共查询到20条相似文献,搜索用时 156 毫秒
1.
Tsiamis G Tzagkaraki G Chamalaki A Xypteras N Andersen G Vayenas D Bourtzis K 《Current microbiology》2012,64(2):197-203
Culture-dependent and -independent approaches were employed to identify the bacterial community structure from olive-mill
wastewater produced from three olive-fruit varieties. The 233 bacterial isolates recovered were phylogenetically related to
38 members of Firmicutes, Actinobacteria, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, and Bacteroidetes. Employing a novel microarray-based approach (PhyloChip) a high bacterial diversity was revealed consisting of 18 different
phyla with representatives from 99 different families. The bacterial diversity in olive-mill wastewater from the three olive
tree varieties was dominated by α-, β-, γ-, δ-, ε-Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi,
Cyanobacteria, and Actinobacteria. This in-depth analysis of the indigenous microbiota indicated a cultivar-specific bacterial profile. Interestingly, the
common bacterial taxa present in all three varieties examined were restricted indicating that the bacterial communities present
in the olive-mill wastewater are greatly influenced by the olive-fruit variety. 相似文献
2.
Maria Blaina Mirjana Najdek Dragica Fuks Ana Ruso Mauro tifani Dinko Pavlini 《Ecological Indicators》2009,9(6):1265-1270
This study reports the development of a tool to characterise and differentiate northern Adriatic waters, particularly oligotrophic, high-salinity waters, based on the cellular fatty acids of culturable heterotrophic bacterioplankton. The growth abilities and population dominance were observed for particle-attached and free-living bacteria cultured in three types of media: Marine Broth, diluted Marine Broth (1:10) and R2 broth. Three groups of water layers were distinguished by hierarchical clustering analysis: eutrophic, oligotrophic and oligotrophic nutrient-selected. Significant differences between the resulting groups were tested by two-way ANOVA (with replication). Eutrophic layers were characterised by readily culturable particle-attached and free-living fractions of the bacterial community in all three media, all dominated by fast-growing γ-Proteobacteria. In contrast, oligotrophic water layers with low productivity had a much weaker culturability and a different population dominance for the free-living community, as compared to their attached or growth-arrested counterparts, for all media. The free-living bacteria from strictly oligotrophic environments demonstrated minimum culturability in Marine Broth, while those from selective oligotrophic environments were culturable and were dominated either by Cytophaga–Flavobacter complex, α-Proteobacteria or γ-Proteobacteria. The conclusive evidence regarding the selective and refractory nature of organic compounds in these waters demonstrates the dominant culturability of the Cytophaga–Flavobacter complex and α-Proteobacteria in free-living communities in all growth-media. The response of fatty acid dominance ratios depends significantly on the trophic state and fraction (p < 0.05), although the effect of the trophic state is completely different in attached and free fractions. Both fractions were tested separately, demonstrating a significant influence of the trophic state (p < 0.05), while the effect of the media on the fatty acid response was not significant (p > 0.05). An interaction between media and trophic status was present in the attached fraction (p < 0.05), yet this was not observed in the free fraction (p > 0.05), indicating that any systematic difference between trophic states was the same for each media tested. Accordingly, the free-living fraction of bacterioplankton is a more informative attribute and can be used solely as an indicator of the water layer trophic condition. 相似文献
3.
Olapade OA 《Microbial ecology》2012,63(1):96-102
The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed
location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence
in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed
the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than
the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene
sequences of unknown bacteria (32% to 73%), however, the operational taxonomic units from members of the α-Proteobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria were also well represented during the four tidal events examined. Comparatively, sequence diversity was highest in OT, lowest
in low tide, and very similar between HT and incoming tide. The results indicate that the dynamics of bacterial occurrence
and diversity appeared to be more pronounced during HT and OT, further indicative of the ecological importance of several
environmental variables including temperature, light intensity, and nutrient availability that are also concurrently fluctuating
during these tidal events in marine systems. 相似文献
4.
Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input 总被引:2,自引:0,他引:2
Udiković-Kolić N Devers-Lamrani M Petrić I Hršak D Martin-Laurent F 《Applied microbiology and biotechnology》2011,90(4):1547-1554
We evaluated the effects of variations in atrazine input on the evolution of a bacterial culture adapted to a low atrazine
concentration. This initial culture (M3-K) was subjected to weekly subculturing in the presence of a high concentration of
atrazine as the only N source (100 mg l−1). After four subculturing, M3-K evolved to a new bacterial culture (M3) which exhibited a significant increase in the extent
of atrazine mineralization in comparison with the initial culture. Molecular analyses of M3-K and M3 cultures by cloning,
restriction analysis, and sequencing of the 16S rRNA genes revealed significant differences in culture structure and composition.
M3-K culture comprised mainly Actinobacteria (40%), β-Proteobacteria (26%), and Bacteroidetes (16%). After exposure to a high atrazine concentration, the dominance of Actinobacteria decreased (14%), Bacteroidetes increased (27%), and β-Proteobacteria were replaced by γ-Proteobacteria (32%). Quantitative PCR revealed that the abundance of atzB and atzC genes relative to total bacteria decreased by a factor of 3–4 following the increase in atrazine concentration, while the
relative abundance of trzD increased significantly (≈400 times). Presented study shows that variations in atrazine input drive both functional and compositional
shifts in the atrazine-degrading bacterial culture. 相似文献
5.
Streptococcus pneumoniae is one of the most common causes of bacterial pneumonias in humans. Neutrophil migration into lungs infected with S. pneumoniae is central to the host defense but the mechanisms of neutrophil recruitment, as mediated by S. pneumoniae, into lungs are incompletely understood. Therefore, we have assessed the role of integrin αvβ3 by evaluating its subunit
β3 in a mouse model of lung inflammation induced by S. pneumonia. Integrin subunit β3 knockout (β3-/-) and wild-type (WT) mice were intratracheally instilled with either S. pneumoniae or saline. Other groups of WT mice were treated intraperitoneally with 25 μg or 50 μg of antibody against integrin β3 or
with isotype-matched antibody at 1 h before instillation of S. pneumoniae. Mice were killed 24 h after infection. Flow cytometry confirmed the absence or presence of integrin subunit β3 on peripheral
blood neutrophils in β3-/- or WT mice, respectively. Neutrophil numbers in bronchoalveolar lavage (BAL) from infected β3-/- and WT mice showed no differences. Neutrophil numbers in BAL of infected WT mice treated with β3 antibody were lower compared
with those without antibody but similar to those of mice administered isotype-matched antibody. Many neutrophils were present
in the perivascular spaces of the lungs in β3-/- mice. Lungs from infected β3-/- mice had negligible mitogen-activated protein kinase expression compared with those of infected WT mice. Thus, integrin β3
or its heterodimer αvβ3 is not critical for neutrophil migration into lungs infected with S. pneumoniae. 相似文献
6.
The influence of stream sediment particle size on bacterial abundance and community composition 总被引:1,自引:0,他引:1
Sediment features may play a major role in determining benthic bacterial community structure. In this study, sediment samples
were collected on four dates over the course of a year from a Northeast Ohio stream and fractionated into different particle
size classes. Abundance of bacteria of various taxa on differentially sized sediment fractions was determined using fluorescent
in situ hybridization which relies on taxon-specific oligonucleotide probes that hybridize to rRNA in intact cells. The differences
among the size classes were generally small in comparison to the large seasonal changes observed. These seasonal changes differed
greatly among taxa; for some, peaks in the number of cells hybridizing a particular probe were in the spring (Domain Bacteria,
α-Proteobacteria), while others peaked in the summer/fall (γ-Proteobacteria and the Cytophaga-Flavobacterium). At the species level, the abundances of Burkholderia cepacia and Acinetobacter calcoaceticus were highest in the summer on sediments of all sizes. Seasonal differences appeared to be more of a factor driving community
differences than sediment particle size. 相似文献
7.
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
8.
Temporary rivers are characterized by recurrent dry phases, and global warming will stress their hydrology by amplifying extreme
events. Microbial degradation and transformation of organic matter (OM) in riverbed sediment are key processes with regard
to carbon and nutrient fluxes. In this study, we describe structural and functional changes of benthic microbial communities
in a riverine environment subject to hydrological fluctuation. Sampling was carried out in the outlet section of the Mulargia
River (Sardinia, Italy) under various water regimes, including one flood event. Overall, sediments were characterized by low
bacterial cell abundance (range 0.6–1.8 × 109 cell g−1) as a consequence of their low nutrient and OM concentrations. No major differences were found in the community composition.
