scholarly journals Anaerobic Digestion of Renewable Biomass: Thermophilic Temperature Governs Methanogen Population Dynamics

2010 ◽  
Vol 76 (6) ◽  
pp. 1842-1850 ◽  
Author(s):  
Niclas Krakat ◽  
A. Westphal ◽  
S. Schmidt ◽  
P. Scherer
Keyword(s):  
Anaerobic Digestion ◽  
Fluorescence Microscopy ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Temperature Dependent ◽  
Renewable Biomass ◽  
Operational Taxonomic Units ◽  
Methanogen Population ◽  
Gene Restriction

ABSTRACT Beet silage and beet juice were digested continuously as representative energy crops in a thermophilic biogas fermentor for more than 7 years. Fluorescence microscopy of 15 samples covering a period of 650 days revealed that a decrease in temperature from 60°C to 55°C converted a morphologically uniform archaeal population (rods) into a population of methanogens exhibiting different cellular morphologies (rods and coccoid cells). A subsequent temperature increase back to 60°C reestablished the uniform morphology of methanogens observed in the previous 60°C period. In order to verify these observations, representative samples were investigated by amplified rRNA gene restriction analysis (ARDRA) and fluorescence in situ hybridization (FISH). Both methods confirmed the temperature-dependent population shift observed by fluorescence microscopy. Moreover, all samples investigated demonstrated that hydrogenotrophic Methanobacteriales dominated in the fermentor, as 29 of 34 identified operational taxonomic units (OTUs) were assigned to this order. This apparent discrimination of acetoclastic methanogens contradicts common models for anaerobic digestion processes, such as anaerobic digestion model 1 (ADM1), which describes the acetotrophic Euryarchaeota as predominant organisms.

scholarly journals Mesophilic Fermentation of Renewable Biomass: Does Hydraulic Retention Time Regulate Methanogen Diversity?

2010 ◽  
Vol 76 (18) ◽  
pp. 6322-6326 ◽  
Author(s):  
Niclas Krakat ◽  
Stefan Schmidt ◽  
Paul Scherer
Keyword(s):  
Ribosomal Rna ◽  
Retention Time ◽  
Hydraulic Retention Time ◽  
Restriction Analysis ◽  
Term Study ◽  
Renewable Biomass ◽  
Long Term Study ◽  
Gene Restriction

ABSTRACT The present long-term study (about 1,100 days) monitored the diversity of methanogens during the mesophilic, anaerobic digestion of beet silage. Six fermentor samples were analyzed by ribosomal RNA gene restriction analysis, fluorescence in situ hybridization, and fluorescence microscopy. Hydrogenotrophic methanogens dominated within the population in all samples analyzed. Multidimensional scaling revealed that a rapid decrease in hydraulic retention time resulted in increased species richness, which in turn led to slightly higher CH4 yields.

scholarly journals Bacterial Symbionts of the Brown Planthopper, Nilaparvata lugens (Homoptera: Delphacidae)

2010 ◽  
Vol 76 (6) ◽  
pp. 1740-1745 ◽  
Author(s):  
Ming Tang ◽  
Lu Lv ◽  
Shengli Jing ◽  
Lili Zhu ◽  
Guangcun He
Keyword(s):  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Rrna Gene ◽  
Rice Varieties ◽  
Ovipositor Sheath ◽  
Operational Taxonomic Units ◽  
Metaseiulus Occidentalis ◽  
High Virulence ◽  
Gene Libraries

