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Titel:Colonization of the rice rhizosphere by microbial communities involved in the syntrophic degradation of rhizodeposits to methane
Autor:Vogel, Dirk
Weitere Beteiligte: Conrad, Ralf (Prof. Dr.)
Veröffentlicht:2017
URI:https://archiv.ub.uni-marburg.de/diss/z2017/0241
URN: urn:nbn:de:hebis:04-z2017-02419
DOI: https://doi.org/10.17192/z2017.0241
DDC:500 Naturwissenschaften
Titel(trans.):Besiedlung der Reis-Rhizosphäre durch am syntrophen Abbau von Rhizodepositen zu Methan beteiligte mikrobielle Lebensgemeinschaften
Publikationsdatum:2017-12-14
Lizenz:https://creativecommons.org/licenses/by-nc-sa/4.0

Dokument

Schlagwörter:
Rhizosphäre, Rhizodeposition, organic matter degradation, rhizosphere, Methanogenese, methanogenesis, Abbau von organischen Substanzen, Methanogenese, rhizodeposition, Rhizosphäre

Summary:
Roots represent the primary site of direct interaction between rice plants and soil microorganisms. The influence of the plant on the soil microbial community includes the translocation of photosynthetically fixed carbon into the rhizosphere as rhizodeposition. This extends to the rhizosphere of rice plants, which is colonized by a syntrophic microbial community, which in turn is able to degrade root derived carbon to methane. Each plant species is thought to select a specific microbial community composition as root microbiome. A general understanding of microbial colonization of the rice rhizosphere and the consequential impact on the emission of methane originating from rhizodeposits is still uncertain, since the majority of the studies have so far focused exclusively on rice roots planted in rice paddy soils. Therefore, we used different initial soil microbial communities available for colonization of the rice roots. In order to do this, an inert sand-vermiculite matrix was inoculated with rice paddy soil and digested sludge, respectively, and was afterwards planted with rice. The microbial activity essential for the formation of methane from those soil-systems was tested in pre-experiments and the colonization of the rice rhizosphere was determined afterwards in plant-soil microcosms. Each of the microcosms possessed an individually structured microbial community, which served as a seed bank for the colonization of the rice roots. We analyzed the impact of the community composition on the emission of methane by combining 13CO2 pulse-labeling with illumina sequencing and quantitative PCR, targeting the 16S rRNA as phylogenetic-, as well as mcrA and pmoA as functional marker genes for methanogenic archaea and methane-oxidizing bacteria. The degradation of rhizodeposits to methane in the different microcosms was dependent on the bacterial and methanogenic community structure, but not on their absolute abundance in the rhizosphere. Like the colonization of the rhizosphere by bacteria and methanogenic archaea, the translocation of photosynthetically fixed carbon depended upon the initial microbial communities. Nevertheless, the rice rhizosphere was found to be a distinct habitat for bacteria and methanogenic archaea. We were able to identify a methanogenic community which was linked to the degradation of rhizodeposits to methane across the rhizosphere of all microcosms. Besides hydrogenotrophic Methanocella and Methanobacteriaceae, acetoclastic Methanosaeta could also be assigned to this community. Nevertheless, most methanogens which contribute to the emission of methane originating from root derived carbon were found to belong to those with a hydrogenotrophic pathway. Within the methanogenic community linked to the formation of methane from rhizodeposits, the root surface was mainly colonized by hydrogenotrophic methanogens, while those able to perform acetoclastic methanogenesis were highly abundant in the rhizospheric soil. This was true of the colonization of the rice rhizosphere by methanogenic archaea in general. Furthermore, we were able to identify methanogens which were ubiquitous in the rhizosphere of all microcosms. Those were considered as methanogenic community selected by the rice plant on its roots. Representatives of Methanobacteriaceae, Methanosaeta and Methanosarcina colonized the overall rhizosphere, while Methanocella were found to be present in the rhizospheric soil of all microcosms. In addition to this, all methanogenic archaea which were linked to the degradation of root derived carbon to methane also belonged to this root associated community. Hence, the methanogenic community selected on the rice root also contributed to the formation of methane from rhizodeposits. Besides methanogens, we were also able to identify certain bacterial groups, which are linked to the degradation of root derived carbon to methane. These includes representatives of Kineosporiaceae, Anaeromyxobacter, Bradyrhizobium, and Bacteroidales. A higher abundance of Kineosporiaceae also resulted in an increased conversion of root derived carbon compounds to acetate, CO2, and propionate. Therefore, at least the family of Kineosporiaceae was thought to be actively involved in the degradation of rhizodeposition to precursors for methanogenesis. Nevertheless, we were not able to determine bacteria which contributed to the emission of methane originating from root derived carbon and which were ubiquitous in the rhizosphere of all soil-systems. This resulted from the fact that the microbial community structure of the rhizosphere also depended on the initial pool of microorganisms available for root colonization.

