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1.
Numerical Dominance and Phylotype Diversity of Marine Rhodobacter Species during Early Colonization of Submerged Surfaces in Coastal Marine Waters as Determined by 16S Ribosomal DNA Sequence Analysis and Fluorescence In Situ Hybridization 总被引:2,自引:0,他引:2
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Early stages of surface colonization in coastal marine waters appear to be dominated by the marine Rhodobacter group of the α subdivision of the division Proteobacteria (α-Proteobacteria). However, the quantitative contribution of this group to primary surface colonization has not been determined. In this study, glass microscope slides were incubated in a salt marsh tidal creek for 3 or 6 days. Colonizing bacteria on the slides were examined by fluorescence in situ hybridization by employing DNA probes targeting 16S or 23S rRNA to identify specific phylogenetic groups. Confocal laser scanning microscopy was then used to quantify and track the dynamics of bacterial primary colonists during the early stages of surface colonization and growth. More than 60% of the surface-colonizing bacteria detectable by fluorescence staining (Yo-Pro-1) could also be detected with the Bacteria domain probe EUB338. Archaea were not detected on the surfaces and did not appear to participate in surface colonization. Of the three subdivisions of the Proteobacteria examined, the α-Proteobacteria were the most abundant surface-colonizing organisms. More than 28% of the total bacterial cells and more than 40% of the cells detected by EUB338 on the surfaces were affiliated with the marine Rhodobacter group. Bacterial abundance increased significantly on the surfaces during short-term incubation, mainly due to the growth of the marine Rhodobacter group organisms. These results demonstrated the quantitative importance of the marine Rhodobacter group in colonization of surfaces in salt marsh waters and confirmed that at least during the early stages of colonization, this group dominated the surface-colonizing bacterial assemblage. 相似文献
2.
Microbial community structures in conventional activated sludge system and membrane bioreactor (MBR)
The microbial community structures of a conventional activated sludge and MBR systems treating the municipal wastewater were
studied using Fluorescent in-situ Hybridization (FISH) analysis to identify differences in both systems. The oligonucleotide probes specific for overall bacteria,
including α-, β-, and γ-subclasses of Proteobacteria, ammonia-oxidizing bacteria (Nitrosomonas), and nitrite-oxidizing bacteria (Nitrobacter) were used to compare the microbial community structure of both systems. A trend of less hybridization with bacteria-specific
probe EUB338 was observed in MBR systems operated under aerobic condition, compared to conventional activated sludge system.
The less hybridization trend with the probes could be associated with low ribosomal RNA (rRNA) content in the biomass, which
suggests that the biomass in the MBR system was not in a physiological state characteristic for growth due to low substrate
per unit biomass 相似文献
3.
Biodegradation of nonylphenol in a continuous bioreactor at low temperatures and effects on the microbial population 总被引:6,自引:0,他引:6
A packed-bed bioreactor inoculated with a mixed culture obtained from a contaminated site was used to continuously treat a
saturated solution of nonylphenol. The reactor was operated at feeding rates of 13–112 ml h−1 and temperatures of 5.5, 10, and 15°C. Optimal bioreactor performance was achieved at 10°C and at a feeding rate of 84 ml
h−1 (with a removal rate of 43 mg l−1 day−1 of nonylphenol). No endocrine activity was observed in the effluent of the bioreactor at any of the temperatures tested,
and the only metabolic products found were branched carboxylic acids and alkanes (lacking an aromatic ring). The study of
the microbial populations in the biofilm at the three temperatures tested using fluorescence in situ hybridization showed
that all the bacterial species that could be identified belonged to the phylum Proteobacteria. The most abundant class identified at all three temperatures was β-Proteobacteria. The proportions of bacteria that bound to the specific probes among the total population, identified with the bacterial
probe EUB338MIX, were 60, 43, and 24% at 15, 10, and 5.5°C, respectively. 相似文献
4.
