Effect of the addition of rice straw on microbial community in a sewage sludge digester

2014 ◽  
Vol 70 (5) ◽  
pp. 819-827 ◽  
Author(s):  
E. Nakakihara ◽  
R. Ikemoto-Yamamoto ◽  
R. Honda ◽  
S. Ohtsuki ◽  
M. Takano ◽  
...  
Keyword(s):  
Sewage Sludge ◽  
Rice Straw ◽  
Dna Sequences ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Shannon Index ◽  
Methanosarcina Barkeri ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Digested Sludge ◽  
Capillary Suction

Rice straw was added to a sewage sludge digester and its effects on methane production, dewatering characteristics, and microbial communities in the digested sludge were examined by a continuous digestion experiment under mesophilic conditions (35 °C). Stable gas generation was monitored in all digestion experiments. Methane yield from raw sludge, chopped rice straw and softened rice straw were estimated to be 0.27, 0.18 and 0.26 NL/g total solids load, respectively. The capillary suction time of digested sludge was decreased by the addition of rice straw. Archaeal and bacterial communities in the sludge were elucidated by PCR-DGGE (polymerase chain reaction – denaturing gradient gel electrophoresis) targeting 16S rRNA genes. The Shannon index of DGGE profiles indicated that bacterial diversity increased with the addition of softened rice straw. DNA sequences of significant bands of the digested sludge were most closely related to Methanosaeta concilii (97.4% identity) and Methanoculleus bourgensis (100% identity). Meanwhile, those in the co-digested sludge with rice straw were most closely related to Methanosarcina barkeri (98.4% identity) and Methanoculleus bourgensis (99.3% identity). Although both Methanosaeta spp. and Methanosarcina spp. metabolize acetate to methane, Methanosarcina spp. have a competitive advantage at acetate concentrations of >70 mg/L. Results suggested that the quantity of acetate produced during rice straw degradation may change the archaeal community.

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 Variability of the Sheep Lung Microbiota

2016 ◽  
Vol 82 (11) ◽  
pp. 3225-3238 ◽  
Author(s):  
Laura Glendinning ◽  
Steven Wright ◽  
Jolinda Pollock ◽  
Peter Tennant ◽  
David Collie ◽  
...  
Keyword(s):  
Spatial Variability ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Large Animal ◽  
Local Factors ◽  
Adult Sheep ◽  
Sequencing Technologies ◽  
Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

scholarly journals Phylogenetic and Morphological Diversity of Cyanobacteria in Soil Desert Crusts from the Colorado Plateau

2001 ◽  
Vol 67 (4) ◽  
pp. 1902-1910 ◽  
Author(s):  
Ferran Garcia-Pichel ◽  
Alejandro López-Cortés ◽  
Ulrich Nübel
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Colorado Plateau ◽  
Morphological Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Filamentous Cyanobacteria ◽  
Phylogenetic Cluster ◽  
Field Samples ◽  
Gradient Gel Electrophoresis ◽  
Well Differentiated

ABSTRACT We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of Microcoleus vaginatus Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named “Xeronema,” grouped a series of thin filamentousPhormidium-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanicalPhormidium and Schizothrix spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.

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.

Perchlorate removal using two component biodegradable carriers in particle-fixed biofilm reactor

2014 ◽  
Vol 49 (3) ◽  
pp. 234-244
Author(s):  
Fang He ◽  
Fusheng Li ◽  
Haihong Zhou ◽  
Lingling Niu ◽  
Liguo Wang
Keyword(s):  
Carbon Source ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Polymer Particle ◽  
Biofilm Reactor ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Biofilm Reactors ◽  
Gradient Gel Electrophoresis ◽  
Perchlorate Removal ◽  
Fixed Biofilm

In this research, biocompounds designed out of two polymers having different degradability was investigated for use as the sole carbon source and biofilm carrier to remove perchlorate in particle-fixed biofilm reactors. Both laboratory batch and column experiments were conducted with perchlorate contaminated groundwater. Batch experiments demonstrated clearly that ClO4– was removed from the aqueous phase readily and the degradation rate constants (k) changed in the range of 0.23–0.37 mg/L h as ClO4– concentration increased from 2 to 8 mg/L. Simultaneous perchlorate and nitrate degradation occurred in the polymer bioreactor. Effluent concentrations of perchlorate varied positively with temperature and fitted the Arrhenius equation expression as k=k20•100.0316(t–20) over the range of 13–30 °C. No perchlorate was detected in the effluent of polymer columns after 20 days’ startup. Complete perchlorate removal was observed at a hydraulic loading rate doubled to 1.8 mL/min. Images prove the concept of the pore and filament structure within the biocompounds, which provide both a heterotrophic biofilm and carbon source. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes indicated that formerly reported perchlorate-reducing bacteria were present in the polymer particle-fixed biofilm reactors.

