualities of L. japonicus include a small genome size of approximately 450 Mb, diploid genetics, six chromosome pairs, genomic colinearity to different legume crops, self-fertile flowers, a short seed-to-seed generation time, ample seed production, small seeds, simple straight (nonspiral) seed pod like soybean, large flowers enabling manual crossing, described transformation procedures using Agrobacterium tumefaciens of Agrobacterium rhizogenes, described in vitro tissue culture and regeneration procedures, effective nodulation and mycorrhization, perennial life cycle, regrowth from stem base, propagation from nodal cuttings, and production of cyanogenic glucosides, isoflavonoids, tannin, and other secondary metabolites ( Fig. 1 ).

Fig. 1 . Lotus japonicus plants grown for seed production in the greenhouse.

Simbiose

Most legumes develop root nodules in symbiosis with nitrogen-fixing soil bacteria collectively called rhizobia, and nodulated legume plants can use atmospheric dinitrogen as their sole nitrogen source. The interaction between the bacterial microsymbionts and legumes is selective. Individual species of rhizobia have a characteristic host range allowing nodulation of a particular set of legume plants. Mesorhizobium loti and the broad host range Rhizobium sp. NGR234 induce root nodules on L. japonicus. Roots of L. japonicus are also effectively colonized by symbiotic arbuscular mycorrhizal fungi, for example, Glomus intraradices en Gigaspora margarita. These fungi invade the root tissue by intercellular and intracellular hyphal growth and form arbuscules in cortical cells where metabolic interchanges take place. Mycorrhizal hypha increase the root surface and improves phosphor uptake. Identification of single gene plant mutations impairing both colonization by mycorrhiza and rhizobial invasion demonstrates that the two interactions share common steps during the early infection processes. Extending this observation may open a broader approach to the understanding of plant–microbe interactions, where symbiotic studies contribute not only to realization of the potential of symbiosis, but also to our understanding of, for example, plant–pathogen interactions. One of the interests of the plant science community is to use L. japonicus in the molecular genetic analysis of symbiosis. For this purpose, tools and resources for molecular analysis have been established. Insertion mutagenesis is possible with T-DNA or the maize transposon Rek. Ethyl methanesulfonate (EMS) is effective for chemical mutagenesis and a TILLING population for reverse genetics has been established as a service for the legume community and the plant community at large (TILLING, targeting-induced local lesions in genomes). More recently, an endogenous retransposon, LORE1, was shown to generate independent new insertions in the pollen germ line of regenerated plants and a large LORE1 insertion population has been established. This population is a new resource for forward genetics screening for interesting phenotypes and reverse genetics to identify insertion mutants in genes of interest.

Equally important, it can be used for identifying insertions in genes of interest using reverse genetics based on large-scale sequencing of insertion sites in a structured population connecting insertion sites in genes with plants and seeds carrying the individual insertions.

Genetics of Symbiotic Pathways

Like soybean, L. japonicus develops the determinate type of nodules. In contrast to, for example, pea nodules with a persistent meristem, the meristematic activity ceases early in determinate nodules developing on L. japonicus . After the initial phase with meristematic cell proliferation, determinate nodules grow by expansion giving a typical spherical shape. All developmental stages, from root hair curling to nodule senescence, are consequently phased in time. Root nodule development is a rare example of induced and dispensable organ formation in plants. Nodulation mutants can be rescued on nitrogen-containing nutrient solution, and developmental control genes that would compromise plant development and completion of the life cycle in other organogenic processes could thus be identified from nodulation mutants. Screening of the EMS, T-DNA, LORE1 and Rek populations of L. japonicus has so far identified more than 40 symbiotic loci. The phenotypes of these developmental plant mutants divide them roughly into three classes: non-nodulating mutants arrested in bacterial recognition or nodule initiation nodule development mutants arrested at consecutive stages of the organogenic process and autoregulatory mutants where the plant control of root nodule numbers is nonfunctional and spontaneous nodulating mutant plant developing root nodules in the absence of the rhizobial microsymbiont. Development of root nodules can thus be divided into a series of genetically separable steps. Taking advantage of the genetic and genomic resources available, genes involved in these different steps have been cloned and characterized. A novel class of LysM receptor kinases perceiving the rhizobial Nod-factor signals triggering the development of root nodules has been identified and shown to be involved in deciphering the structure of the Nod-factor signal molecule, thus contributing to the determination of the plant–bacterial host specificity, which in older literature is described as cross-inoculation groups. Another LysM receptor kinase was recently shown to distinguish between compatible and incompatible bacterial exopolysaccharides thus regulating rhizobial infection.