Phylogenetic Analysis and In Situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog 总被引:3,自引:0,他引:3
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Svetlana N. Dedysh Timofei A. Pankratov Svetlana E. Belova Irina S. Kulichevskaya Werner Liesack 《Applied microbiology》2006,72(3):2110-2117
The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 107 and 1.1 × 107 cells g−1 peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity. 相似文献
5.
Rakia Chouari Denis Le Paslier Patrick Daegelen Catherine Dauga Jean Weissenbach Abdelghani Sghir 《Microbial ecology》2010,60(2):272-281
A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge
from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified
by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249
almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before
and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives
of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S
rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples.
The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within
the anoxic basin. 相似文献
6.
Berchtold M Chatzinotas A Schonhuber W Brune A Amann R Hahn D Konig H 《Archives of microbiology》1999,172(6):407-416
We examined the abundance and spatial distribution of major phylogenetic groups of the domain Bacteria in hindguts of the
Australian lower termite Mastotermes darwiniensis by using in situ hybridization with group-specific, fluorescently labeled, rRNA-targeted oligonucleotide probes. Between
32.0 ± 7.2% and 52.3 ± 8.2% of the DAPI-stained cells in different hindgut fractions were detected with probe EUB338, specific
for members of the domain Bacteria. About 85% of the prokaryotic cells were associated with the flagellates of the thin-walled
anterior region (P3a) and the thick wall of the posterior region (P3b/P4) of the hindgut, as shown by DAPI staining. At most,
half of the EUB338-detected cells hybridized with one of the other probes that targeted a smaller assemblage within the bacterial
domain. In most fractions, cells were found in varying numbers with probe ALF1b, which targeted members of the α-Proteobacteria,
whereas substantial amounts of sulfate-reducing bacteria, gram-positive bacteria with a high DNA G+C content and members of
the Cytophaga-Flavobacterium cluster of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum could be detected only in the wall fraction of P3b/P4. This clearly indicates that the hindgut microhabitats
differ in the composition of their microbial community. In situ hybridization of cryosections through the hindgut showed only
low numbers of bacteria attached to the P3a wall. In contrast, the wall of P3b was densely colonized by rod- and coccus-shaped
bacteria, which could be assigned to the Cytophaga-Flavobacterium cluster of the CFB phylum and to the group of gram-positive bacteria with a high DNA G+C content, respectively. Oxygen concentration
profiles determined with microelectrodes revealed steep oxygen gradients both in P3a and P3b. Oxygen was consumed within 100
μm below the gut surface, and anoxic conditions prevailed in the central portions of both gut regions, indicating that oxygen
consumption in the hindgut does not depend on the presence of a biofilm on the hindgut wall.
Received: 17 May 1999 / Accepted: 16 September 1999 相似文献
7.
The diversity and the community structure of sulfate-reducing bacteria (SRB) in an anaerobic continuous bioreactor used for
treatment of a sulfate-containing wastewater were investigated by fluorescence in situ hybridization. Hybridization to the 16S rRNA probe EUB338 for the domain Bacteria was performed, followed by a nonsense probe
NON338 as a control for nonspecific staining. Sulfate-reducing consortia were identified by using five nominally genus-specific
probes (SRB129 for Desulfobacter, SRB221 for Desulfobacterium, SRB228 for Desulfotomaculum, SRB660 for Desulfobulbus, and SRB657 for Desulfonema) and four group-specific probes (SRB385 as a general SRB probe, SRB687 for Desulfovibrioaceae, SRB814 for Desulfococcus group, and SRB804 for Desulfobacteriaceae). The total prokaryotic population was determined by 4′,6-diamidino-2-phenylindole staining. Hybridization analysis using
these 16S rRNA-targeted oligonucleotide probes showed that, of those microbial groupings investigated, Desulfonema, Desulfobulbus, spp., and Desulfobacteriaceae group were the main sulfate-reducing bacteria in the bioreactor when operated at steady state at 35°C, pH 7.8, and a 2.5-day
residence time with feed stream containing 2.5 kg m−3 sulfate as terminal electron acceptor and 2.3 kg m−3 acetate as carbon source and electron donor. 相似文献
8.
