Die Effizienz von Biogasreaktoren hängt im wesentlichen Maße von der Substratverwertung durch die beteiligte Mikroflora ab. Die genaue Zusammensetzung der mikrobiellen Gemeinschaft ist jedoch bislang nur oberflächlich charakterisiert. In dieser Studie wird daher eine Übersicht über die mikrobielle Diversität in verschiedenen Biogasreaktorentypen (Rührkesselreaktor, Leach-bed-Reaktor, Festbett-Anaerobfilter) während der Fermentation verschiedener pflanzlicher Substrate (Mais-, Rüben-, Triticum-Ganzpflanzensilage, teilweise in Kofermentation mit Rindergülle) gegeben. Die Charakterisierung der Mikrobiologie erfolgte mittels der Entwicklung und nachfolgenden bioinformatischen Analyse von 16S rDNA Bibliotheken. Es wurden insgesamt sechs 16S rDNA Bibliotheken konstruiert. Insgesamt umfassten diese sechs 16S rDNA Bibliotheken 627 Klone. Mittels der zugehörigen fingerprint-Muster (amplified rDNA restriction analysis, ARDRA) wurden innerhalb der sechs 16S rDNA Bibliotheken 223 taxonomische Gruppen (operational taxonomic units, OTU) detektiert. Zur Erfassung der Archaea wurden 402 Klone analysiert. Für die Erfassung der Bacteria wurden 283 Klone untersucht. Damit wurden 114 Archaea OTU sowie 109 Bacteria OTU detektiert. Die Dominanz von hydrogenotrophen Methanbildnern in den Archaeaspezifischen 16S rDNA Bibliotheken sowie deren große Diversität sind Indizien für eine verstärkte Bildung von Methan durch Oxidation von CO2. In diesem Falle würde die Verwertung des Acetats überwiegend durch syntrophe Bacteria erfolgen. Die Analyse der Diversität innerhalb der Domäne Bacteria ergab für den Rührkesselreaktor bei der Kofermentation von Maissilage und Gülle im Normalzustand eine hohe Diversität unter den Vertretern der Phyla Firmicutes mit dem Genus Clostridium. / The efficiency of biogas reactors depends on the substrate utilisation by the involved microbial community. However, the exact composition of the microbial biocoenosis was rudimental characterized. In this study an overview of the microbial diversity in different anaerobic biogas reactor types (completly stirred tank reactor, leach bed reactor, fixed bed anaerobic filter) is given for the fermentation of different substrates (corn-, carrots-, triticale whole crop silage as renewable raw materials, partly in co-fermentation with cattle liquid manure). The characterisation of the microbial community was conducted via the construction of 16S rDNA libraries for both, methanogenic Archaea and fermentative Bacteria. Individual taxonomic groups within the 16S rDNA libraries were determined by means of amplified rDNA restriction analysis (ARDRA). The taxonomic classification of these groups was performed via a phylogenetic analysis of representative 16S rDNA sequences. In total six 16S rDNA libraries with 627 clones were developed. Together 223 taxonomic groups were detected; from these 114 was assigned to the domain Archaea and further 109 was assigned to the domain Bacteria. Within the examined biogas reactors a high diversity was found within the hydrogenotrophic methane producing Archaea, acetotrophic methane producing Archaea appears only with a comparatively small diversity. From the domain Bacteria fermentative species of phylum Firmicutes especially of the genus Clostridium were found to be dominant in the microbial community.

Aufgrund der ökologischen und ökonomischen Problematik der chemischen Phosphatfällung ist eine Optimierung der Effizienz und Stabilität der biologischen Verfahren zur Phosphat-elimination erforderlich. Hierfür ist jedoch ein fundiertes Wissen über die daran beteiligten Organismen eine entscheidende Vorraussetzung. Das Ziel der vorliegenden Arbeit war es, die mikrobielle Populationstruktur von zwei Belebtschlamm-anlagen im Labormaßstab mit Hilfe von drei unterschiedlichen 16S rDNA basierenden molekular-biologischen Methoden zu charakterisieren. Ein besonderer Schwer-punkt ist hierbei die Analyse der Bakterien, die mit der erhöhten biologischen Phosphat-elimination in Verbindung gebracht werden. Dies sind Vertreter der Rhodocyclus-Gruppe, der Gattung Tetrasphaera und der Gattung Acinetobacter. Als Untersuchungsobjekte wurden zwei Hauptstromverfahren zur erhöhten biologischen Phosphatelimination gewählt, die sich im Schlamm-alter, der Schlammbelastung und der sich daraus resultierenden Nitrifikationsleistung unterscheiden. Aufgrund der gewählten Verfahrensweisen wurde der Einfluss der Nitrifikation auf die Zusammensetzung der Belebtschlammbiozönose ebenfalls untersucht. Um praxisnahe Verhältnisse zu erreichen, wurden die Anlagen mit kommunalem Abwasser beschickt. Für einen Vergleich sollten Proben aus kommunalen Kläranlagen mit deutlich anderen Verfahrensweisen in die Untersuchungen mit einbezogen werden.