Likewise, a signal transduction pathway shared with mycorrhizal infection frequently called the common pathway has been defined. This knowledge inspired the cloning of the chitin receptor from the Arabidopsis model plant and the role of this receptor in plant–pathogen interaction is now studied intensively. In a similar development, the information from identification and functional analysis of plant genes required for Nod-factor perception, downstream signaling, or functional symbiosis has been used to identify the corresponding genes in cultivated legumes such as pea, bean, and soybean. More recently, the availability of both loss-of-function and gain-of-function mutants made it possible to investigate the role of individual genes in the highly synchronized infection and organogenic pathways leading to the development of functional nitrogen fixing root nodules. Combining loss-of-function and gain-of-function mutations in synthetic mutants showed that L. japonicus possess three different infection routes reflecting the different bacterial entry pathways in the legume family. The genetic requirement for single-cell peg entry, crack entry, and infection thread infection was defined by this analysis, which provides support for the origin of rhizobial infection through direct intercellular epidermal invasion and subsequent evolution of crack entry and root hair invasions observed in most extant legumes.

Translational Genetics and Genomics

Several resources for genetic and genomic research in L. japonicus have been developed, and an integrated genetic map of Lotus has been assembled. The Gifu and Miyakojima ecotypes of L. japonicus were used to develop the genetic linkage map together with the closely related cross-fertile Lotus burtii en Lotus filicaulis. In addition, recombinant inbreed lines have been developed from a Gifu×Miyakojima cross, from a L. japonicus Gifu×Lotus burtii cross and from an L. japonicus Gifu×Lotus filicaulis kwaad. In order to transfer this genetic information and gene discoveries to crops unfit for genetic analysis, a bioinformatics-based legume anchor marker design was developed and applied to bean (Phaseolus vulgaris) and groundnut (Arachis). This has revealed a high degree of colinearity, and a substantial synteny exists toward the genomes of other legumes such as pea, common bean, and peanut. Another observation from these studies suggests that the gene space in Papilionoid legumes may be divided into two broadly defined components: more conserved regions, which tend to have low retrotransposon densities and are relatively stable during evolution and, variable regions, which tend to have high retrotransposon densities and whose frequent rearrangement may contribute toward evolution of some gene families.

Genome and Proteome Resources

For further studies, the following genome resources have been developed: a general genetic map and bacterial artificial chromosome (BAC) libraries for positional cloning of untagged mutants recombinant inbred lines and inventories of expressed sequence tags (ESTs) sampling the gene expression profiles from several tissues and growth conditions. Deep sequencing is now contributing to defining transcribed regions, intron–exon structures, alternative splicing, and microRNAs (miRNAs), thus annotating the genome. Sequencing of the gene space of the L. japonicus genome is almost complete and the latest release of genome sequence provides 98% coverage with updates still to come. The full genome sequence of the bacterial M. loti MAFF 303099 strain and the symbiosis island of the M. loti R7A strain, including bacterial genes required for nodulation and nitrogen fixation, are available, together with a wide selection of rhizobial mutants. Lotus has over the last decade contributed to the discovery of novel genes involved in diverse biological processes. High-throughput transcriptome, proteome, and metabolome studies have been performed and the information made available in public databases. As an example, a large-scale proteomics analysis of seeds and seed pods through the different developmental stages into maturation of the seeds and senescence of the seed pod has been performed in order to improve our understanding of the developmental and metabolic processes leading to the production of the protein- and oil-rich legume seeds that is a major source of food and feed.


Kyk die video: De cellen van de 4 rijken - planten, dieren, schimmels en bacteriën (September 2022).


Kommentaar:

  1. Chanan

    Ek dink dit is die wonderlike idee

  2. Dourr

    Waar is die infa

  3. Shalar

    Ek dink dat jy 'n fout begaan. Kom ons bespreek. Skryf vir my in PM, ons sal praat.



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