共查询到20条相似文献,搜索用时 31 毫秒
1.
Federici E Pepi M Esposito A Scargetta S Fidati L Gasperini S Cenci G Altieri R 《Bioresource technology》2011,102(23):10965-10972
In this study, physico-chemical modifications and community dynamics and functional role of the resident microbiota during composting of humid husk from a two-phase extraction system (TPOMW) were investigated. High mineralization and humification of carbon, low loss of nitrogen and complete degradation of polyphenols led to the waste biotransformation into a high-quality compost. Viable cell counts and denaturing gradient gel electrophoresis (DGGE) profiling of the 16S rRNA genes showed that the thermophilic phase was characterized by the strongest variations of cell number, the highest biodiversity and the most variable community profiles. The isolation of tannin-degrading bacteria (e.g. Lysinibacillus fusiformis, Kocuria palustris, Tetrathiobacter kashmirensis and Rhodococcus rhodochrous) suggested a role of this enzymatic activity during the process. Taken together, the results indicated that the composting process, particularly the thermophilic phase, was characterized by a rapid succession of specialized bacterial populations with key roles in the organic matter biotransformation. 相似文献
2.
The contents of fed-batch composting (FBC) reactors often aggregate after prolonged operation. This process leads to irreversible
breakdown of the decomposition reaction and possible alteration of the bacterial communities. We compared the structures of
bacterial communities in reactors under aggregate and optimal conditions. The results of 16S rRNA gene clone analysis showed
that populations of the family Bacillaceae (such as Bacillus spp., Cerasibacillus spp., Gracilibacillus spp.), which dominate (98%) under optimal condition, were significantly decreased under aggregate condition. In contrast,
populations of the family Staphylococcaceae considerably increased after aggregation and accounted for 53% of the total. Phylogenetic analysis also showed that anaerobes
or facultative anaerobes related to Tetragenococcus halophilus, Atopostipes suicloacalis, Jeotgalicoccus pinnipedialis, and Staphylococcus spp. were dominant in the aggregates. These results suggested that aerobic Gram-positive bacteria mainly contributed to organic
degradation and that aggregation created some anaerobic environment, which promoted the growth of bacterial communities usually
not found in well-functioning FBC reactors. 相似文献
3.
The microbial diversity of Japanese- and Chinese-fermented soybean pastes was investigated using nested PCR–denaturing gradient
gel electrophoresis (DGGE). Five Japanese-fermented soybean paste samples and three Chinese-fermented soybean paste samples
were analyzed for bacteria and fungi. Extracted DNA was used as a template for PCR to amplify 16S rRNA and 18S rRNA genes.
The nearly complete 16S rRNA and 18S rRNA genes were amplified using universal primers, and the resulting products were subsequently
used as a template in a nested PCR to obtain suitable fragments for DGGE. Tetragenococcus halophilus and Staphylococcus gallinarum were found to dominate the bacterial microbiota in Japanese samples, whereas Bacillus sp. was detected as the predominant species in Chinese samples. DGGE analysis of fungi in soybean pastes determined the presence
of Aspergillus oryzae and Zygosaccharomyces rouxii in most of the Chinese and Japanese samples. Some differences were observed in the bacterial diversity of Japanese- and Chinese-fermented
soybean pastes. 相似文献
4.
J. A. Narváez-Zapata R. A. Rojas-Herrera I. C. Rodríguez-Luna C. P. Larralde-Corona 《Current microbiology》2010,61(5):444-450
Mezcal is an alcoholic beverage obtained from the distillation of fermented juices of cooked Agave spp. plant stalks (agave must), and each region in Mexico with denomination of origin uses defined Agave species to prepare mezcal with unique organoleptic characteristics. During fermentation to produce mezcal in the state of
Tamaulipas, not only alcohol-producing yeasts are involved, but also a lactic acid bacterial community that has not been characterized
yet. In order to address this lack of knowledge on this traditional Mexican beverage, we performed a DGGE-16S rRNA analysis
of the lactic acid bacterial diversity and metabolite accumulation during the fermentation of a typical agave must that is
rustically produced in San Carlos County (Tamaulipas, Mexico). The analysis of metabolite production indicated a short but
important malolactic fermentation stage not previously described for mezcal. The denaturing gradient gel electrophoresis (DGGE)
analysis of the 16S rRNA genes showed a distinctive lactic acid bacterial community composed mainly of Pediococcus parvulus, Lactobacillus brevis, Lactobacillus composti, Lactobacillus parabuchneri, and Lactobacillus plantarum. Some atypical genera such as Weissella and Bacillus were also found in the residual must. Our results suggest that the lactic acid bacteria could strongly be implicated in the
organoleptic attributes of this traditional Mexican distilled beverage. 相似文献
5.