α- and β-Proteobacteria Control the Consumption and Release of Amino Acids on Lake Snow Aggregates
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Bernhard Schweitzer Ingrid Huber Rudolf Amann Wolfgang Ludwig Meinhard Simon 《Applied microbiology》2001,67(2):632-645
We analyzed the composition of aggregate (lake snow)-associated bacterial communities in Lake Constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes of various specificity. In addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. Generally, between 40 and more than 80% of the microbes enumerated by DAPI staining (4′,6′-diamidino-2-phenylindole) were detected as Bacteria by the probe EUB338. At a depth of 25 m, 10.5% ± 7.9% and 14.2% ± 10.2% of the DAPI cell counts were detected by probes specific for α- and β-Proteobacteria. These proportions increased to 12.0% ± 3.3% and 54.0% ± 5.9% at a depth of 50 m but decreased again at the sediment surface at 110 m to 2.7% ± 1.4% and 41.1% ± 8.4%, indicating a clear dominance of β-Proteobacteria at depths of 50 and 110 m, where aggregates have an age of 3 to 5 and 8 to 11 days, respectively. From 50 m to the sediment surface, cells detected by a Cytophaga/Flavobacteria-specific probe (CF319a) comprised increasing proportions up to 18% of the DAPI cell counts. γ-Proteobacteria always comprised minor proportions of the aggregate-associated bacterial community. Using only two probes highly specific for clusters of bacteria closely related to Sphingomonas species and Brevundimonas diminuta, we identified between 16 and 60% of the α-Proteobacteria. In addition, with three probes highly specific for close relatives of the β-Proteobacteria Duganella zoogloeoides (formerly Zoogloea ramigera), Acidovorax facilis, and Hydrogenophaga palleroni, bacteria common in activated sludge, 42 to 70% of the β-Proteobacteria were identified. In the early phase (<20 h) of 11 of the 15 experimental incubations of aggregates, dissolved amino acids were consumed by the aggregate-associated bacteria from the surrounding water. This stage was followed by a period of 1 to 3 days during which dissolved amino acids were released into the surrounding water, paralleled by an increasing dominance of β-Proteobacteria. Hence, our results show that lake snow aggregates are inhabited by a community dominated by a limited number of α- and β-Proteobacteria, which undergo a distinct succession. They successively decompose the amino acids bound in the aggregates and release substantial amounts into the surrounding water during aging and sinking. 相似文献
9.
Abstract
The phylogenetic composition, three-dimensional structure and dynamics of bacterial communities in river biofilms generated
in a rotating annular reactor system were studied by fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). Biofilms grew on independently removable polycarbonate
slides exposed in the reactor system with natural river water as inoculum and sole nutrient and carbon source. The microbial
biofilm community developed from attached single cells and distinct microcolonies via a more confluent structure characterized
by various filamentous bacteria to a mature biofilm rich in polymeric material with fewer cells on a per-area basis after
56 days. During the different stages of biofilm development, characteristic microcolonies and cell morphotypes could be identified
as typical features of the investigated lotic biofilms. In situ analysis using a comprehensive suite of rRNA-targeted probes visualized individual cells within the alpha-, beta-, and gamma-Proteobacteria as well as the Cytophaga–Flavobacterium group as major parts of the attached community. The relative abundance of these major groups was determined by using digital
image analysis to measure specific cell numbers as well as specific cell area after in situ probing. Within the lotic biofilm community, 87% of the whole bacterial cell area and 79% of the total cell counts hybridized
with a Bacteria specific probe. During initial biofilm development, beta-Proteobacteria dominated the bacterial population. This was followed by a rapid increase of alpha-Proteobacteria and bacteria affiliated to the Cytophaga–Flavobacterium group. In mature biofilms, alpha-Proteobacteria and Cytophaga–Flavobacteria continued to be the prevalent bacterial groups. Beta-Proteobacteria constituted the morphologically most diverse group within the biofilm communities, and more narrow phylogenetic staining
revealed the importance of distinct phylotypes within the beta1-Proteobacteria for the composition of the microbial community. The presence of sulfate-reducing bacteria affiliated to the Desulfovibrionaceae and Desulfobacteriaceae confirmed the range of metabolic potential within the lotic biofilms.