Zusammenfassung:
Die Pflanzenwurzel stellt die primäre Zone für Interaktionen zwischen Reispflanzen und Bodenmikroorganismen dar. Pflanzen nehmen unter anderem durch Translokation von photosynthetisch fixiertem Kohlenstoff in die Rhizosphäre als Rhizodeposition Einfluss auf die im Boden vorkommenden mikrobiellen Gemeinschaften. Dies gilt auch für Reiswurzeln, welche von einer syntrophen mikrobiellen Lebensgemeinschaft besiedelt sind, die Methan aus wurzelbürtigen organischen Kohlenstoffverbindungen bilden kann. Es konnte bereits gezeigt werden, dass jede Pflanzenart eine spezifische mikrobielle Gemeinschaft an ihren Wurzeln selektiert. Ein generelles Verständnis über die Kolonisierung der Rhizosphäre von Reispflanzen und der sich daraus ergebende Einfluss auf den Abbau von Rhizodepositen zu Methan fehlt jedoch, da der Großteil der veröffentlichen Studien das Augenmerk ausschließlich auf solche Wurzeln legt, die auch in Reisfeldböden herangewachsen sind. Daher haben wir für diese Studie verschiedene mikrobielle Ausgangs-Boden-Gemeinschaften erstellt, welche zur Besiedlung der Reiswurzeln zur Verfügung standen. Dazu wurde eine inerte Sand-Vermiculit Matrix mit Reisfeldboden, bzw. Faulschlamm inokuliert und anschließend mit Reis bepflanzt. Die mikrobielle Aktivität der Boden-Systeme zur Bildung von Methan wurde in Vorversuchen getestet und die Besiedlung der Reis-Rhizosphäre daraufhin in bepflanzten Mikrokosmen untersucht. Diese enthielten jeweils eine unterschiedlich strukturierte mikrobielle Gemeinschaft, welche zur Wurzelbesiedlung zur Verfügung stand. Die Bedeutung der mikrobiellen Gemeinschaften für die Bildung von Methan aus pflanzenbürtigem Kohlenstoff wurde durch eine Kombination aus 13CO2 pulse-labeling mit Illumina Sequenzierung und quantitativer PCR untersucht. Die molekularbiologischen Analysen richteten sich hierbei auf die 16S rRNA als phylogenetisches, bzw. mcrA und pmoA als funktionale Marker-Gene für methanogene Archaeen und methanotrophe Bakterien. Die Bildung von Methan, sowie der generelle Abbau des wurzelbürtigen organischen Kohlenstoffs in den verschiedenen Mikrokosmen, war abhängig von der Zusammensetzung der bakteriellen und methanogenen Lebensgemeinschaften, jedoch nicht von deren absoluter Abundanz innerhalb der Rhizosphäre. Die Besiedlung der Rhizosphäre durch Bakterien und methanogene Archaeen fand in Abhängigkeit von den Ausgangs-Boden-Gemeinschaften statt, genauso wie die Translokation des photosynthetisch fixierten Kohlenstoffs. Dennoch zeigte sich anhand der an den Wurzeln vorkommenden mikrobiellen Zusammensetzung, dass die Rhizosphäre von Reispflanzen ein eigenständiges Habitat für Bakterien und methanogene Archaeen darstellt. Es konnte eine methanogene Lebensgemeinschaft identifiziert werden, welche über die Rhizosphäre aller Mikrokosmen hinweg mit der Bildung von Methan aus Rhizodeposition verknüpft war. Neben den hydrogenotrophen Methanocella und Methanobacteriaceae konnten auch Vertreter der acetoklastischen Methanosaeta dieser Gemeinschaft zugeordnet werden. Dennoch gehörten die meisten der Methanogenen, welche zur Methanemission aus Rhizodeposition beigetragen haben, zu denen mit hydrogenotrophem Stoffwechselweg. Innerhalb der methanogenen Gemeinschaft, die maßgeblich an der Bildung von Methan aus Rhizodeposition beteiligt war, wurden die Wurzeloberflächen stärker mit hydrogenotrophen Organismen besiedelt, während jene, die zur acetoklastischen Methanogenese befähigt sind, vornehmlich den Rhizosphären-Boden kolonisierten. Dies galt ebenfalls für die Besiedlung der Reis-Rhizosphäre durch Methanogene im Allgemeinen. Darüber hinaus konnten Methanogene ermittelt werden, die ubiquitär in der Rhizosphäre aller Mikrokosmen vertreten waren. Diese wurden somit als methanogene Lebensgemeinschaft verstanden, welche Reispflanzen an ihren Wurzeln selektieren. Hierbei besiedelten Vertreter von Methanobacteriaceae, Methanosaeta und Methanosarcina die gesamte Rhizosphäre, während Methanocella im Rhizosphären-Boden aller Mikrokosmen vorhanden waren. Des Weiteren konnte gezeigt werden, dass alle methanogenen Vertreter, welche an der Bildung von Methan aus wurzelbürtigem Kohlenstoff beteiligt waren, dieser der Reiswurzel assoziierten Gemeinschaft angehörten. Somit war die an der Reiswurzel selektierte methanogene Lebensgemeinschaft auch an der Bildung von Methan aus pflanzenbürtigem Kohlenstoff beteiligt. Neben methanogenen konnten auch bakterielle Gruppen identifiziert werden, die an der Entstehung von Methan aus Rhizodeposition beteiligt waren. Hierzu gehörten Vertreter von Kineosporiaceae, Anaeromyxobacter, Bradyrhizobium und Bacteroidales. Es konnte gezeigt werden, dass ein erhöhtes Vorkommen von Kineosporiaceae auch zu einer verstärkten Umsetzung von wurzelbürtigem Kohlenstoff zu Acetat, CO2 und Propionat führte. Daher ist davon auszugehen, dass zumindest die Familie der Kineosporiaceae aktiv an der Umsetzung von Rhizodeposition zu Vorprodukten für die Methanogenese beteiligt war. Dennoch konnten keine Bakterien identifiziert werden, welche sowohl zur Bildung von Methan aus wurzelbürtigem Kohlenstoff beigetragen haben, als auch ubiquitär in der Rhizosphäre aller Boden-Systeme präsent waren. Dies könnte darin begründet liegen, dass die Zusammensetzung der mikrobiellen Gemeinschaft in der Rhizosphäre auch maßgeblich von der Verfügbarkeit bestimmter funktionaler Gruppen in den Ausgangs-Boden-Gemeinschaften abhängig war.

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