Mikrobielle Prozesse spielen eine wichtige Rolle im Sediment von Talsperren und Seen. Demgegenüber stehen nur unzureichende Erkenntnisse über die Zusammensetzung mikrobieller Biozönosen in Sedimenten sowie deren Aktivität zur Verfügung. Das Ziel dieser Studie war die Untersuchung und der Vergleich der Zusammensetzung und der Struktur mikrobieller Gemeinschaften in Sedimenten um eine Abschätzung der mikrobiellen Diversität in Talsperrensedimenten unterschiedlicher Trophie zu erreichen. Durch die Kombination der in dieser Arbeit verwendeten Methoden (Vergleichende 16S rDNA Analyse, Fingerprinttechniken, klassische Methoden) konnte eine Charakterisierung der mikrobiellen Zusammensetzung der obersten 5 cm von den Talsperrensedimenten Neunzehnhain, Muldenberg, Quitzdorf und Saidenbach erzielt werden. Die vergleichende 16S rDNA Analyse offenbarte in 2541 analysierten rekombinanten Klonen 528 verschiedene Sequenztypen, welche zu 293 OTUs zusammengefaßt werden konnten. Obwohl die Gemeinschaften der verschiedenen Talsperren nur schwach auf der Ebene der phylogenetischen Gruppen differierten, konnte durch die Verwendung von Ähnlichkeitsindices gezeigt werden, dass jede Talsperre eine spezifische mikrobielle Sedimentgemeinschaft aufweist. Über 60% aller Klone zeigten Ähnlichkeiten von mehr als 97% zu 16S rDNA-Sequenzen kultivierter Organismen oder phylogenetisch eingeordneten Sequenzen (14 bekannte phylogenetische Gruppen). Alle anderen Klone zeigten hohe Sequenzhomologien zu unidentifizierten, phylogenetisch bisher nicht eingeordneten Bakterien. Diese Bakterien waren mit Anteilen zwischen 19,8% (Muldenberg) und 54,6% (Saidenbach) in den 16S rDNA Bibliotheken repräsentiert. Mittels Fingerprinttechniken (DGGE, T-RFLP, ARISA) konnten komplexe Muster der mikrobiellen Diversität erzeugt werden. Dabei konnten die Ergebnisse der 16S rDNA Analyse bestätigt werden. Durch die verwendeten Methoden konnte eine komplexe mikrobielle Diversität in den Sedimenten aufgedeckt werden und die Ergebnisse weisen darauf hin, dass die mikrobielle Diversität in Sedimenten wesentlich höher ist als bisher angenommen.

No description available.