ABSTRACT The brown planthopper (Nilaparvata lugens Stål), the most destructive pest of rice, has been identified, including biotypes with high virulence towards previously resistant rice varieties. There have also been many reports of a yeast-like symbiont of N. lugens, but little is known about the bacterial microbes. In this study, we examined the bacterial microbes in N. lugens and identified a total of 18 operational taxonomic units (OTUs) representing four phyla (Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes) by sequencing and analyzing 16S rRNA gene libraries obtained from three populations of N. lugens, which were maintained on the rice varieties TN1, Mudgo, and ASD7. Several of the OTUs were similar to previously reported secondary symbionts of other insects, including an endosymbiont of the psyllid Glycapsis brimblecombei, an Asaia sp. found in the mosquito Anopheles stephensi, and Wolbachia, found in the mite Metaseiulus occidentalis. However, the species and numbers of the detected OTUs differed substantially among the N. lugens populations. Further, in situ hybridization analysis using digoxigenin-labeled probes indicated that OTU 1 was located in hypogastrium tissues near the ovipositor and ovary in biotype 1 insects, while OTU 2 was located in the front of the ovipositor sheath in biotype 2 insects. In addition, masses of bacterium-like organisms were observed in the tubes of salivary sheaths in rice plant tissues that the insects had fed upon. The results provide indications of the diversity of the bacterial microbes harbored by the brown planthopper and of possible associations between specific bacterial microbes and biotypes of N. lugens.

scholarly journals Diversity of Lactic Acid Bacteria Associated with Fish and the Fish Farm Environment, Established by Amplified rRNA Gene Restriction Analysis

2007 ◽  
Vol 73 (9) ◽  
pp. 2947-2955 ◽  
Author(s):  
Christian Michel ◽  
Claire Pelletier ◽  
Mekki Boussaha ◽  
Diane-Gaëlle Douet ◽  
Armand Lautraite ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Opportunistic Infections ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Fish Food ◽  
Group A ◽  
Gene Restriction

ABSTRACT Lactic acid bacteria have become a major source of concern for aquaculture in recent decades. In addition to true pathogenic species of worldwide significance, such as Streptococcus iniae and Lactococcus garvieae, several species have been reported to produce occasional fish mortalities in limited geographic areas, and many unidentifiable or ill-defined isolates are regularly isolated from fish or fish products. To clarify the nature and prevalence of different fish-associated bacteria belonging to the lactic acid bacterium group, a collection of 57 isolates of different origins was studied and compared with a set of 22 type strains, using amplified rRNA gene restriction analysis (ARDRA). Twelve distinct clusters were delineated on the basis of ARDRA profiles and were confirmed by sequencing of sodA and 16S rRNA genes. These clusters included the following: Lactococcus raffinolactis, L. garvieae, Lactococcus l., S. iniae, S. dysgalactiae, S. parauberis, S. agalactiae, Carnobacterium spp., the Enterococcus “faecium” group, a heterogeneous Enterococcus-like cluster comprising indiscernible representatives of Vagococcus fluvialis or the recently recognized V. carniphilus, V. salmoninarum, and Aerococcus spp. Interestingly, the L. lactis and L. raffinolactis clusters appeared to include many commensals of fish, so opportunistic infections caused by these species cannot be disregarded. The significance for fish populations and fish food processing of three or four genetic clusters of uncertain or complex definition, namely, Aerococcus and Enterococcus clusters, should be established more accurately.

scholarly journals Proof that Burkholderia Strains Form Effective Symbioses with Legumes: a Study of Novel Mimosa-Nodulating Strains from South America

2005 ◽  
Vol 71 (11) ◽  
pp. 7461-7471 ◽  
Author(s):  
Wen-Ming Chen ◽  
Sergio M. de Faria ◽  
Rosângela Straliotto ◽  
Rosa M. Pitard ◽  
Jean L. Simões-Araùjo ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Consensus Sequences ◽  
Mimosa Pigra ◽  
Green Fluorescent ◽  
Gene Restriction ◽  
Single Cluster ◽  
The 16S Rrna Gene

ABSTRACT Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.