Received: 24 September 1998; Accepted: 17 February 1999 相似文献
10.
Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria 总被引:22,自引:13,他引:9
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Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to heterotrophic bacteria in marine samples. Penetration of the HRP molecule into bacterial cells requires permeabilization procedures that cause high and most probably species-selective cell loss. Here we present an improved protocol for CARD-FISH of marine planktonic and benthic microbial assemblages. After concentration of samples onto membrane filters and subsequent embedding of filters in low-gelling-point agarose, no decrease in bacterial cell numbers was observed during 90 min of lysozyme incubation (10 mg ml−1 at 37°C). The detection rates of coastal North Sea bacterioplankton by CARD-FISH with a general bacterial probe (EUB338-HRP) were significantly higher (mean, 94% of total cell counts; range, 85 to 100%) than that with a monolabeled probe (EUB338-mono; mean, 48%; range, 19 to 66%). Virtually no unspecific staining was observed after CARD-FISH with an antisense EUB338-HRP. Members of the marine SAR86 clade were undetectable by FISH with a monolabeled probe; however, a substantial population was visualized by CARD-FISH (mean, 7%; range, 3 to 13%). Detection rates of EUB338-HRP in Wadden Sea sediments (mean, 81%; range, 53 to 100%) were almost twice as high as the detection rates of EUB338-mono (mean, 44%; range, 25 to 71%). The enhanced fluorescence intensities and signal-to-background ratios make CARD-FISH superior to FISH with directly labeled oligonucleotides for the staining of bacteria with low rRNA content in the marine environment. 相似文献
11.
The incorporation of [3H-methyl] thymidine (3H-TdR) by Eubacteria, bacterial groups (α- and β-Proteobacteria, Cytophaga–Flavobacter), and Archaea was measured according to temperature (7 and 17°C) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (Sep, France). Short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. Irrespective of the temperatures and nutrients studied, all the major phylogenetic bacterial groups assimilated 3H-TdR, and in most of the treatments studied, the proportion of β-Proteobacteria taking up 3H-TdR was higher than those in the other bacterial groups. The proportion of Bacteria and different bacterial groups studied incorporating 3H-TdR were significantly increased, approximately 1.5-fold, by temperature except for α-Proteobacteria (7.6-fold). The nutrient effect was not the same for the different bacterial groups according to the temperatures studied. The proportions of α-Proteobacteria (at both temperatures) and Cytophaga–Flavobacter (at 7°C) taking up 3H-TdR were significantly decreased and increased by adding N and P, respectively. Also, adding N, P, and C increased and decreased the percentage of β-Proteobacteria incorporating 3H-TdR at 7 and 17°C, respectively. The archaeal community showed a similar proportion of active cells (i.e., 3H-TdR) to the bacterial community, and uptake of 3H-TdR by Archaea was significantly increased (P < 0.05) by both temperature and nutrients. Thus, the assimilation of 3H-TdR by bacterial groups and Archaea in lacustrine system is significantly controlled by both temperature and nutrients. 相似文献
12.