Made available in DSpace on 2017-07-10T18:13:20Z (GMT). No. of bitstreams: 1 Rafael Henrique da Rocha.pdf: 1457832 bytes, checksum: 601a9b8393782cd1f8fee92a45fbe86c (MD5) Previous issue date: 2016-04-06 / Fundação Araucária / Siluriforms is one of the most significant orders and greater diversity of species in the Neotropics, being Corydoras genus with the highest number of species. This group has color patterns and external morphology very similar among species. In this context, the present study used the cytogenetics and morphometry to characterize and differentiate Corydoras carlae and Corydoras sp. B of the Iguassu River basin. The diploid number found was 46 chromosomes, with karyotype formula of 22m + 22sm + 2st, and NF equal to 92. The impregnation with silver nitrate showed two bearing-NORs chromosomes and fluorescent hybridization with 18S ribosomal probe confirmed this result, charactering simple NORs system for species. Furthermore, the 5S rDNA was co-located with the 18S rDNA for Corydoras carlae and Corydoras sp. B. However, Corydoras sp. B have an extra marking 5S rDNA, located in interstitial position on the short arm of one submetacentric chromosome. The heterochromatin constitutive was found in centromeric and pericentomeric regions for both species, but with differences in the bearing chromosomes. The morphometric traits showed morphological differences between the two species, provided by indices: body height / standard length; interorbital distance / length of the head; horizontal diameter of orbit / length of the head. The results demonstrate that although both species have the same diploid number,e same karyotype formula and simple NORs system, C. carlae e Corydoras sp. B are different how much the location of the heterochromatin constitutive and in the 5S rDNA number bearing chromosomes, and present morphological differences which distinguish the two species. / Siluriformes é uma das ordens mais representativas e com maior diversidade de espécies da região Neotropical, sendo Corydoras o gênero com o maior número de espécies. Esse grupo apresenta padrões de coloração e morfologia externa muito semelhantes entre as espécies. Nesse contexto, o presente estudo utilizou a citogenética e a morfometria para caracterizar e diferenciar as espécies Corydoras carlae e Corydoras sp. B da bacia do rio Iguaçu. O número diplóide encontrado foi de 46 cromossomos, com fórmula cariotípica de 22m+22sm+2st e NF igual a 92 para ambas as espécies. A impregnação com o nitrato de prata revelou dois cromossomos portadores de RONs e a hibridização in situ fluorescente com sonda ribossomal 18S confirmou este resultado, caracterizando sistema de RONs simples para as espécies. Além disso, o DNAr 5S foi co-localizado com o DNAr 18S para Corydoras carlae e Corydoras sp. B. No entanto, Corydoras sp. B tem uma marcação extra de DNAr 5S, localizada em posição intersticial no braço curto de um cromossomo submetacêntrico. A heterocromatina constitutiva foi evidenciada em regiões centroméricas e pericentoméricas para ambas espécies, porém com diferenças nos cromossomos portadores. Os caracteres morfométricos avaliados demonstraram diferenças morfológicas entre as duas espécies, proporcionada pelos índices: altura do corpo/comprimento padrão; distância interorbital/comprimento da cabeça; diâmetro horizontal da orbita/comprimento da cabeça. Os resultados demonstram que, apesar das espécies apresentarem o mesmo número diplóide, mesma fórmula cariotípica e sistema de RONs simples, C. carlae e Corydoras sp. B são diferentes quanto a localização da heterocromatina constitutiva e o número de cromossomos portadores de DNAr 5S, além de apresentarem diferenças morfológicas que separam as duas espécies.

Aufgrund der ökologischen und ökonomischen Problematik der chemischen Phosphatfällung ist eine Optimierung der Effizienz und Stabilität der biologischen Verfahren zur Phosphat-elimination erforderlich. Hierfür ist jedoch ein fundiertes Wissen über die daran beteiligten Organismen eine entscheidende Vorraussetzung. Das Ziel der vorliegenden Arbeit war es, die mikrobielle Populationstruktur von zwei Belebtschlamm-anlagen im Labormaßstab mit Hilfe von drei unterschiedlichen 16S rDNA basierenden molekular-biologischen Methoden zu charakterisieren. Ein besonderer Schwer-punkt ist hierbei die Analyse der Bakterien, die mit der erhöhten biologischen Phosphat-elimination in Verbindung gebracht werden. Dies sind Vertreter der Rhodocyclus-Gruppe, der Gattung Tetrasphaera und der Gattung Acinetobacter. Als Untersuchungsobjekte wurden zwei Hauptstromverfahren zur erhöhten biologischen Phosphatelimination gewählt, die sich im Schlamm-alter, der Schlammbelastung und der sich daraus resultierenden Nitrifikationsleistung unterscheiden. Aufgrund der gewählten Verfahrensweisen wurde der Einfluss der Nitrifikation auf die Zusammensetzung der Belebtschlammbiozönose ebenfalls untersucht. Um praxisnahe Verhältnisse zu erreichen, wurden die Anlagen mit kommunalem Abwasser beschickt. Für einen Vergleich sollten Proben aus kommunalen Kläranlagen mit deutlich anderen Verfahrensweisen in die Untersuchungen mit einbezogen werden.