Denaturing gradient gel electrophoresis (DGGE) analysis
of bacterial community composition in deep-sea sediments of the South China Sea 总被引:5,自引:0,他引:5
Xintian Lai Xiaofan Zeng Shu Fang Yali Huang Lixiang Cao Shining Zhou 《World journal of microbiology & biotechnology》2006,22(12):1337-1345
The South China Sea, which is one of the largest marginal seas in the world, is predicted to have suitable accumulation conditions and exporting prospects for natural gas hydrate. The aim of this study was to explore the bacterial community composition of deep-sea sediments from such an ecosystem. DNA was extracted by five different methods and used as templates for PCR amplification of the V3 regions of the 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) was used to separate the amplified products and analyse the 16S rRNA gene diversity of sediment samples. The results of DGGE indicated that the bacterial community composition is influenced by DNA extraction methods. Sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belong to Proteobacteria, Bacteroidetes, gram-positive bacteria and Archaea. Integrating different DNA extraction procedures are needed to analyse the actual bacterial diversity from environment when the amplification of 16S rRNA gene and construction of representative clone library were adopted. 相似文献
6.
We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure
of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing
gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal
microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas
the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota
of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized
using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was
significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of
the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal
eukaryotic microorganisms were almost identical. 相似文献
7.
Xiao Y Zeng GM Yang ZH Ma YH Huang C Xu ZY Huang J Fan CZ 《Bioresource technology》2011,102(2):1383-1388
Actinomycetes degrade cellulose and solubilize lignin during composting. Changes in the diversity of the actinomycetal communities and the 16S rDNA copy numbers of actinomycetes were monitored by denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR), respectively, during continuous thermophilic composting (CTC) and traditional composting (TC). qPCR indicated that the copy numbers from the CTC samples were 25-80% higher than those from the TC samples during similar phases of active composting and they were lower than 3×10(9) gene copies/g (dry weight) in the mature compost from both runs. DGGE showed a more diverse actinomycetal community in the CTC than in TC, averaging 16 bands as compared to 12 bands, at the post peak temperature phase. The study suggested that temperatures higher than 50 °C in CTC benefited the growth of actinomycetes. 相似文献
8.
Zhuhong Liu Lei Gao Yuyang Zhang Jingjing Pei Chunhua Ren 《Marine Biology Research》2016,12(10):1101-1108
Serious bleaching events have been observed in Acropora solitaryensis, one of the main species of reef-building coral in the area of the Xisha islands in the South China Sea, during 2008–2011. The microbial communities of healthy and bleached coral samples were compared to explore the difference in the bacterial composition using 16S rRNA gene sequencing and denaturing gradient gel electrophoresis (DGGE). Analysis of 16S rRNA gene sequences showed that the diversity of bacteria from the corals was different between the healthy and the bleached. Albeit both the healthy coral and bleached coral displayed similar dominant bacterial species (α- and γ-proteobacteria), the ratio of Vibrio spp. increased sharply in the latter. As the bleaching developed, the diversity of the microbial community was dramatically decreased and the dominant species were replaced by γ-proteobacteria where Vibrio spp. and Escherichia spp. overwhelmed other genera. Similar results were gained by the DGGE technique though the abundance was lower. Furthermore, in the bleached tissues, Vibrio coralliilyticus was identified using both methods. These results indicated that pathogenic Vibrio spp. might be one of the factors causing A. solitaryensis bleaching in the coral reef of the Xisha islands. 相似文献
9.
Rod J. Dillon Gordon Webster Andrew J. Weightman A. Keith Charnley 《Antonie van Leeuwenhoek》2010,97(1):69-77
Here we report the effects of starvation and insect age on the diversity of gut microbiota of adult desert locusts, Schistocerca gregaria, using denaturing gradient gel electrophoretic (DGGE) analysis of bacterial 16S rRNA genes. Sequencing of excised DGGE bands
revealed the presence of only one potentially novel uncultured member of the Gammaproteobacteria in the guts of fed, starved, young or old locusts. Most of the 16S rRNA gene sequences were closely related to known cultured
bacterial species. DGGE profiles suggested that bacterial diversity increased with insect age and did not provide evidence
for a characteristic locust gut bacterial community. Starved insects are often more prone to disease, probably because they
compromise on immune defence. However, the increased diversity of Gammaproteobacteria in starved locusts shown here may improve defence against enteric threats because of the role of gut bacteria in colonization
resistance. 相似文献
10.