Tay Tiong-Lee Stephen Ivanov Volodymyr Kim In Soo Feng Lin Tay Joo-Hwa 《World journal of microbiology & biotechnology》2001,17(6):583-589
16S rRNA-targeted oligonucleotide probes for Bacteria (Eub338) and Archaea (Arc915) were used for whole-cell, fluorescence in situ hybridization (FISH) to quantify the ratio of these microbial groups in an anaerobic digester. The quantity of specifically bound (hybridized) probe was measured by fluorescence spectrometry and evaluated by analysing the dissociation curve of the hybrids, by the measurement of the binding with a nonsense probe, and by the competitive inhibition of the binding of the labelled probe by the corresponding unlabelled probe. Specific binding of oligonucleotide probes with the biomass of anaerobes was 40–50% of their total binding. The ratio of Arc915 and Eub338 probes hybridized with rRNAs of the cells in anaerobic sludge was 0.50. Measurement of FISH by fluorescence spectrometry appears to be a suitable method for quantification of the microbial community of anaerobes. 相似文献
13.
14.
The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. 总被引:39,自引:0,他引:39
H Daims A Brühl R Amann K H Schleifer M Wagner 《Systematic and applied microbiology》1999,22(3):434-444
In situ hybridization with rRNA-targeted oligonucleotide probes has become a widely applied tool for direct analysis of microbial population structures of complex natural and engineered systems. In such studies probe EUB338 (AMANN et al., 1990) is routinely used to quantify members of the domain Bacteria with a sufficiently high cellular ribosome content. Recent reevaluations of probe EUB338 coverage based on all publicly available 16S rRNA sequences, however, indicated that important bacterial phyla, most notably the Planctomycetales and Verrucomicrobia, are missed by this probe. We therefore designed and evaluated two supplementary versions (EUB338-II and EUB338-III) of probe EUB338 for in situ detection of most of those phyla not detected with probe EUB338. In situ dissociation curves with target and non-target organisms were recorded under increasing stringency to optimize hybridization conditions. For that purpose a digital image software routine was developed. In situ hybridization of a complex biofilm community with the three EUB338 probes demonstrated the presence of significant numbers of probe EUB338-II and EUB338-III target organisms. The application of EUB338, EUB338-II and EUB338-III should allow a more accurate quantification of members of the domain Bacteria in future molecular ecological studies. 相似文献
15.
Biofilms were grown in annular reactors supplied with drinking water enriched with 235 microg C/L. Changes in the biofilms with ageing, disinfection, and phosphate treatment were monitored using fluorescence in situ hybridization. EUB338, BET42a, GAM42a, and ALF1b probes were used to target most bacteria and the alpha (alpha), beta (beta), and gamma (gamma) subclasses of Proteobacteria, respectively. The stability of biofilm composition was checked after the onset of colonization between T = 42 days and T = 113 days. From 56.0% to 75.9% of the cells detected through total direct counts with DAPI (4'-6-diamidino-2-phenylindole) were also detected with the EUB338 probe, which targets the 16S rRNA of most bacteria. Among these cells, 16.9%-24.7% were targeted with the BET42a probe, 1.8%-18.3% with the ALF1b probe, and <2.5% with the GAM42a probe. Phosphate treatment induced a significant enhancement to the proportion of gamma-Proteobacteria (detected with the GAM42a probe), a group that contains many health-related bacteria. Disinfection with monochloramine for 1 month or chlorine for 3 days induced a reduction in the percentage of DAPI-stained cells that hybridized with the EUB338 probe (as expressed by percentages of EUB338 counts/DAPI) and with any of the ALF1b, BET42a, and GAM42a probes. The percentage of cells detected by any of the three probes (ALF1b+BET42a+GAM42a) tended to decrease, and reached in total less than 30% of the EUB338-hybridized cells. Disinfection with chlorine for 7 days induced a reverse shift; an increase in the percentage of EUB338 counts targeted by any of these three probes was noted, which reached up to 87%. However, it should be noted that the global bacterial densities (heterotrophic plate counts and total direct counts) tended to decrease over the duration of the experiment. Therefore, those bacteria that could be considered to resist 7 days of chlorination constituted a small part of the initial biofilm community, up to the point at which the other bacterial groups were destroyed by chlorination. The results suggest that there were variations in the kinetics of inactivation by disinfectant, depending on the bacterial populations involved. 相似文献
16.