Mikrobielle Prozesse spielen eine wichtige Rolle im Sediment von Talsperren und Seen. Demgegenüber stehen nur unzureichende Erkenntnisse über die Zusammensetzung mikrobieller Biozönosen in Sedimenten sowie deren Aktivität zur Verfügung. Das Ziel dieser Studie war die Untersuchung und der Vergleich der Zusammensetzung und der Struktur mikrobieller Gemeinschaften in Sedimenten um eine Abschätzung der mikrobiellen Diversität in Talsperrensedimenten unterschiedlicher Trophie zu erreichen. Durch die Kombination der in dieser Arbeit verwendeten Methoden (Vergleichende 16S rDNA Analyse, Fingerprinttechniken, klassische Methoden) konnte eine Charakterisierung der mikrobiellen Zusammensetzung der obersten 5 cm von den Talsperrensedimenten Neunzehnhain, Muldenberg, Quitzdorf und Saidenbach erzielt werden. Die vergleichende 16S rDNA Analyse offenbarte in 2541 analysierten rekombinanten Klonen 528 verschiedene Sequenztypen, welche zu 293 OTUs zusammengefaßt werden konnten. Obwohl die Gemeinschaften der verschiedenen Talsperren nur schwach auf der Ebene der phylogenetischen Gruppen differierten, konnte durch die Verwendung von Ähnlichkeitsindices gezeigt werden, dass jede Talsperre eine spezifische mikrobielle Sedimentgemeinschaft aufweist. Über 60% aller Klone zeigten Ähnlichkeiten von mehr als 97% zu 16S rDNA-Sequenzen kultivierter Organismen oder phylogenetisch eingeordneten Sequenzen (14 bekannte phylogenetische Gruppen). Alle anderen Klone zeigten hohe Sequenzhomologien zu unidentifizierten, phylogenetisch bisher nicht eingeordneten Bakterien. Diese Bakterien waren mit Anteilen zwischen 19,8% (Muldenberg) und 54,6% (Saidenbach) in den 16S rDNA Bibliotheken repräsentiert. Mittels Fingerprinttechniken (DGGE, T-RFLP, ARISA) konnten komplexe Muster der mikrobiellen Diversität erzeugt werden. Dabei konnten die Ergebnisse der 16S rDNA Analyse bestätigt werden. Durch die verwendeten Methoden konnte eine komplexe mikrobielle Diversität in den Sedimenten aufgedeckt werden und die Ergebnisse weisen darauf hin, dass die mikrobielle Diversität in Sedimenten wesentlich höher ist als bisher angenommen.

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. / Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

O presente trabalho teve por objetivo compreender e analisar os mecanismos genéticos e epigenéticos da expressão diferencial de regiões organizadoras do nucléolo - RONs através do estudo de dois acessos (CRT-1 e CRT-2) de Crotalaria retusa. O acesso CRT-1 é uma cultivar, enquanto que o acesso CRT-2 é proveniente de uma população periférica da orla marítima de Ilhéus BA. Por serem temporalmente e espacialmente separados, acredita-se que os acessos foram submetidos a pressões seletivas diferentes, resultando em alterações dos padrões epigenéticos, principalmente nas RONs. Para o desenvolvimento deste trabalho foram realizadas medidas cromossômicas e nucleolares a partir de células coradas pelo método de Feulgen e por nitrato de prata, coloração com fluorocromos específicos às regiões cromossômicas ricas em nucleotídeos GC e AT, mapeamento físico dos locos de DNA ribossômico 45S por hibridação in situ fluorescente, análise qualitativa e quantitativa de modificações pós-traducionais de histonas por Western blot e eletroforese bidimensional de extrato protéico radicular com enfoque em proteínas envolvidas nos mecanismos epigenéticos. As análises citológicas demonstraram uma grande semelhança nos cariótipos dos dois acessos, diferindo apenas no tamanho do segmento proximal do braço curto do cromossomo 1. Em ambos os acessos foi observada uma expressão nucleolar diferencial em, aproximadamente, 50% das células; contudo, a expressão diferencial em CRT-2 apresentou-se consideravelmente maior. Além disso, os dois acessos demonstraram diferenças quantitativas nas modificações pós-traducionais de histonas e em proteínas possivelmente envolvidas em mecanismos epigenéticos. Uma vez que as variações epigenéticas podem ser modificadas por fatores ambientais, sugere-se que as diferenças nos padrões de modificações de histonas e nos perfis protéicos encontradas entre os acessos, como também a expressão diferencial mais expressiva em CRT-2, sejam devidas às diferentes pressões seletivas as quais as populações originais foram submetidas. O estudo dos mecanismos genéticos e epigenéticos na dominância nucleolar possibilita uma maior compreensão da ação do remodelamento da cromatina no controle da expressão gênica do rDNA, como também da expressão gênica em geral. / The aim of this present work was to understand and analyze the genetic