Alpha-Proteobacteria dominated during the whole year (range 21–30%) followed by Beta-Proteobacteria, Gamma-Proteobacteria, and Cytophaga-Flavobacteria which always contributed <18%. Planctomycetes and Firmicutes were found in smaller amounts (<7%). In spring, when the highest total organic carbon content was also detected (0.42% w/w),
both bacterial abundance and C production (BCP, 170 nmol C h−1 g−1) reached relatively high values. During the flood event, an increase in BCP and the highest values of community respiration
(CR, 74 nmol C h−1 g−1) were observed. Moreover, most of the extracellular enzyme activities (EEA) changed significantly during the flood. The variation
of the water flow itself can explain part of these changes and other factors also come into play. The presence of different
patterns of functional parameters could suggest that the quality of the OM could be the major driving force in nutrient flux. 相似文献
9.
Analysis of Endophytic Bacterial Communities of Potato by Plating and Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA Based PCR Fragments 总被引:12,自引:0,他引:12
The diversity of endophytic bacterial populations of potato (Solanum tuberosum cv Desirée) was assessed using a combination of dilution plating of plant macerates followed by isolation and characterization
of isolates, and direct PCR-DGGE on the basis of DNA extracted from plants. The culturable endophytic bacterial communities
detected in potato stem bases as well as in roots were in most cases on the order 103 to 105 CFU g−1 of fresh plant tissue. Dilution plating revealed that a range of bacterial types dominated these populations. Dominant isolates
fell into the α and γ subgroups of the Proteobacteria, as well as in the Flavobacterium/Cytophaga group. Different representatives of the Firmicutes were also found. The most frequently isolated strains (>5% of the total) were characterized as different Pseudomonas spp. (including P. aureofaciens, P. corrugata, and P. putida), Agrobacterium radiobacter, Stenotrophomonas maltophilia, and Flavobacterium resinovorans, using fatty acid methyl ester (FAME) analysis and/or sequencing of their partial 16S ribosomal RNA genes. Other Proteobacteria or Firmicutes were also found, albeit infrequently, and mainly in potato stem tissue. The fate of three putative potato endophytes, Stenotrophomonas maltophilia, Bacillus sp., and Sphingomonas paucimobilis, was monitored following their release into potato plants via injection, via root dipping, or via the soil. Following stem
injection, the S. maltophilia and Bacillus inoculants could be tracked over time periods of, respectively, 22 and 1 day(s) by dilution plating as well as via PCR-DGGE.
However, only S. maltophilia was able to colonize, and persist in, plant tissue from soil or dipped roots. S. paucimobilis was never recovered from the plant irrespective of the mode of introduction. The diversity of the indigenous bacterial flora
associated with potato was then monitored via PCR-DGGE. The patterns obtained revealed the existence of bacterial communities
of limited complexity, with communities from potato stems typically differing from those from stem peel and roots. Evidence
was obtained for the endophytic occurrence of a range of organisms falling into the α, β, and γ subgroups of the Proteobacteria as well as in the Firmicutes. Several of the sequences found matched those from isolates, suggesting that the molecular evidence reported culturable organisms.
However, a number of sequences did not have matching sequences from isolates, suggesting that non-culturable or as-yet-uncultured
endophytic organisms were being detected. 相似文献
10.