Keiko Watanabe Norio Nagao Tatsuki Toda Norio Kurosawa 《World journal of microbiology & biotechnology》2009,25(5):803-811
Bacterial community succession in the start-up of a large-scale, completely-mixed composting reactor was analyzed by 16S rRNA
gene (16S rDNA) clone analysis and denaturing gradient gel electrophoresis (DGGE) combined with measurements of temperature,
pH, moisture contents, and decomposing rate. DGGE analysis and physicochemical parameters showed that bacterial community
succession occurred in four phases; (1) at the start of operation and pH decreasing period (day 0–3), (2) pH decreased and
increased period (day 4–11), (3) middle term, moisture content decreasing and maximum temperature increased period (day 12–16)
and (4) latter term, temperature decreasing period (day 17–24). Lactobacillus spp. and Bacillus coagulans were detected from the initial phase and middle term, respectively. 16S rDNA clone analysis showed that the dominant bacteria
shifted from the order “Lactobacillales” to Bacillales and Actinomycetales. The order “Lactobacillales” was unique which may be caused by using the plastic bottle flakes (polyethylene terephthalate, PET) as bulking agent. 相似文献
11.
Valérie Bru-Adan Nathalie Wéry Marina Moletta-Denat Patrick Boiron Jean-Philippe Delgènes Jean-Jacques Godon 《Current microbiology》2009,59(3):326-335
This article outlines a comprehensive analysis of the microbial diversity of aerosols produced during screening in a green
waste composting plant using both culture and molecular techniques. Bacteria, thermophilic actinomycetes and fungi were quantified
in the aerosols. The structure of the microbial community was examined using a fingerprint technique and DNA libraries. The
results show: (i) the very high diversity of bacteria and fungi in aerosols produced during the composting screening stage,
(ii) the low percentage of cultivability for bacteria in aerosols, (iii) the abundance of Thermoactinomyces spp. and Aspergillus spp. in compost aerosols. 相似文献
12.
Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes
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Sabine Peters Stefanie Koschinsky Frank Schwieger Christoph C. Tebbe 《Applied microbiology》2000,66(3):930-936
A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of γ-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process. 相似文献
13.
DGGE and T-RFLP Analysis of Bacterial Succession during Mushroom Compost Production and Sequence-aided T-RFLP Profile of Mature Compost 总被引:6,自引:0,他引:6
The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting
the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored,
and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable
properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient
gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods
were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE
bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting
processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together
and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature
compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were
uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the
dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora. 相似文献
14.
This study examined bacterial community structure of biofilms on stainless steel and polycarbonate in seawater from the Delaware
Bay. Free-living bacteria in the surrounding seawater were compared to the attached bacteria during the first few weeks of
biofilm growth. Surfaces exposed to seawater were analyzed by using 16S rDNA libraries, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE). Community structure of the free-living bacterial
community was different from that of the attached bacteria according to FISH and DGGE. In particular, alpha-proteobacteria
dominated the attached communities. Libraries of 16S rRNA genes revealed that representatives of the Rhodobacterales clade were the most abundant members of biofilm communities. Changes in community structure during biofilm growth were also
examined by DGGE analysis. We hypothesized that bacterial communities on dissimilar surfaces would initially differ and become
more similar over time. In contrast, the compositions of stainless steel and polycarbonate biofilms were initially the same,
but differed after about 1 week of biofilm growth. These data suggest that the relationship between surface properties and
biofilm community structure changes as biofilms grow on surfaces such as stainless steel and polycarbonate in estuarine water. 相似文献
15.
In order to obtain the diversity and temporal–spatial distribution of Bacillus community during the swine manure composting, we utilized traditional culture methods and the modern molecular biology techniques
of polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and –denaturing gradient gel electrophoresis
(PCR-DGGE). Bacillus species were firstly isolated from the composting. Based on temperature changes, the temporal–spatial characteristics of
total culturable Bacillus were remarkable that the number of the culturable Bacillus detected at the high-temperature stage was the highest in each layer of the pile and that detected in the middle layer was
the lowest at each stage of composting respectively. The diversity of cultivated Bacillus species isolated from different composting stages was low. A total of 540 isolates were classified by the RFLP method and
partial 16S rDNA sequences. They affiliated to eight species including Bacillus subtilis, Bacillus cereus, Bacillus thuringiensis, Bacillus anthracis, Bacillus megaterium, Bacillus licheniformis, Bacillus pumilus, and Bacillus circulans. The predominant species was B. subtilis, and the diversity of culturable Bacillus isolated in the middle-level samples at temperature rising and cooling stages was the highest. The DGGE profile and clone
library analysis revealed that the temporal–spatial distribution of Bacillus community was not obvious, species belonging to the Bacillus were dominant (67%) with unculturable bacteria and B. cereus was the second major culturable Bacillus species. This study indicated that a combination of culture and culture-independent approaches could be very useful for monitoring
the diversity and temporal–spatial distribution of Bacillus community during the composting process. 相似文献
16.
