scholarly journals Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

Archaea ◽  
2005 ◽  
Vol 1 (6) ◽  
pp. 391-397 ◽  
Author(s):  
Atsuo Sugano ◽  
Hidetaka Tsuchimoto ◽  
Tun Cho Cho ◽  
Makoto Kimura ◽  
Susumu Asakawa
Keyword(s):  
Rice Straw ◽  
Rice Field ◽  
Previous History ◽  
Methanogenic Archaea ◽  
Leaf Sheath ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Crop Season ◽  
Rdna Sequencing ◽  
Archaeal Communities

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related toMethanomicrobialesand Rice cluster I.Methanomicrobiales, Rice cluster I andMethanosarcinaleswere major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related toMethanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals

2016 ◽  
Vol 74 (4) ◽  
pp. 824-835 ◽  
Author(s):  
Janet Jiménez ◽  
Susanne Theuerl ◽  
Ingo Bergmann ◽  
Michael Klocke ◽  
Gilda Guerra ◽  
...  
Keyword(s):  
Rice Straw ◽  
Community Dynamics ◽  
Swine Manure ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutritional Conditions ◽  
Continuously Stirred Tank Reactor ◽  
Positive Effect ◽  
Methanosarcina Species

The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

scholarly journals Identification and Quantification of Methanogenic Archaea in Adult Chicken Ceca

2006 ◽  
Vol 73 (1) ◽  
pp. 353-356 ◽  
Author(s):  
Suwat Saengkerdsub ◽  
Robin C. Anderson ◽  
Heather H. Wilkinson ◽  
Woo-Kyun Kim ◽  
David J. Nisbet ◽  
...  
Keyword(s):  
16S Rrna ◽  
Copy Number ◽  
Methanogenic Archaea ◽  
Molecular Methods ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Adult Chicken ◽  
Wet Weight ◽  
Identification And Quantification

ABSTRACT By using molecular methods for the identification and quantification of methanogenic archaea in adult chicken ceca, 16S rRNA genes of 11 different phylotypes, 10 of which were 99% similar to Methanobrevibacter woesei, were found. Methanogen populations, as assessed by cultivation, and the 16S rRNA copy number were between 6.38 and 8.23 cells/g (wet weight) and 5.50 and 7.19 log10/g (wet weight), respectively.

scholarly journals Effect of Temperature on Carbon and Electron Flow and on the Archaeal Community in Methanogenic Rice Field Soil

2000 ◽  
Vol 66 (11) ◽  
pp. 4790-4797 ◽  
Author(s):  
Axel Fey ◽  
Ralf Conrad
Keyword(s):  
Steady State ◽  
Rice Field ◽  
Electron Flow ◽  
Rflp Analysis ◽  
Archaeal Community ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Field Soil ◽  
Rice Field Soil ◽  
Different Temperatures

ABSTRACT Temperature is an important factor controlling CH4production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37°C or in a temperature gradient block covering the same temperature range at intervals of 1°C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH4 production rates increased with temperature, with an apparent activation energy of 61 kJ mol−1. Steady-state partial pressures of the methanogenic precursor H2 also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H2 plus CO2-dependent methanogenesis was kept at −20 to −25 kJ mol of CH4 −1 over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 μM. Simultaneously, the relative contribution of H2 as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to 14CH4, so that the carbon and electron flow to CH4 was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae,Methanomicrobiaceae, Methanosaetaceae,Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I andMethanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

scholarly journals The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

2023 ◽  
Vol 83 ◽  
Author(s):  
A. Belmok ◽  
T. Rodrigues-Oliveira ◽  
F.A.C. Lopes ◽  
R.H. Krüger ◽  
C.M. Kyaw
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Rrna Gene ◽  
Natural Habitats ◽  
16S Rdna Pcr ◽  
Archaeal Communities

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

scholarly journals Methanogenic Community Dynamics during Anaerobic Utilization of Agricultural Wastes

Acta Naturae ◽  
2012 ◽  
Vol 4 (4) ◽  
pp. 91-97 ◽  
Author(s):  
A. M. Ziganshin ◽  
E. E. Ziganshina ◽  
S. Kleinsteuber ◽  
J. Pröter ◽  
O. N. Ilinskaya
Keyword(s):  
16S Rrna ◽  
Anaerobic Degradation ◽  
Community Dynamics ◽  
Biological Diversity ◽  
Biogas Production ◽  
Rflp Analysis ◽  
Methanogenic Archaea ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene

This work is devoted to the investigation of the methanogenic archaea involved in anaerobic digestion of cattle manure and maize straw on the basis of terminal restriction fragment length polymorphism (TRFLP) analysis of archaeal 16S rRNA genes. The biological diversity and dynamics of methanogenic communities leading to anaerobic degradation of agricultural organic wastes with biogas production were evaluated in laboratory-scale digesters. T-RFLP analysis, along with the establishment of archaeal 16S rRNA gene clone libraries, showed that the methanogenic consortium consisted mainly of members of the genera Methanosarcina and Methanoculleus, with a predominance of Methanosarcina spp. throughout the experiment.

scholarly journals Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

2020 ◽  
Vol 42 ◽  
pp. e49877
Author(s):  
Keyla Vitoria Marques Xavier ◽  
Eden Silva e Souza ◽  
Erick de Aquino Santos ◽  
Michely Correia Diniz
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Descriptive Analysis ◽  
Methanogenic Archaea ◽  
Ribosomal Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Terrestrial Environments ◽  
Methyl Coenzyme M Reductase ◽  
Potential Use

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.