An DS Cui CH Sung BH Yang HC Kim SC Lee ST Im WT Kim SG 《Applied microbiology and biotechnology》2012,94(3):673-682
The gene encoding an α-l-arabinofuranosidase that could biotransform ginsenoside Rc {3-O-[β-d-glucopyranosyl-(1–2)-β-d-glucopyranosyl]-20-O-[α-l-arabinofuranosyl-(1–6)-β-d-glucopyranosyl]-20(S)-protopanaxadiol} to ginsenoside Rd {3-O-[β-d-glucopyranosyl-(1–2)-β-d-glucopyranosyl]-20-O-β-d-glucopyranosyl-20(S)-protopanaxadiol} was cloned from a soil bacterium, Rhodanobacter ginsenosidimutans strain Gsoil 3054T, and the recombinant enzyme was characterized. The enzyme (AbfA) hydrolyzed the arabinofuranosyl moiety from ginsenoside
Rc and was classified as a family 51 glycoside hydrolase based on amino acid sequence analysis. Recombinant AbfA expressed
in Escherichia coli hydrolyzed non-reducing arabinofuranoside moieties with apparent K
m values of 0.53 ± 0.07 and 0.30 ± 0.07 mM and V
max values of 27.1 ± 1.7 and 49.6 ± 4.1 μmol min−1 mg−1 of protein for p-nitrophenyl-α-l-arabinofuranoside and ginsenoside Rc, respectively. The enzyme exhibited preferential substrate specificity of the exo-type
mode of action towards polyarabinosides or oligoarabinosides. AbfA demonstrated substrate-specific activity for the bioconversion
of ginsenosides, as it hydrolyzed only arabinofuranoside moieties from ginsenoside Rc and its derivatives, and not other sugar
groups. These results are the first report of a glycoside hydrolase family 51 α-l-arabinofuranosidase that can transform ginsenoside Rc to Rd. 相似文献
11.
Microbial Diversity in Sediments of Saline Qinghai Lake, China: Linking Geochemical Controls to Microbial Ecology 总被引:2,自引:0,他引:2
Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial
diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom
of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline
(pH 9.4) and is located on the Qinghai–Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the
core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40–70 mM) and dissolved
organic carbon (1596–5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were ∼2 and <0.5%, respectively.
Acridine orange direct count data indicated that cell numbers decreased from 4 × 109 cells/g at the water–sediment interface to 6× 107 cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore
water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in
the bacterial community with depth. Whereas the α-, β-, and γ-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water–sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but thepresence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and
clone sequences could be grouped inthe Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments.
Acetate-utilizing methanogens were isolated from sediment incubations, and α- and γ-proteobacterial isolates were obtained
from a water sample from the lakebottom (23 m). Our data collectively showed that the observed diversity and shift in the
community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor
and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results
reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments. 相似文献
12.
Isolation of the exoelectrogenic denitrifying bacterium Comamonas denitrificans based on dilution to extinction 总被引:2,自引:0,他引:2
Defeng Xing Shaoan Cheng Bruce E. Logan John M. Regan 《Applied microbiology and biotechnology》2010,85(5):1575-1587
The anode biofilm in a microbial fuel cell (MFC) is composed of diverse populations of bacteria, many of whose capacities
for electricity generation are unknown. To identify functional populations in these exoelectrogenic communities, a culture-dependent
approach based on dilution to extinction was combined with culture-independent community analysis. We analyzed the diversity
and dynamics of microbial communities in single-chamber air-cathode MFCs with different anode surfaces using denaturing gradient
gel electrophoresis based on the 16S rRNA gene. Phylogenetic analyses showed that the bacteria enriched in all reactors belonged
primarily to five phylogenetic groups: Firmicutes, Actinobacteria, α-Proteobacteria, β-Proteobacteria, and γ-Proteobacteria. Dilution-to-extinction experiments further demonstrated that Comamonas denitrificans and Clostridium aminobutyricum were dominant members of the community. A pure culture isolated from an anode biofilm after dilution to extinction was identified
as C. denitrificans DX-4 based on 16S rRNA sequence and physiological and biochemical characterizations. Strain DX-4 was unable to respire using
hydrous Fe(III) oxide but produced 35 mW/m2 using acetate as the electron donor in an MFC. Power generation by the facultative C. denitrificans depends on oxygen and MFC configuration, suggesting that a switch of metabolic pathway occurs for extracellular electron
transfer by this denitrifying bacterium. 相似文献
13.