scholarly journals Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

2004 ◽  
Vol 70 (2) ◽  
pp. 804-813 ◽  
Author(s):  
Christian Winter ◽  
Arjan Smit ◽  
Gerhard J. Herndl ◽  
Markus G. Weinbauer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Tropical Atlantic ◽  
Viral Lysis ◽  
Batch Cultures ◽  
Operational Taxonomic Units ◽  
The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

scholarly journals Ecology of Uncultivated Oscillospira Species in the Rumen of Cattle, Sheep, and Reindeer as Assessed by Microscopy and Molecular Approaches

2003 ◽  
Vol 69 (11) ◽  
pp. 6808-6815 ◽  
Author(s):  
Roderick I. Mackie ◽  
Rustam I. Aminov ◽  
Wenping Hu ◽  
Athol V. Klieve ◽  
Diane Ouwerkerk ◽  
...  
Keyword(s):  
Rumen Bacterium ◽  
Rrna Gene ◽  
Hybridization Probe ◽  
Morphological Form ◽  
Operational Taxonomic Units ◽  
Specific Pcr ◽  
Molecular Approaches ◽  
Definition Of ◽  
Cattle And Sheep

ABSTRACT The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.

Evaluation of 16S rRNA Gene Restriction Analysis for the Identification of Cultured Organisms of Clinically ImportantClostridiumSpecies

Anaerobe ◽  
1996 ◽  
Vol 2 (4) ◽  
pp. 249-256 ◽  
Author(s):  
Mario Vaneechoutte ◽  
Charles P. Cartwright ◽  
Esther C. Williams ◽  
Birgit Jäger ◽  
Hans-Volker Tichy ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Gene Restriction

scholarly journals Differentiation of lactococci by rRNA gene restriction analysis

1991 ◽  
Vol 84 (3) ◽  
pp. 307-312 ◽  
Author(s):  
Gerwald Köhler ◽  
Wolfgang Ludwig ◽  
Karl Heinz Schleifer
Keyword(s):  
Restriction Analysis ◽  
Rrna Gene ◽  
Gene Restriction

scholarly journals Analysis of Vaginal Lactobacilli from Healthy and Infected Brazilian Women

2008 ◽  
Vol 74 (14) ◽  
pp. 4539-4542 ◽  
Author(s):  
Rafael C. R. Martinez ◽  
Sílvio A. Franceschini ◽  
Maristela C. Patta ◽  
Silvana M. Quintana ◽  
Álvaro C. Nunes ◽  
...  
Keyword(s):  
Bacterial Vaginosis ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Restriction Analysis ◽  
Rrna Gene ◽  
Vaginal Lactobacilli ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Gene Restriction ◽  
Culture Dependent

ABSTRACT Culture-dependent PCR-amplified rRNA gene restriction analysis and culture-independent (PCR-denaturing gradient gel electrophoresis) methodologies were used to examine vaginal lactobacilli from Brazilian women who were healthy or had been diagnosed with vulvovaginal candidiasis (VVC) or bacterial vaginosis. Only Lactobacillus crispatus was detected accordingly by both methods, and H2O2-producing lactobacilli were not associated with protection against VVC.

scholarly journals Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm

2017 ◽  
Vol 27 (5) ◽  
pp. 306-317 ◽  
Author(s):  
Liliana Pampillón-González ◽  
Nadia L. Ortiz-Cornejo ◽  
Marco Luna-Guido ◽  
Luc Dendooven ◽  
Yendi E. Navarro-Noya
Keyword(s):  
Community Structure ◽  
Anaerobic Digestion ◽  
Biogas Production ◽  
Waste Product ◽  
Archaeal Community ◽  
Pig Manure ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Sampling Locations ◽  
Pig Farm

Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e<i>.</i>, methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, <i>Methanosarcina</i>, <i>Methanolobus</i>, <i>Methanosaeta</i>, and <i>Methanospirillum</i>) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria <i>Candidatus</i> Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic <i>Methanosaeta</i> and the hydrogenothrophic <i>Methanoculleus</i> and <i>Methanospirillum</i>. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.

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