scholarly journals Annual Variations in the Diversity, Viability, and Origin of Airborne Bacteria

2010 ◽  
Vol 76 (9) ◽  
pp. 3015-3025 ◽  
Author(s):  
Camilla Fahlgren ◽  
Åke Hagström ◽  
Douglas Nilsson ◽  
Ulla Li Zweifel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Seasonal Pattern ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Clone Libraries ◽  
Probable Number ◽  
Annual Variations ◽  
Annual Survey ◽  
Cultured Bacteria

ABSTRACT The presence of bacteria in aerosols has been known for centuries, but information on their identity and role in dispersing microbial traits is still limited. This study monitored the airborne bacterial community during an annual survey using samples collected from a 25-m tower near the Baltic Sea coast. The number of CFU was estimated using agar plates while the most probable number (MPN) of viable bacteria was estimated using dilution-to-extinction culturing assays (DCAs). The MPN and CFU values produced quantitatively similar results, displaying a pronounced seasonal pattern, with the highest numbers in winter. The most dominant bacteria growing in the DCAs all formed colonies on agar plates, were mostly pigmented (80%), and closely resembled (>97%) previously cultured bacteria based on their 16S rRNA gene sequences. 16S rRNA gene clone libraries were constructed on eight occasions during the survey; these revealed a highly diverse community with a few abundant operational taxonomic units (OTUs) and a long tail of rare OTUs. A majority of the cloned sequences (60%) were also most closely related to previously “cultured” bacteria. Thus, both culture-dependent and culture-independent techniques indicated that bacteria able to form colonies on agar plates predominate in the atmosphere. Both the DCAs and clone libraries indicated the dominance of bacteria belonging to the genera Sphingomonas sp. and Pseudomonas sp. on several sampling occasions. Potentially pathogenic strains as well as sequences closely resembling bacteria known to act as ice nuclei were found using both approaches. The origin of the sampled air mass was estimated using backward trajectories, indicating a predominant marine source.

Characterization and Identification of Numerically Abundant Culturable Bacteria from the Anoxic Bulk Soil of Rice Paddy Microcosms

1999 ◽  
Vol 65 (11) ◽  
pp. 5042-5049 ◽  
Author(s):  
Kuk-Jeong Chin ◽  
Dittmar Hahn ◽  
Ulf Hengstmann ◽  
Werner Liesack ◽  
Peter H. Janssen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dry Weight ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Most Probable Number ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Probable Number ◽  
Clostridial Cluster

ABSTRACT Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 × 108 cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4′,6-diamidino-2-phenylindole staining, was 4.8 × 108cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the divisionVerrucomicrobia, theCytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050–5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.

scholarly journals Specific Detection, Isolation, and Characterization of Selected, Previously Uncultured Members of the Freshwater Bacterioplankton Community

2005 ◽  
Vol 71 (10) ◽  
pp. 5908-5919 ◽  
Author(s):  
Frederic Gich ◽  
Karin Schubert ◽  
Alke Bruns ◽  
Herbert Hoffelner ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Light Harvesting Complexes ◽  
Probable Number ◽  
Bacterioplankton Community ◽  
Isolation And Characterization

ABSTRACT High-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. A total of 570 bacterial cultures were obtained by employing the most probable number and MicroDrop techniques. The majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the α-Proteobacteria, β-Proteobacteria, Actinobacteria, Firmicutes, or Flavobacteria-Cytophaga lineage. Correspondingly, the natural bacterioplankton community was analyzed by high-resolution phylogenetic fingerprinting of these five bacterial lineages. 16S rRNA gene fragments were generated for each lineage and subsequently separated by denaturing gradient gel electrophoresis. By the combination of five group-specific PCR protocols, the total number of 16S rRNA gene fingerprints generated from the natural communities was increased sixfold compared to conventional (eubacterial) fingerprinting. Four of the environmental α-Proteobacteria 16S rRNA gene sequences obtained from the natural community were found to be identical to those of bacterial isolates. One of these phylotypes was detected in 14 different cultures and hence represented the most frequently cultured bacterium. Three of these 14 strains were characterized in detail. Their complete 16S rRNA gene sequences showed only 93% similarity to that of Sandaracinobacter sibiricus, the closest relative described so far. The novel phylotype of bacterium is a strict aerobe capable of using numerous organic carbon substrates and contains bacteriochlorophyll a bound to two different photosynthetic light-harvesting complexes. Dot blot hybridization revealed that the strains occur in lakes of different trophic status and constitute up to 2% of the microbial community.

