scholarly journals Nitrogen Cycling and Community Structure of Proteobacterial β-Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments

1999 ◽  
Vol 65 (1) ◽  
pp. 213-220 ◽  
Author(s):  
Allison E. McCaig ◽  
Carol J. Phillips ◽  
John R. Stephen ◽  
George A. Kowalchuk ◽  
S. Martyn Harvey ◽  
...  
Keyword(s):  
Community Structure ◽  
Nitrogen Cycling ◽  
Marine Fish ◽  
Fish Farm ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Probable Number ◽  
Oligonucleotide Hybridization ◽  
Pcr Products

ABSTRACT A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial β-subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marineNitrosomonas group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novelNitrosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.

Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment

1991 ◽  
Vol 37 (11) ◽  
pp. 828-833 ◽  
Author(s):  
W. T. Smorczewski ◽  
E. L. Schmidt
Keyword(s):  
Lake Sediment ◽  
Environmental Changes ◽  
Ammonia Oxidation ◽  
Eutrophic Lake ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Probable Number ◽  
Nitrite Oxidizers

The microbiological and chemical potential for ammonia oxidation in a freshwater, eutrophic lake sediment was examined in relation to environmental changes caused by seasonal, dimictic circulation. Poulations of both ammonia and nitrite oxidizers as estimated by most probable number (MPN) were sustained throughout extended anaerobic summer intervals, with nitrite oxidizers outnumbering ammonia oxidizers by a factor ranging from 3.0 to 8.1. Ammonia oxidation potential on a per cell basis was affected by seasonal changes and was seen to decrease as oxygen was removed from the sediments. Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira. These strains did not react with known ammonia-oxidizer serotypes and, therefore, extend the serological diversity of this group of bacteria. An immunofluorescence analysis of MPN tubes from sediment collected during a period of lake stratification revealed progressive changes in the diversity of the ammonia-oxidizer population. The genera Nitrosomonas, Nitrosolobus, and Nitrosospira, including the novel serotype of Nitrosospira isolated from the sediment a year earlier, were found to coexist in well-oxygenated sediment. This diversity was seen to disappear, with Nistrosomonas surviving, as anaerobic conditions persisted. Key words: ammonia oxidizers, lake sediments, nitrifiers, nitrification.

scholarly journals Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

1999 ◽  
Vol 65 (2) ◽  
pp. 396-403 ◽  
Author(s):  
George A. Kowalchuk ◽  
Zinaida S. Naoumenko ◽  
Piet J. L. Derikx ◽  
Andreas Felske ◽  
John R. Stephen ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Transformations ◽  
Rt Pcr ◽  
Gene Encoding ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Almost All

ABSTRACT Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteriain a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms.

Microbiological aspects of ammonia oxidation of swine waste

1991 ◽  
Vol 37 (12) ◽  
pp. 918-923 ◽  
Author(s):  
S. St-Arnaud ◽  
J. -G. Bisaillon ◽  
R. Beaudet
Keyword(s):  
Ammonia Oxidation ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Swine Waste ◽  
Anaerobic Conditions ◽  
Rotating Biological Contactor ◽  
Probable Number ◽  
Inorganic Medium ◽  
Number Of Cells ◽  
Microbiological Aspects

Ammonia-oxidizing bacteria were present at 102 MPN/mL (most probable number per millilitre) in swine waste, and they were outnumbered by a factor of 105 by the heterotrophs of the indigenous flora. To study these ammonia-oxidizing bacteria we attempted to isolate them in pure culture. We succeeded in increasing the concentration of these bacteria by successive transfers to an inorganic medium, but the heterotrophs were always dominant. To overcome this problem Nitrosomonas europaea ATCC 19718 was adapted to grow in stabilized swine waste. With this adapted strain it was shown that the number of cells inoculated into swine waste rapidly decreased both under the aerobic conditions used to oxidize the organic matter of swine waste and under the anaerobic conditions found in stored swine waste. Ammonia oxidation was delayed when adapted N. europaea was inoculated into a partially stabilized swine waste as compared with results in a completely stabilized waste. A biofilm of 107 MPN/cm2 of N. europaea was developed after 114 days of incubation at 29 °C on polyvinyl chloride discs covered with geotextile in a rotating biological contactor using an inorganic medium. This biofilm was gradually adapted to stabilized swine waste and the rate of disappearance of ammonia reached 270 mg∙L−1∙day−1 in the compartment of the reactor containing 2.5 L of waste. Key words: amonia-oxidizing bacteria, swine waste, ammonia oxidation, biofilm, most probable number.

scholarly journals Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures

2003 ◽  
Vol 69 (10) ◽  
pp. 6152-6164 ◽  
Author(s):  
Sharon Avrahami ◽  
Ralf Conrad
Keyword(s):  
Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Change ◽  
Effect Of Temperature ◽  
Ammonia Oxidizer ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Moist Soil ◽  
Α Subunit ◽  
Mean Temperature

ABSTRACT The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the α subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer.

scholarly journals Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

2000 ◽  
Vol 66 (12) ◽  
pp. 5410-5418 ◽  
Author(s):  
Carol J. Phillips ◽  
Dave Harris ◽  
Sherry L. Dollhopf ◽  
Katherine L. Gross ◽  
James I. Prosser ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Deciduous Forest ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizers ◽  
Probable Number ◽  
Gradient Gel Electrophoresis ◽  
And Function

ABSTRACT The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4 +-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.