scholarly journals “Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

2012 ◽  
Vol 78 (23) ◽  
pp. 8245-8253 ◽  
Author(s):  
Kristina Paul ◽  
James O. Nonoh ◽  
Lena Mikulski ◽  
Andreas Brune
Keyword(s):  
16S Rrna ◽  
Methanogenic Archaea ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Published Data ◽  
Gene Trees ◽  
Specific Sequence ◽  
Content Type ◽  
Marine Habitats ◽  
Seventh Order

ABSTRACTTheEuryarchaeotacomprise both methanogenic and nonmethanogenic orders and many lineages of uncultivated archaea with unknown properties. One of these deep-branching lineages, distantly related to theThermoplasmatales, has been discovered in various environments, including marine habitats, soil, and also the intestinal tracts of termites and mammals. By comparative phylogenetic analysis, we connected this lineage of 16S rRNA genes to a large clade of unknownmcrAgene sequences, a functional marker for methanogenesis, obtained from the same habitats. The identical topologies of 16S rRNA andmcrAgene trees and the perfect congruence of all branches, including several novel groups that we obtained from the guts of termites and cockroaches, strongly suggested that they stem from the same microorganisms. This was further corroborated by two highly enriched cultures of closely related methanogens from the guts of a higher termite (Cubitermes ugandensis) and a millipede (Anadenobolussp.), which represented one of the arthropod-specific clusters in the respective trees. Numerous other pairs of habitat-specific sequence clusters were obtained from the guts of other termites and cockroaches but were also found in previously published data sets from the intestinal tracts of mammals (e.g., rumen cluster C) and other environments. Together with the recently describedMethanomassiliicoccus luminyensisisolated from human feces, which falls into rice cluster III, the results of our study strongly support the idea that the entire clade of “unculturedThermoplasmatales” in fact represents the seventh order of methanogenic archaea, for which the provisional name “Methanoplasmatales” is proposed.

scholarly journals Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

2001 ◽  
Vol 67 (3) ◽  
pp. 1318-1327 ◽  
Author(s):  
Sabine Weber ◽  
Stephan Stubner ◽  
Ralf Conrad
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Rice Straw ◽  
Paddy Soil ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Blot Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Dot Blot ◽  
Cell Counts

ABSTRACT Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), andAcidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to theCytophaga-Flavobacterium cluster of theCytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the α, β, and γ Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.

scholarly journals Pyrosequencing ofmcrAand Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

2014 ◽  
Vol 81 (2) ◽  
pp. 604-613 ◽  
Author(s):  
David Wilkins ◽  
Xiao-Ying Lu ◽  
Zhiyong Shen ◽  
Jiapeng Chen ◽  
Patrick K. H. Lee
Keyword(s):  
Anaerobic Digestion ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Methanogenic Archaea ◽  
16S Rrna Gene Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTMethanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes.Methanobacteriales,Methanomicrobiales, andMethanosarcinaleswere detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of themcrAgenes suggested that these digesters were dominated by acetoclastic methanogens, particularlyMethanosarcinales, while the other digesters were dominated by hydrogenotrophicMethanomicrobiales. The proposed euryarchaeotal orderMethanomassiliicoccalesand the uncultured WSA2 group were detected with the 16S rRNA gene, and potentialmcrAgenes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using themcrAgene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance ofmcrAtranscripts in digesters treating sludge and wastewater samples, supporting themcrAgene as a biomarker for methane yield.

scholarly journals Earthworms and rice straw enhanced soil bacterial diversity and promoted the degradation of phenanthrene

2020 ◽  
Vol 32 (1) ◽  
Author(s):  
Ali Mohamed Elyamine ◽  
Chengxiao Hu
Keyword(s):  
16S Rrna ◽  
Rice Straw ◽  
Diversity Index ◽  
Shannon Diversity Index ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenanthrene Degradation ◽  
Shannon Diversity ◽  
Polycyclic Aromatic ◽  
Degradation In Soil

Abstract Background Since the industrial revolution, the contamination of agricultural soils by polycyclic aromatic hydrocarbons (PAHs) has increasingly become of serious global environmental concern and poses a huge threat to human beings and natural ecosystems. Microbial degradation is a proved technology mostly used to depollute polycyclic aromatic hydrocarbon (PAH) in the environment. However, very limited information is available regarding the interaction of earthworms with rice straw on the soil microbial community and the degradation of phenanthrene. This study was performed to enlighten the rice straw and earthworms’ interaction on soil bacterial abundance and structure and phenanthrene removal. Results Result about functional gene information revealed that both rice straw and earthworm enhanced phenanthrene degradation. Subsequently, both Shannon diversity index (r2 = − 0.8807, p < 0.001) and bacterial 16S rRNA genes (r2 = − 0.7795, p < 0.001) negatively correlated with the remaining phenanthrene concentration in soil. The application of both rice straw and earthworms in soil had the lowest ratio of soil remaining phenanthrene concentration (0.16 ± 0.02), the highest Shannon diversity index (6.45 ± 0.2) and the highest bacterial 16S rRNA genes. This implied that both earthworms and rice straw might improve the phenanthrene metabolism by increasing soil bacteria diversity. The abundance of genera Pseudomonas, Luteimonas, Rhodanobacter, Sphingomonas, Gemmatimonas, Flavobacterium, and Leifsonia was significantly increased in the presence of both earthworms and rice straw and was found to negatively correlate with the remaining phenanthrene concentration in soil. Conclusion Based on these results, this study offers clear and strong evidences that the positive interaction between earthworms and rice straw could promote phenanthrene degradation in soil. These finding will improve our understanding on the importance of the natural resources forsaken and how they can interact with the soil macro- and microorganisms to change soil structure and enhance PAH degradation in soil.

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