Jong-Shik Kim Robert S. Dungan Soon-Wo Kwon Hang-Yeon Weon 《World journal of microbiology & biotechnology》2006,22(12):1267-1273
The objective of this study was to characterize the bacterial community composition in the bulk soil, rhizosphere soil and root tissue of the tomato plant (Lycopersicum esculentum Mill). 16S ribosomal DNA (rDNA) from the bacterial community was amplified using PCR, and sequence analysis of 16S rDNA clones was subsequently used for bacterial identification and phylogenetic classification. Phylogenetic analysis of clones (total of 68) from the bulk soil, rhizosphere and root tissues showed that about 50% of the bacteria belonged to the α-, β-, γ-, and δ-Proteobacteria or Cytophaga–Flavobacterium–Bacteroides (CFB) phyla, with only one high G+C clone identified. A number of diverse bacteria were identified within Proteobacteria, while 87% of the bacteria belonged to the genus Flavobacterium within the CFB phylum, which is a unique finding for tomato plants. Our results will be of interest to those wanting to identify bacteria that can promote plant growth or resistance to diseases. 相似文献
17.
Cultivable Bacterial Community from South China Sea Sponge as Revealed by DGGE Fingerprinting and 16S rDNA Phylogenetic Analysis 总被引:2,自引:0,他引:2
The cultivable bacterial communities associated with four South China Sea sponges—Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis in mixed cultures—were investigated by microbial community DNA-based DGGE fingerprinting and 16S rDNA phylogenetic analysis.
Diverse bacteria such as α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes were cultured, some of which were previously uncultivable bacteria, potential novel strains with less than 95% similarity
to their closest relatives and sponge symbionts growing only in the medium with the addition of sponge extract. According
to 16S rDNA BLAST analysis, most of the bacteria were cultured from sponge for the first time, although similar phyla of bacteria
have been previously recognized. The selective pressure of sponge extract on the cultured bacterial species was suggested,
although the effect of sponge extract on bacterial community in high nutrient medium is not significant. Although α- and γ-Proteobacteria appeared to form the majority of the dominant cultivable bacterial communities of the four sponges, the composition of the
cultivable bacterial community in the mixed culture was different, depending on the medium and sponge species. Greater bacterial
diversity was observed in media C and CS for Stelletta tenuis, in media F and FS for Halichondria rugosa and Craniella australiensis. S. tenuis was found to have the highest cultivable bacterial diversity including α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes, followed by sponge Dysidea avara without δ-Proteobacteria, sponge Halichondria rugosa with only α-, γ-Proteobacteria and Bacteroidetes, and sponge C. australiensis with only α-, γ-Proteobacteria and Firmicutes. Based on this study, by the strategy of mixed cultivation integrated with microbial community DNA-based DGGE fingerprinting
and phylogenetic analysis, the cultivable bacterial community of sponge could be revealed effectively. 相似文献
18.
Detection of nitrifying bacteria in activated sludge by fluorescent in situ hybridization and fluorescence spectrometry 总被引:2,自引:0,他引:2
16S rRNA-targeted oligonucleotide probes for eubacteria (EUB338), ammonium-oxidizing bacteria (Nsm156) and nitrite-oxidizing bacteria (Nb1000) were used for the rapid detection of nitrifying bacteria in the activated sludge of a pilot nitrifying reactor by whole-cell, fluorescent in situ hybridization (FISH). Emission scanning and synchronous scanning fluorescence spectrometry were used to measure the hybridization. The binding of the probes at a temperature significantly lower than the melting temperature of the hybrids was conventionally considered as non-specific. Total binding of the probes at a temperature significantly higher than the melting temperature of the hybrids was conventionally considered as the sum of non-specific and specific binding (hybridization). Non-specific binding of the oligonucleotide probes with a biomass of activated sludge was 37% of the total binding of the EUB338 probe, 54% of the total binding of the Nsm156 probe, and 69% of the total binding of the Nb1000 probe. The ratio of the specific binding of the Nsm156 and Nb1000 probes was 2.3:1. The ratio of the numbers of ammonium-oxidizing bacteria to nitrite-oxidizing bacteria, determined by microbiological methods, was 2.4:1. Measuring fluorescent in situ hybridization by fluorescence spectrometry appears to be a practical tool for monitoring the microbial communities that contain nitrifying bacteria. However, a method that accounts for the non-specific binding of the probes more easily and reliably should be developed for practical application. 相似文献
19.