Archaeal and bacterial communities of heavy metal contaminated acidic waters from zinc mine residues in Sepetiba Bay 总被引:2,自引:0,他引:2
Welington I. Almeida Ricardo P. Vieira Alexander Machado Cardoso Cynthia B. Silveira Rebeca G. Costa Alessandra M. Gonzalez Rodolfo Paranhos João A. Medeiros Flávia A. Freitas Rodolpho M. Albano Orlando B. Martins 《Extremophiles : life under extreme conditions》2009,13(2):263-271
Mining of metallic sulfide ore produces acidic water with high metal concentrations that have harmful consequences for aquatic
life. To understand the composition and structure of microbial communities in acid mine drainage (AMD) waters associated with
Zn mine tailings, molecular diversity of 16S genes was examined using a PCR, cloning, and sequencing approach. A total of
78 operational taxonomic units (OTUs) were obtained from samples collected at five different sites in and around mining residues
in Sepetiba Bay, Brazil. We analyzed metal concentration, physical, chemical, and microbiological parameters related to prokaryotic
diversity in low metal impacted compared to highly polluted environments with Zn at level of gram per liter and Cd–Pb at level
of microgram per liter. Application of molecular methods for community structure analyses showed that Archaea and Bacteria
groups present a phylogenetic relationship with uncultured environmental organisms. Phylogenetic analysis revealed that bacteria
present at the five sites fell into seven known divisions, α-Proteobacteria (13.4%), β-Proteobacteria (16.3%), γ-Proteobacteria (4.3%), Sphingobacteriales (4.3%), Actinobacteria (3.2%) Acidobacteria (2.1%), Cyanobacteria (11.9%), and unclassified bacteria (44.5%). Almost all archaeal clones were related to uncultivated Crenarchaeota species,
which were shared between high impacted and low impacted waters. Rarefaction curves showed that bacterial groups are more
diverse than archaeal groups while the overall prokaryotic biodiversity is lower in high metal impacted environments than
in less polluted habitats. Knowledge of this microbial community structure will help in understanding prokaryotic diversity,
biogeography, and the role of microorganisms in zinc smelting AMD generation and perhaps it may be exploited for environmental
remediation procedures in this area. 相似文献
14.
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
15.
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
16.
Carvalho de Souza A Ganchev DN Snel MM van der Eerden JP Vliegenthart JF Kamerling JP 《Glycoconjugate journal》2009,26(4):457-465
Cell aggregation in the marine sponge Microciona prolifera is mediated by a multimillion molecular-mass aggregation factor, termed MAF. Earlier investigations revealed that the cell
aggregation activity of MAF depends on two functional domains: (i) a Ca2+-independent cell-binding domain and (ii) a Ca2+-dependent proteoglycan self-interaction domain. Structural analysis of involved carbohydrate fragments of the proteoglycan
in the self-association established a sulfated disaccharide β-d-GlcpNAc3S-(1→3)-α-l-Fucp and a pyruvated trisaccharide β-d-Galp4,6(R)Pyr-(1→4)-β-d-GlcpNAc-(1→3)-α-l-Fucp. Recent UV, SPR, and TEM studies, using BSA conjugates and gold nanoparticles of the synthetic sulfated disaccharide, clearly
demonstrated self-recognition on the disaccharide level in the presence of Ca2+-ions. To determine binding forces of the carbohydrate–carbohydrate interactions for both synthetic MAF oligosaccharides,
atomic force microscopy (AFM) studies were carried out. It turned out that, in the presence of Ca2+-ions, the force required to separate the tip and sample coated with a self-assembling monolayer of thiol-spacer-containing
β-d-GlcpNAc-(1→3)-α-l-Fucp-(1→O)(CH2)3S(CH2)6S- was found to be quantized in integer multiples of 30 ± 6 pN. No binding was observed between the two monolayers in the
absence of Ca2+-ions. Cd2+-ions could partially induce the self-interaction. In contrast, similar AFM experiments with thiol-spacer-containing β-d-Galp4,6(R)Pyr-(1→4)-β-d-GlcpNAc-(1→3)-α-l-Fucp-(1→O)(CH2)3S(CH2)6S- did not show a binding in the presence of Ca2+-ions. Also TEM experiments of gold nanoparticles coated with the pyruvated trisaccharide could not make visible aggregation
in the presence of Ca2+-ions. It is suggested that the self-interaction between the sulfated disaccharide fragments is stronger than that between
the pyruvated trisaccharide. 相似文献
17.