and epigenetic mechanisms of differential expression of the nucleolus organizer regions - NORs through the study of two accesses (CRT-1 and CRT-2) of Crotalaria retusa. Access CRT-1 is a cultivar, while access CRT-2 is from a peripheral population of the shoreline of Ilhéus BA. Because they are temporally and spatially separated, it is believed that the accesses were submitted to different selective pressures, resulting in changes in epigenetic patterns, primarily in NORs. To develop this work, it was carried out chromosomal and nucleolar measurements from cell stained by Feulgen method and silver nitrate, staining with specific fluorochromes to chromosomal regions rich in GC and AT nucleotides, physical mapping of 45S ribosomal DNA loci by fluorescent in situ hybridization, qualitative and quantitative analysis of post-translational histone modifications by western blot, and two-dimensional electrophoresis of root extract protein focusing on proteins involved in epigenetic mechanisms. The cytological analysis showed a great similarity in karyotypes of two accessions, differing only in size of the proximal segment of the sort arm of chromosome 1. In both accesses, it was observed a differential nucleolar expression in approximately 50% of the cells; however, the differential expression in CRT-2 showed considerably larger. Furthermore, the two accesses showed quantitative differences in the posttranslational histone modifications, and in a protein possibly involved in epigenetic mechanisms. Since epigenetic variations can be modified by environmental factors, it is suggested that differences in patterns of histone modifications and protein profiles found between the accesses, but also the most significant differential expression in CRT-2, are due to different selective pressures to which the original populations were submitted. Studies of the epigenetic mechanisms in nucleolar dominance allows a better understanding of the action of the remodeling of chromatin in controlling the dosage of rRNA genes, but also in the control of gene expression in general.

O nucléolo é uma organela nuclear responsável pela produção dos ribossomos, através das Regiões Organizadoras do Nucléolo (NORs). Espécies que possuem mais de um par de cromossomos contendo NORs terão, obrigatoriamente, pelo menos um par ativo, sendo as demais NORs funcionais de acordo com a demanda celular. O mecanismo de compensação de dose é visualizado e bem estabelecido em híbridos interespecíficos, conhecido como dominância nucleolar, com a inativação de NORs de um dos parentais por outras homeólogas ativas que as dominam. A arquitetura da cromatina nas NORs e o controle da sua expressão foram estudados com o objetivo de se entender os mecanismos envolvidos no fenômeno da dominância nucleolar em espécies diplóides que possuem múltiplas NORs. A espécie modelo utilizada neste estudo foi Crotalaria juncea (Leguminosae-Papilionoideae), caracterizada por conter 2n=2x=16, e NORs no braço curto do cromossomo 1, sendo este o principal organizador do nucléolo, e no braço longo do cromossomo 4 adjacente à heterocromatina centromérica, sendo este um sítio adicional (sítio menor) e de expressão facultativa, previamente determinada. Nas raízes de C. juncea sincronizadas, observou-se que a nucleologênese tem seu início durante o final da telófase, em que os 4 sítios de genes ribossomais podem ter atividade e formar até 4 nucléolos, os quais tendem a se fundir durante a interfase. A Hibridação in situ fluorescente (FISH) permitiu estudos da arquitetura da cromatina, com a visualização dos territórios cromossômicos, onde a cromatina não está organizada de forma aleatória dentro do núcleo, e consequentemente o rDNA 45S dentro do nucléolo. Observou-se também que todos os sítios de rDNA 45S possuem diferença no tamanho do arranjo repetitivo. Assim sendo, a hierarquia de dominância está de acordo com o tamanho de cada arranjo (sítio), e estes são ativados de acordo com a demanda celular. As análises das modificações nas histonas mostraram que a H3K9Met1 apresentou marcas fracas no nucléolo, enquanto no restante da cromatina nuclear sua marcação foi intensa. Já a H3K9Met2 apresentou marcação fortemente associada à cromatina presente no nucléolo, com alguns pequenos pontos heterocromáticos dispersos no núcleo. Pela observação entende-se que ambas metilações controlam diferentes tipos de heterocromatinas, ou seja, a H3K9Met2 controla principalmente heterocromatinas associadas aos genes ribossomais, e a H3K9Met controla heterocromatinas não associadas ao rDNA. O rDNA é