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 Bioaugmentation of Activated Sludge by an Indigenous 3-Chloroaniline-Degrading Comamonas testosteroni Strain, I2gfp

2000 ◽  
Vol 66 (7) ◽  
pp. 2906-2913 ◽  
Author(s):  
Nico Boon ◽  
Johan Goris ◽  
Paul De Vos ◽  
Willy Verstraete ◽  
Eva M. Top
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Activated Sludge ◽  
Microbial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dynamic Change ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Adaptation Period ◽  
Comamonas Testosteroni

ABSTRACT A strain identified as Comamonas testosteroni I2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-CA). During the mineralization, a yellow intermediate accumulated temporarily, due to the distalmeta-cleavage of chlorocatechol. This strain was tested for its ability to clean wastewater containing 3-CA upon inoculation into activated sludge. To monitor its survival, the strain was chromosomally marked with the gfp gene and designated I2gfp. After inoculation into a lab-scale semicontinuous activated-sludge (SCAS) system, the inoculated strain maintained itself in the sludge for at least 45 days and was present in the sludge flocs. After an initial adaptation period of 6 days, complete degradation of 3-CA was obtained during 2 weeks, while no degradation at all occurred in the noninoculated control reactor. Upon further operation of the SCAS system, only 50% 3-CA removal was observed. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes revealed a dynamic change in the microbial community structure of the activated sludge. The DGGE patterns of the noninoculated and the inoculated reactors evolved after 7 days to different clusters, which suggests an effect of strain inoculation on the microbial community structure. The results indicate that bioaugmentation, even with a strain originating from that ecosystem and able to effectively grow on a selective substrate, is not permanent and will probably require regular resupplementation.

scholarly journals Phylogenetic Composition of Arctic Ocean Archaeal Assemblages and Comparison with Antarctic Assemblages

2004 ◽  
Vol 70 (2) ◽  
pp. 781-789 ◽  
Author(s):  
Nasreen Bano ◽  
Shomari Ruffin ◽  
Briana Ransom ◽  
James T. Hollibaugh
Keyword(s):  
Arctic Ocean ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
The Arctic ◽  
Rrna Genes ◽  
Specific Primers ◽  
Group I ◽  
The Arctic Ocean ◽  
Gradient Gel Electrophoresis ◽  
Phylogenetic Composition

ABSTRACT Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota.

scholarly journals Effects of Lactococcus lactis on Composition of Intestinal Microbiota: Role of Nisin

2006 ◽  
Vol 72 (1) ◽  
pp. 239-244 ◽  
Author(s):  
Nete Bernbom ◽  
Tine Rask Licht ◽  
Carl-Henrik Brogren ◽  
Birthe Jelle ◽  
Anette H. Johansen ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Intestinal Microbiota ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Enzyme Linked Immunosorbent Assay ◽  
Gradient Gel Electrophoresis ◽  
Intact Molecule ◽  
Human Flora

ABSTRACT This study examined the ability of (i) pure nisin, (ii) nisin-producing Lactococcus lactis strain CHCC5826, and (iii) the non-nisin-producing L. lactis strain CHCH2862 to affect the composition of the intestinal microbiota of human flora-associated rats. The presence of both the nisin-producing and the non-nisin-producing L. lactis strains significantly increased the number of Bifidobacterium cells in fecal samples during the first 8 days but decreased the number of enterococci/streptococci in duodenum, ileum, cecum, and colon samples as detected by selective cultivation. No significant changes in the rat fecal microbiota were observed after dosage with nisin. Pearson cluster analysis of denaturing gradient gel electrophoresis profiles of the 16S rRNA genes present in the fecal microbial population revealed that the microbiota of animals dosed with either of the two L. lactis strains were different from that of control animals dosed with saline. However, profiles of the microbiota from animals dosed with nisin did not differ from the controls. The concentrations of nisin estimated by competitive enzyme-linked immunosorbent assay (ELISA) were approximately 10-fold higher in the small intestine and 200-fold higher in feces than the corresponding concentrations estimated by a biological assay. This indicates that nisin was degraded or inactivated in the gastrointestinal tract, since fragments of this bacteriocin are detected by ELISA while an intact molecule is needed to retain biological activity.

scholarly journals Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

2011 ◽  
Vol 77 (7) ◽  
pp. 2264-2274 ◽  
Author(s):  
Ji Young Jung ◽  
Se Hee Lee ◽  
Jeong Myeong Kim ◽  
Moon Su Park ◽  
Jin-Woo Bae ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Leuconostoc Mesenteroides ◽  
16S Rrna Genes ◽  
Read Length ◽  
Rrna Genes ◽  
Genetic Profile ◽  
Average Read Length ◽  
Metabolic Potential ◽  
Fermentation Products

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

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