N. V. Potekhina G. M. Streshinskaya Yu. I. Kozlova E. B. Kudryashova S. N. Senchenkova A. S. Shashkov L. N. Anan’ina 《Biochemistry. Biokhimii?a》2009,74(12):1368-1374
Cell walls of Bacillus subtilis VKM B-760 and VKM B-764 are characterized by heterogeneous composition of teichoic acids. Polymer I with structure -6)-β-D-Galp-(1→1)-sn-Gro-(3-P-, polymer II with structure -6)-α-D-Glcp-(1→1)-sn-Gro-(3-P-, and a small amount of unsubstituted 1,3-poly(glycerol phosphate) were detected in strain VKM B-760. Strain VKM
B-764 contains an analogous set of teichoic acids, but a characteristic feature of polymer II is the presence of disubstituted
glycerol residue with α-glucopyranose localization in the integral chain at C-1 hydroxyl and β-glucopyranose as a side branch
at C-2 hydroxyl (polymer III): -6)-α-D-Glcp-(1→1)-[β-D-Glcp-(1→2)]-sn-Gro-(3-P-. The structures of polymer I in bacilli and polymer III in Gram-positive bacteria are described for the first time.
Teichoic acids were studied by chemical methods and on the basis of combined analysis of one-dimensional 1H-, 13C-, and 31P-NMR spectra, homonuclear two-dimensional 1H/1H COSY, TOCSY, and ROESY, and heteronuclear two-dimensional 1H/13C gHSQC- and HMQC-TOCSY experiments. Simultaneous presence of several different structure teichoic acids in the bacillus cell
walls as well as chemotaxonomical perspectives of the application of these polymers as species-specific markers for members
of the Bacillus genus is discussed. 相似文献
18.
The glycoside hydrolase family 57 (GH57) contains α-amylase and a few other amylolytic specificities. It counts ~400 members
from Archaea (1/4) and Bacteria (3/4), mostly of extremophilic prokaryotes. Only 17 GH57 enzymes have been biochemically characterized. The main goal of
the present bioinformatics study was to analyze sequences having the clear GH57 α-amylase features. Of the 107 GH57 sequences,
59 were evaluated as α-amylases (containing both GH57 catalytic residues), whereas 48 were assigned as GH57 α-amylase-like
proteins (having a substitution in one or both catalytic residues). Forty-eight of 59 α-amylases were from Archaea, but 42 of 48 α-amylase-like proteins were of bacterial origin. The catalytic residues were substituted in most cases in
Bacteroides and Prevotella by serine (instead of catalytic nucleophile glutamate) and glutamate (instead of proton donor aspartate). The GH57 α-amylase
specificity has thus been evolved and kept enzymatically active mainly in Archaea. 相似文献
19.
NOEs between the β-protons of cysteine residues across disulfide bonds in proteins provide direct information on the connectivities
and conformations of these important cross-links, which are otherwise difficult to investigate. With conventional [U-13C, 15N]-proteins, however, fast spin diffusion processes mediated by strong dipolar interactions between geminal β-protons prohibit the quantitative measurements and thus the analyses of long-range NOEs across disulfide bonds. We describe
a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β-13C; α,β-2H2] Cys and (2R, 3R)-[β-13C; α,β-2H2] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of
the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even
with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at
high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NOE information, the disulfide
bond connectivities can be unambiguously established for proteins with multiple disulfide bonds. In addition, the conformations
around disulfide bonds, namely χ2 and χ3, can be determined based on the precise proton distances of the four β-proton pairs, by quantitative measurements of the
NOEs across the disulfide bonds. The feasibility of this method is demonstrated for bovine pancreatic trypsin inhibitor, which
has three disulfide bonds. 相似文献
20.
Cobucci-Ponzano B Conte F Rossi M Moracci M 《Extremophiles : life under extreme conditions》2008,12(1):61-68
Glycoside hydrolases form hyperthermophilic archaea are interesting model systems for the study of catalysis at high temperatures
and, at the moment, their detailed enzymological characterization is the only approach to define their role in vivo. Family
29 of glycoside hydrolases classification groups α-l-fucosidases involved in a variety of biological events in Bacteria and Eukarya. In Archaea the first α-l-fucosidase was identified in Sulfolobus solfataricus as interrupted gene expressed by programmed −1 frameshifting. In this review, we describe the identification of the catalytic
residues of the archaeal enzyme, by means of the chemical rescue strategy. The intrinsic stability of the hyperthermophilic
enzyme allowed the use of this method, which resulted of general applicability for β and α glycoside hydrolases. In addition,
the presence in the active site of the archaeal enzyme of a triad of catalytic residues is a rather uncommon feature among
the glycoside hydrolases and suggested that in family 29 slightly different catalytic machineries coexist. 相似文献