hiperacetilado dentro do nucléolo para a H3K14. Não foi observada marcação nucleolar para H4K8ac, mas pôde ser observadas regiões hiperacetiladas em outras regiões da cromatina. A metilação do DNA esteve diretamente associada à diferentes níveis de organização da cromatina das NORs. As heterocromatinas adjacentes ao nucléolo apareceram fortemente metiladas, enquanto a cromatina distendida dentro do nucléolo apresentou marcação dispersa, com algumas regiões mais fortemente marcadas, onde a cromatina apresentava-se mais condensada e provavelmente não associados com a cromatina ativa. As fibras estendidas permitiram uma análise de alta resolução, onde foi possível observar que regiões não metiladas apareciam intercaladas entre grandes regiões fortemente metiladas, sugerindo que estas regiões hipometiladas estão, possivelmente, associadas com as alças de transcrição dentro do nucléolo. 12 Esses resultados contribuem para o entendimento sobre o controle genético e epigenético na arquitetura da cromatina ribossomal, bem como seu controle na expressão dos genes ribossomais no genoma das plantas. / The nucleolus is a nuclear organelle responsible for the ribosomes production, by Nucleolus Organizer Regions (NORs). Species presenting more than one chromosome pair with NORs should present, one pair expressing the genes, at least; while the other pairs expressing their genes accordingly to cellular demand. Dosage compensation mechanism is visualized and well established of interspecific hybrids as a well-described phenomena named nucleolar dominance, where a NOR from one parental could lead to inactivation of a NOR from the other parental which is dominated. The chromatin architecture and expression of the NORs were studied to address the mechanism involved in the nucleolar dominance of diploid species containing multiple sites of 45S rDNA. The model species used in the present study was the crop Crotalaria juncea (Leguminosae-Papilionoideae) characterized by 2n=2x=16 chromosomes, being the main NOR mapped into chromosome 1 short arm and presenting an additional site (minor site) in the chromosome 4 long arm adjacent to a centromeric heterochromatin and facultatively expressed. Synchronized meristematic root tip cells determined to nucleologenesis starts during the late-telophase, often expressing every ribosomal gene sites, when up to four nucleoli could be observed and these become merged during interphases. FISH allowed nucleolar chromatin architecture be accessed revealing distinct chromosomal domains (territories), suggesting a non-random distribution of the 45S rDNA, even between homologous chromosomes, into the nucleolus. The 45S rDNA sites from both chromosome pairs 1 and 4 of C. juncea showed differences in their array sizes. The differences in the 45S rDNA array sizes and the order of loci expression suggest a hierarchy of dominance, a feature of nucleolar dominance; being the small RONs activated only on demand. Immunodetection of histone modifications showed different patterns to methylation distribution across the chromatin as a whole; where H3K9Met1 was found mainly distributed along the nuclear chromatin without an evident signal into nucleolus, while H3K9Met2 was detected as conspicuous dots in the nuclear chromatin and highly accumulated into the nucleolus. The results indicate different control on heterochromatin establishment and maintenance, being the modifications specific to certain chromosomal regions. Indeed, H3K9Met is a key component in the nucleolus chromatin architecture and expression. The chromatin inside the nucleolus showed a high accumulation of H3K14ac, with a weak fluorescent signal along the nucleus; on the other hand H4K8ac showed a strong signal homogenously distributed across the nuclear chromatin, but without evident signals inside the nucleolus. DNA methylation was directly associated with different levels of chromatin organization of the NORs. The heterochromatic regions associated to RON are highly methylated, while the chromatin inside the nucleolus showed weaker signals, with some bright spots probably in condensed regions and related to chromatin inactivity. Extended DNA fiber allowed a higher resolution mapping that revealed long methylated regions intermingled by nomethylated ones, being the last probably associated to transcriptional loops of rRNA genes into the nucleolus. The results presented herein contributes to a better understand about the nucleolar chromatin architecture and the genetic and epigenetic control of the ribosomal genes expression on plant genomes.