17.
Huys G Vanhoutte T Joossens M Mahious AS De Brandt E Vermeire S Swings J 《Current microbiology》2008,56(6):553-557
The main aim of this study was to evaluate the specificity of three commonly used 16S rRNA gene-based polymerase chain reaction
(PCR) primer sets for bacterial community analysis of samples contaminated with eukaryotic DNA. The specificity of primer
sets targeting the V3, V3-V5, and V6-V8 hypervariable regions of the 16S rRNA gene was investigated in silico and by community fingerprinting of human and fish intestinal samples. Both in silico and PCR-based analysis revealed cross-reactivity of the V3 and V3-V5 primers with the 18S rRNA gene of human and sturgeon. The consequences of this primer anomaly were illustrated by denaturing
gradient gel electrophoresis (DGGE) profiling of microbial communities in human feces and mixed gut of Siberian sturgeon.
DGGE profiling indicated that the cross-reactivity of 16S rRNA gene primers with nontarget eukaryotic DNA might lead to an
overestimation of bacterial biodiversity. This study has confirmed previous sporadic indications in literature indicating
that several commonly applied 16S rRNA gene primer sets lack specificity toward bacteria in the presence of eukaryotic DNA.
The phenomenon of cross-reactivity is a potential source of systematic error in all biodiversity studies where no subsequent
analysis of individual community amplicons by cloning and sequencing is performed. 相似文献
18.
《Journal of microbiological methods》2010,80(3):321-328
The present study was conducted to identify and characterize the thermophilic bacteria isolated from various hot springs in Turkey by using phenotypic and genotypic methods including fatty acid methyl ester and rep-PCR profilings, and 16S rRNA sequencing. The data of fatty acid analysis showed the presence of 17 different fatty acids in 15 bacterial strains examined in this study. Six fatty acids, 15:0 iso, 15:0 anteiso, 16:0, 16:0 iso, 17:0 iso, and 17:0 anteiso, were present in all strains. The bacterial strains were classified into three phenotypic groups based on fatty acid profiles which were confirmed by genotypic methods such as 16S rRNA sequence analysis and rep-PCR genomic fingerprint profiles. After evaluating several primer sets targeting the repetitive DNA elements of REP, ERIC, BOX and (GTG)5, the (GTG)5 and BOXA1R primers were found to be the most reliable technique for identification and taxonomic characterization of thermophilic bacteria in the genera of Geobacillus, Anoxybacillus and Bacillus spp. Therefore, rep-PCR fingerprinting using the (GTG)5 and BOXA1R primers can be considered as a promising genotypic tool for the identification and characterization of thermophilic bacteria from species to strain level. 相似文献
19.
Dohrmann AB Baumert S Klingebiel L Weiland P Tebbe CC 《Applied microbiology and biotechnology》2011,89(6):1991-2004
Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy
production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include
bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended
growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters
affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up
during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both
were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation
using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic
profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were
highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from
SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant
community members in biogas reactors fed with manure. 相似文献
20.
Microbial communities thriving at two hot springs, Hammam Pharaon (Pharaoh's Bath) and Oyoun Mossa (Moses springs), in Egypt was studied by cultural and molecular methods. Thirteen morphologically distinct strains of facultative anaerobic thermophilic bacterial isolates have been characterized and identified using phenotypic and genotypic characters including RAPD-PCR, ERIC-PCR typing, plasmid analysis and 16S rRNA sequencing. All isolates produced plasmid DNA with various sizes ranging from 0.7 kb to a larger plasmid 7.2 kb. The bacterial strains could tolerate a temperature range between 45 to 85°C and a pH between 4–11. Also, sulphate-reducing bacteria (SRB) in the thermal springs were investigated with combined biochemical and molecular approaches. A sulphate-reducing bacteria medium containing lactate was used for enrichment and isolation, which yielded Gram negative, rod shaped, anaerobic, non-spore-forming and motile bacteria capable of reducing sulphate to sulphide. These grew at temperatures ranging from 30 to 50°C and could use pyruvate, lactate and ethanol as electron donors. The dissimilatory sulphite reductase (DSR) gene sequences of eleven representative isolates revealed that the strains belonged to the sulphur reducing bacterial species Desulfovibrio vulgaris. 16S rRNA gene partial sequence results indicated the presence of novel or existing species of Bacillus (one species), Anoxybacillus (four species) and Geobacillus (eight species). In this study phenotypic and genotypic diversity were applied for the first time to differentiate thermophilic bacteria of such geothermal sites in Sinai, Egypt. 相似文献