Examination of an acid forest soil for ammonia- and nitrite-oxidizing autotrophic bacteria

1984 ◽  
Vol 30 (9) ◽  
pp. 1125-1132 ◽  
Author(s):  
T. R. Hankinson ◽  
E. L. Schmidt
Keyword(s):  
Forest Soil ◽  
Ammonia Oxidation ◽  
Acid Soil ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizers ◽  
Nitrite Oxidation ◽  
Probable Number ◽  
Acid Forest Soil ◽  
Nitrite Oxidizers

An acid forest soil (pH 3.9 – 4.4) from an undisturbed mixed oak stand in southern Indiana was examined for the occurrence of ammonia- and nitrite- oxidizing chemoautotrophs. Populations of both nitrifiers were detected in pH 7 most-probable-number (MPN) autotrophic media, and a Nitrosospira was isolated from highest dilution ammonia oxidizer MPN tubes. Populations of nitrite oxidizers were 10 to 1000 times higher than those of ammonia oxidizers. In pH 4.0 MPN media, ammonia oxidation was slight and unsustainable on 10% transfer to fresh medium, whereas nitrite oxidation was vigorous and sustainable. In pure culture the Nitrosospira isolate (Np IO1a) was completely inhibited by nitrapyrin at 5 μg mL−1, tolerant of 1.0 and 10.0 mM chlorate, and capable of growth only at pH 6.2 and above. Fluorescent antibodies raised against Np IO1a were used to confirm the predominance of Np IO1a in all MPN series examined. These results suggest that autotrophic ammonia oxidizers may be restricted to circumneutral microsites in this acid soil, whereas autotrophic nitrite oxidizers may not be limited to such sites.

scholarly journals Βιοαντιδραστήρες μεμβρανών για την επεξεργασία βιομηχανικών λυμάτων

2014 ◽  
Author(s):  
Παναγιώτα Μπαμπατσούλη
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Probable Number

Στο α μέρος της παρούσας διατριβής μελετάται μια πιλοτική μονάδα βιολογικού καθαρισμού με βιοαντιδραστήρα μεμβρανών, η οποία επεξεργάζεται τα βιομηχανικά απόβλητα που εισέρχονται στις εγκαταστάσεις του βιολογικού της ΒΙ.ΠΕ Ηρακλείου Κρήτης, χωρίς καμμία προεπεξεργασία, πέραν από αυτή της εσχάρωσης. Το συγκεκριμένο απόβλητο χαρακτηρίζεται κυρίως από το πολύ υψηλό οργανικό φορτίo που περιέχει και τις υψηλές διακυμάνσεις στη σύστασή του. Οι αναλύσεις που πραγματοποιήθηκαν κατά τη διάρκεια της διατριβής στο συγκεκριμένο σύστημα αφορούσαν α) την εξέταση της επίδρασης του χρόνου παραμονής της λάσπης στην ποιότητα της εκροής β) τον προσδιορισμό των διαλυτών και δεσμευμένων εξωκυτταρικών πολυμερών που παράγονται στο σύστημα με στόχο την διερεύνηση της επίδρασης του χρόνου παραμονής της λάσπης στην έμφραξη των μεμβρανών και γ) την εξέταση της επίδρασης του υδραυλικού χρόνου παραμονής τόσο στην ποιότητα εξόδου της εκροής, όσο και στη συσσώρευση των εξωκυτταρικών πολυμερών ενώσεων και των διαλυτών μικροβιακών προϊόντων, σε σταθερό χρόνο παραμονής της λάσπης.Επιπλέον στα πλαίσια αυτής της διατριβής και στα ευρύτερα πλαίσια του όρου ‘βιοαντιδραστήρες μεμβρανών’ στο β μέρος εξετάστηκε ένας αντιδραστήρας προσκολλημένης βιομάζας χρησιμοποιώντας ως μέσο ανάπτυξης των μικροοργανισμών ένα πατενταρισμένο ύφασμα με στόχο τη μελέτη της επεξεργασίας ενός συνθετικού αποβλήτου που προσομοιώνει το ‘βιομηχανικό’ απόβλητο που προέρχεται από την έξοδο θαλασσινών υδατοκαλλιεργειών. Με την πάροδο του χρόνου αναπτύχθηκαν βακτήρια πάνω στο ύφασμα του αντιδραστήρα και κατόπιν πραγματοποιήθηκε ο εμβολιασμός του συστήματος με συγκεκριμένο γένος μικροαλγών για την αποτελεσματικότερη λειτουργία του. Οι αναλύσεις οι οποίες πραγματοποιήθηκαν στο συγκεκριμένο σύστημα είχαν ως στόχο: α) τον προσδιορισμό του βέλτιστου χρόνου λειτουργίας της αντλίας του αντιδραστήρα β) την περιγραφή της μικροβιακής κοινότητας που αποτελούσε το βιοφίλμ που αναπτύχθηκε στο ύφασμα του αντιδραστήρα και που προσδιορίστηκε συγκεκριμένα με τη μέθοδο του Pyrosequencing. γ) τον προσδιορισμό του αριθμού των συνολικών κυττάρων των μικροαλγών και των βακτηρίων ανά τετραγωνικό εκατοστό βιοφίλμ που εκτιμήθηκε με βάση τον αλγόριθμο του πιο πιθανού αριθμού (Most Probable Number - MPN) δ) την αποδοτικότητα του συστήματος (όσον αφορά τις απομακρύνσεις οργανικού υλικού, αζώτου και φωσφόρου) σε διάφορες αναλογίες άνθρακα προς άζωτο του τροφοδοτούμενου αποβλήτου ε) την εξέταση της σταθερότητας της βακτηριακής κοινότητας μέσω της τεχνικής της ηλεκροφόρησης σε πολυακρυλαμίδη σε διαβάθμιση αποδιατακτικών μέσων (DGGE) στ) τη σύνδεση συγκεκριμένων ομάδων μικροοργανισμών με την επεξεργασία του αποβλήτου. Η ποσοτικοποίηση του αριθμού γονιδίων πραγματοποιήθηκε με την τεχνική της Real-Time PCR. Συγκεκριμένα πραγματοποιήθηκε ο πολλαπλασιασμός των οξειδωτών αμμωνίας για τα αρχαία (AOA- ammonia oxidizing archaeal) και τα βακτήρια (AOB- ammonia Oxidizing Bacteria) (γονίδιο amoΑ), καθώς και ο πολλαπλασιασμός των γονιδίων απονιτροποίησης nirK, nirS, and nosZ.