Mahendra Laxman Ahire Savaliram Goga Ghane Vinayak Haribhau Lokhande Penna Suprasanna Tukaram Dayaram Nikam 《In vitro cellular & developmental biology. Plant》2011,47(4):488-495
Uraria picta is extensively used in the Asian traditional systems of medicine. Overexploitation of the species for preparation of the
drug Dashmula has led to the plant becoming rare and endemic. In the present investigation, an efficient micropropagation
protocol has developed from leaf-derived callus of U. picta. Among the various concentrations of cytokinins (6-benzyladenine—BA; kinetin—Kin; and thidiazuron—TDZ) used, a significantly
higher number of shoots per culture (58.8 ± 0.8) was observed on Murashige and Skoog (MS) medium fortified with 4.44 μM BA.
The shoot regeneration frequency was sustained upon transfer to the same fresh medium at 4-wk intervals over a period of 2 yr.
The medium containing various concentrations of auxins (α-napthalene acetic acid (NAA) or indole-3-acetic acid (IAA)) showed
callus interspersed root formation; however, MS basal medium containing 3% sucrose revealed direct root induction from in vitro raised shoots. The acclimatized in vitro grown plants showed almost 98% survival upon transfer to soil in earthen pots and grown ex vitro. Randomly amplified polymorphic DNA analysis of 25 arbitrarily selected regenerants and mother plants revealed 100% uniformity
and true-to-type nature of the regenerants. Methanolic extracts of callus showed strong antibacterial activity against pathogenic
bacteria as compared to leaf and root extracts of in vitro raised plants and wild plants, suggesting the presence of higher concentrations of active chemical constituents (isoflavanoids)
in callus cultures of U. picta. 相似文献
20.
Gupta RS 《Photosynthesis research》2003,76(1-3):173-183
To understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within Bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. Recent analysis of shared conserved
inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in
microbiology. Based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria
can now be defined in clear molecular terms and their relative branching orders logically deduced. For the 82 presently completed
bacterial genomes, the presence or absence of these signatures in various proteins was found to be almost exactly as predicted
by the indel model, with only 11 exceptions observed in 1842 observations. The branching order of different bacterial groups
as deduced using this approach is as follows: low G+C Gram-positive (Heliobacterium chlorum) ↔ high G+C Gram-positive ↔ Clostridium–Fusobacterium–Thermotoga ↔ Deinococcus–Thermus ↔ green nonsulfur bacteria (Chloroflexus aurantiacus) ↔ Cyanobacteria ↔ Spirochetes ↔ Chlamydia–Cytophaga–Flavobacteria–green sulfur bacteria (Chlorobium tepidum) ↔ Aquifex ↔ Proteobacteria (δ and ∈) ↔ Proteobacteria (α) ↔ Proteobacteria (β) and ↔ Proteobacteria (γ). The Heliobacterium species, which contain an Fe–S type of reaction center (RC 1) and represent the sole photosynthetic phylum from the Gram-positive
or monoderm bacteria (i.e., bounded by only a single membrane), is indicated to be the most ancestral of the photosynthetic
lineages. Among the Gram-negative or diderm bacteria (containing both inner and outer cell membranes) the green nonsulfur
bacteria, which contain a pheophytin-quinone type of reaction center (RC 2), are indicated to have evolved first. The later
emerging photosynthetic groups which contain either one or both of these reaction centers could have acquired such genes from
the earlier branching lineages by either direct descent or by means of lateral gene transfer.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献