The Diversity of Benthic Microorganisms in Acidic Mine Lake Sediments

2007 ◽  
Vol 20-21 ◽  
pp. 489-492
Author(s):  
Huynh A. Pham ◽  
Carolyn E. Oldham ◽  
Jason J. Plumb
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Lake Sediments ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Benthic Bacteria ◽  
Different Depths

The sediment microbial communities of a disused coal mine lake, Lake Kepwari (pH~4.5-5) were studied to understand how the natural microbial processes in an oligotrophic acidic mine lake system influence the iron and sulphur cycles. Most probable number (MPN) viable counts were used to enumerate the benthic bacteria at different depths. MPN results revealed an abundance of bacteria that were capable of growing in sulphate reducing medium with numbers in the range of 1 × 107 – 1 × 108 cells.g-1 of wet sediment. In contrast, MPN results showed much lower numbers of bacteria that were capable of growing in ferric reducing medium with 1 × 102 – 2 × 103 cells.g-1 of wet sediment detected. Serial decimal dilution cultures were used to isolate pure strains of benthic bacteria. Strains HP1, HP2 and HP3 were isolated from benthic lake sediments at 18 m, 0 m and 10 m water depths respectively. 16S rRNA gene sequence analysis of strain HP1 showed that the strain belonged to the genus Enterobacter, strain HP2 belonged to the Order Rhizobiales and strain HP3 belonged to the sub-order Micrococcineae. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments was used to profile the diversity of the benthic microbial communities at different depths. DGGE profiling of benthic sediments revealed that sediments contained mostly members of the Proteobacteria, Actinobacteria and Firmicutes phyla.

scholarly journals Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Dimethylmalonate

1999 ◽  
Vol 65 (8) ◽  
pp. 3319-3324 ◽  
Author(s):  
Olaf Kniemeyer ◽  
Christina Probian ◽  
Ramon Rosselló-Mora ◽  
Jens Harder
Keyword(s):  
Sewage Sludge ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Quaternary Carbon ◽  
Probable Number ◽  
Gene Similarity

ABSTRACT The microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. Quantitative growth experiments showed a complete mineralization of dimethylmalonate. According to phylogenetic analysis of the complete 16S rRNA genes, two strains isolated from activated sewage sludge were related to the genusParacoccus within the α-Proteobacteria (98.0 and 98.2% 16S rRNA gene similarity to Paracoccus denitrificans T), and three strains isolated from freshwater ditches were affiliated with the β-Proteobacteria (97.4 and 98.3% 16S rRNA gene similarity to Herbaspirillum seropedicae T andAcidovorax facilis T, respectively). Most-probable-number determinations for denitrifying populations in sewage sludge yielded 4.6 × 104dimethylmalonate-utilizing cells ml−1, representing up to 0.4% of the total culturable nitrate-reducing population.

scholarly journals Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent Genomes and Ecophysiologies

2004 ◽  
Vol 70 (8) ◽  
pp. 4831-4839 ◽  
Author(s):  
Elke Jaspers ◽  
Jörg Overmann
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Niche Overlap ◽  
Most Probable Number ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Probable Number ◽  
Internally Transcribed Spacer

ABSTRACT A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. A set of 11 strains of Brevundimonas alba were isolated from a bacterial freshwater community by conventional plating or by using a liquid most-probable-number (MPN) dilution series. These strains had identical 16S rRNA gene sequences and represented the dominant phylotype in the plateable fraction, as well as in the highest positive dilutions of the MPN series. However, internally transcribed spacer and enterobacterial repetitive intergenic consensus PCR fingerprinting analyses, as well as DNA-DNA hybridization analyses, revealed great genetic diversity among the 11 strains. Each strain utilized a specific combination of 59 carbon substrates, and the niche overlap indices were low, suggesting that each strain occupied a different ecological niche. In dialysis cultures incubated in situ, each strain had a different growth rate and cell yield. We thus demonstrated that the B. alba strains represent distinct populations with genetically determined adaptations and probably occupy different ecological niches. Our results have implications for assessment of the diversity and biogeography of bacteria and increase the perception of natural diversity beyond the level of 16S rRNA gene sequences.

scholarly journals Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater

2006 ◽  
Vol 56 (6) ◽  
pp. 1311-1316 ◽  
Author(s):  
Toby D. Allen ◽  
Paul A. Lawson ◽  
Matthew D. Collins ◽  
Enevold Falsen ◽  
Ralph S. Tanner
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Municipal Wastewater ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Probable Number ◽  
Untreated Wastewater ◽  
Treated Effluent ◽  
The Family

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella–Chryseobacterium–Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G+C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4×105 cells ml−1, and untreated wastewater from a second plant yielded an estimated count of 1.4×104 cells ml−1. Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1T (=CCUG 46293T=CIP 108613T=ATCC BAA-825T=DSM 15886T).

scholarly journals Comparative Diversity of Ammonia Oxidizer 16S rRNA Gene Sequences in Native, Tilled, and Successional Soils