Linking microbial community structure to pollution: Biolog-substrate utilization in and near a landfill leachate plume

2000 ◽  
Vol 41 (12) ◽  
pp. 47-53 ◽  
Author(s):  
W. F. Rüling ◽  
B. M. van Breukelen ◽  
M. Braster ◽  
H. W. van Verseveld
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Functional Diversity ◽  
Microbial Community Structure ◽  
Landfill Leachate ◽  
Substrate Utilization ◽  
Most Probable Number ◽  
Probable Number ◽  
Leachate Plume

Previously, we observed that microbial community structure and functional diversity in aquifers might be enhanced by landfill leachate infiltration. To study this hypothesis, groundwater samples were taken near the Banisveld landfill, The Netherlands. Based on hydrochemical parameters, the samples clustered into two groups. One group corresponded to polluted samples from the plume of landfill leachate and the second group to clean samples from outside the plume. Most Probable Number-Biolog was used to select Eco Biolog plates with similar inoculum densities. Analysis of substrate utilization profiles of these plates revealed that anaerobic microbial communities in polluted samples clustered separately from those in clean samples. Especially substrates containing an aromatic nucleus were more utilized by microbial communities in the leachate plume. Both substrate richness and functional diversity were significantly enhanced in the plume of pollution. This study shows that community-level physiological profiling is a useful and simple tool to distinguish between anaerobic microbial communities in and near a landfill leachate plume.

Enrichment of nitrifying microbial communities from shrimp farms and commercial inocula

2003 ◽  
Vol 48 (8) ◽  
pp. 143-150 ◽  
Author(s):  
C. Paungfoo ◽  
P. Prasertsan ◽  
N. Intrasungkha ◽  
L.L. Blackall ◽  
R. Bhamidimarri
Keyword(s):  
In Situ Hybridisation ◽  
Ammonia Removal ◽  
Microbial Consortia ◽  
Nitrifying Bacteria ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Fluorescence In Situ Hybridisation ◽  
Probable Number ◽  
Shrimp Farm ◽  
Commercial Seed

Nitrifying bacteria were selected from shrimp farm water and sediment (ÒnaturalÓ seed) in Thailand and from commercial seed cultures. The microbial consortia from each source giving the best ammonia removal during batch culture pre-enrichments were used as inocula for two sequencing batch reactors (SBRs). Nitrifiers were cultivated in the SBRs with 100 mg NH4-N/l and artificial wastewater containing 25 ppt salinity. The two SBRs were operated at a 7 d hydraulic retention time (HRT) for 77 d after which the HRT was reduced to 3.5 d. The amounts of ammonia removed from the influent by microorganisms sourced from the natural seed were 85% and 92% for the 7 d HRT and the 3.5 d HRT, respectively. The ammonia removals of microbial consortia from the commercial seed were 71% and 83% for these HRTs respectively. The quantity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was determined in the SBRs using the most probable number (MPN) technique. Both AOB and NOB increased in number over the long-term operation of both SBRs. According to quantitative fluorescence in situ hybridisation (FISH) probing, AOB from the natural seed and commercial seed comprised 21 ± 2% and 30 ± 2%, respectively of all bacteria. NOB could not be detected with currently-reported FISH probes, suggesting that novel NOB were enriched from both sources. Taken collectively, the results from this study provide an indication that the nitrifiers from shrimp farm sources are more effective at ammonia removal than those from commercial seed cultures.

Sign in / Sign up

Export Citation Format

Share Document