1999 ◽  
Vol 65 (7) ◽  
pp. 2994-3000 ◽  
Author(s):  
Mary Ann Bruns ◽  
John R. Stephen ◽  
George A. Kowalchuk ◽  
James I. Prosser ◽  
Eldor A. Paul
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Native Soils

ABSTRACT Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes forNitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospiracluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

scholarly journals Development of a Real-Time PCR Assay for Detection and Quantification of Rhizobium leguminosarum Bacteria and Discrimination between Different Biovars in Zinc-Contaminated Soil

2011 ◽  
Vol 77 (13) ◽  
pp. 4626-4633 ◽  
Author(s):  
Catriona A. Macdonald ◽  
Ian M. Clark ◽  
Penny R. Hirsch ◽  
Fang-Jie Zhao ◽  
Steve P. McGrath
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rhizobium Leguminosarum ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Content Type ◽  
Gene Copies

ABSTRACTPrimers were designed to target 16S rRNA andnodDgenes ofRhizobium leguminosarumfrom DNA extracted from two different soil types contaminated with Zn applied in sewage sludge. Numbers of rhizobia estimated using 16S rRNA gene copy number showed higher abundance than those estimated by bothnodDand the most-probable-number (MPN) enumeration method using a plant trap host. Both 16S rRNA gene copies and the MPN rhizobia declined with increased levels of Zn contamination, as did the abundance of the functional genenodD, providing compelling evidence of a toxic effect of Zn onR. leguminosarumpopulations in the soil. Regression analysis suggested the total Zn concentration in soil as a better predictor of rhizobial numbers than both NH4NO3-extractable and soil solution Zn.R. leguminosarumbv. viciaenodDgene copies were generally less sensitive to Zn thanR. leguminosarumbv. trifoliinodD.The latter were generally below detection limits at Zn levels of >250 mg kg−1. Although there were differences in the actual numbers estimated by each approach, the response to Zn was broadly similar across all methods. These differences were likely to result from the fact that the molecular approaches assess the potential for nodulation while the MPN approach assesses actual nodulation. The results demonstrate that the use of targeted gene probes for assessing environmental perturbations of indigenous soil rhizobial populations may be more sensitive than the conventional plant bioassay and MPN methods.

scholarly journals Microbial Populations Involved in Cycling of Dimethyl Sulfide and Methanethiol in Freshwater Sediments

2001 ◽  
Vol 67 (3) ◽  
pp. 1044-1051 ◽  
Author(s):  
Bart P. Lomans ◽  
Rianne Luderer ◽  
Peter Steenbakkers ◽  
Arjan Pol ◽  
Chris van der Drift ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dimethyl Sulfide ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Mixed Substrates ◽  
Freshwater Sediments ◽  
Probable Number

ABSTRACT Although several microorganisms that produce and degrade methanethiol (MT) and dimethyl sulfide (DMS) have been isolated from various habitats, little is known about the numbers of these microorganisms in situ. This study reports on the identification and quantification of microorganisms involved in the cycling of MT and DMS in freshwater sediments. Sediment incubation studies revealed that the formation of MT and DMS is well balanced with their degradation. MT formation depends on the concentrations of both sulfide and methyl group-donating compounds. A most-probable number (MPN) dilution series with syringate as the growth substrate showed that methylation of sulfide with methyl groups derived from syringate is a commonly occurring process in situ. MT appeared to be primarily degraded by obligately methylotrophic methanogens, which were found in the highest positive dilutions on DMS and mixed substrates (methanol, trimethylamine [TMA], and DMS). Amplified ribosomal DNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis of the total DNA isolated from the sediments and of the DNA isolated from the highest positive dilutions of the MPN series (mixed substrates) revealed that the methanogens that are responsible for the degradation of MT, DMS, methanol, and TMA in situ are all phylogenetically closely related toMethanomethylovorans hollandica. This was confirmed by sequence analysis of the product obtained from a nested PCR developed for the selective amplification of the 16S rRNA gene from M. hollandica. The data from sediment incubation experiments, MPN series, and molecular-genetics detection correlated well and provide convincing evidence for the suggested mechanisms for MT and DMS cycling and the common presence of the DMS-degrading methanogen M. hollandica in freshwater sediments.

scholarly journals Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate

2004 ◽  
Vol 70 (8) ◽  
pp. 4911-4920 ◽  
Author(s):  
Nadia N. North ◽  
Sherry L. Dollhopf ◽  
Lainie Petrie ◽  
Jonathan D. Istok ◽  
David L. Balkwill ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Quantitative Pcr ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clone Libraries ◽  
Subsurface Sediments

ABSTRACT Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the α, β, δ, and γ subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing δ-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the δ-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

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