1
|
Perry MJ. A 50-Year Journey from Phosphate to Autonomous Underwater Vehicles. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:1-22. [PMID: 31525127 DOI: 10.1146/annurev-marine-010419-010945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This narrative is a personal account of my evolution as a student of phytoplankton and the ocean. Initially I focused on phytoplankton nutrient physiology and uptake, later switching to photosynthetic physiology. Better models of photosynthesis naturally require a better understanding of spectral underwater light fields and absorption coefficients, which precipitated my involvement in the nascent field of bio-optical oceanography. Establishment of the now 34-year-old summer graduate course in ocean optics, which continues to attract students from around the globe, is a legacy of my jumping into optics. The importance of social interactions in advancing science cannot be underestimated; a prime example is how a TGIF gathering led to my immersion in the world of autonomous underwater vehicles for the past two decades of my career. Working with people who you like and respect is also critical; I believe collegial friendship played a major role in the great success of the 2008 North Atlantic Bloom Experiment.
Collapse
Affiliation(s)
- Mary Jane Perry
- School of Marine Sciences, University of Maine, Orono, Maine 04469, USA;
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
2
|
Haikara A. Detection ofPectinatusContaminants in Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-43-0043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Auli Haikara
- VTT, Biotechnical Laboratory, SF-02150 Espoo 15, Finland
| |
Collapse
|
3
|
Gares SL, Whiting MS, Ingledew WM, Ziola B. Detection and Identification ofPectinatus CerevisiiphilusUsing Surface-Reactive Monoclonal Antibodies in a Membrane Filter-Based Fluoroimmunoassay. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-51-0158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Sheryl L. Gares
- Department of Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W0
| | - Michael S. Whiting
- Department of Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W0
| | - W. M. Ingledew
- Applied Microbiology and Food Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W0
| | - Barry Ziola
- Department of Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W0
| |
Collapse
|
4
|
Meng J, Li J, Li J, Wang C, Deng K, Sun K. Effect of seed sludge on nitrogen removal in a novel upflow microaerobic sludge reactor for treating piggery wastewater. BIORESOURCE TECHNOLOGY 2016; 216:19-27. [PMID: 27218438 DOI: 10.1016/j.biortech.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/08/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Anaerobic activated sludge (AnaS) and aerobic activated sludge (AerS) were used to start up a novel upflow microaerobic sludge reactor (UMSR), respectively, and the nitrogen removal in the two reactors were evaluated when treating low C/N ratio manure-free piggery wastewater with a COD/TN ration of about 0.85. With the same hydraulic retention time 8h and TN loading rate (NLR) 0.42kg/(m(3)d), the UMSR (R2) inoculated with AerS could reach its steady state earlier and obtained a better TN removal than that in the UMSR (R1) inoculated with AnaS. However, the accumulated AnaS made R1 show a better capability in bearing shock load and demonstrated an excellent NH4(+)-N and TN removal with a NLR as high as 1.07kg/(m(3)d). Microbial community structure of the accumulated AerS and AnaS were observable different. The decreased proportion of nitrifiers restricted the ammonium oxidation in R2, and resulting in a decrease in TN removal.
Collapse
Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jiuling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| |
Collapse
|
5
|
Li J, Meng J, Li J, Wang C, Deng K, Sun K, Buelna G. The effect and biological mechanism of COD/TN ratio on nitrogen removal in a novel upflow microaerobic sludge reactor treating manure-free piggery wastewater. BIORESOURCE TECHNOLOGY 2016; 209:360-368. [PMID: 26972024 DOI: 10.1016/j.biortech.2016.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
A novel upflow microaerobic sludge reactor (UMSR) was constructed to treat manure-free piggery wastewater with high NH4(+)-N concentration and low COD/TN ratio, and the effect and biological mechanism of COD/TN ratio on nitrogen removal were investigated at a constant hydraulic retention time of 8h and 35°C. The results showed that the UMSR could treat the wastewater with a better synchronous removal of COD, NH4(+)-N and TN. The microaerobic UMSR allowed nitrifiers, and heterotrophic and autotrophic denitrifiers to thrive in the flocs, revealing a multiple nitrogen removal mechanism in the reactor. Both the nitrifiers and denitrifiers would be restricted by an influent COD/TN ratio more than 0.82, resulting in a decrease of TN removal in the UMSR. To get a TN removal over 80% with a TN load removal above 0.86kg/(m(3)·d) in the UMSR, the influent COD/TN ratio should be less than 0.70.
Collapse
Affiliation(s)
- Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jiuling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Gerardo Buelna
- Centre de Recherche Industrielle du Québec, 333 Franquet, Québec G1P 4C7, Canada
| |
Collapse
|
6
|
Verhagen FJ, Duyts H, Laanbroek HJ. Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Continuously Percolated Soil Columns. Appl Environ Microbiol 2010; 58:3303-11. [PMID: 16348787 PMCID: PMC183095 DOI: 10.1128/aem.58.10.3303-3311.1992] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the absence of nitrate formation in grassland soils rich in organic matter has often been reported, low numbers of nitrifying bacteria are still found in these soils. To obtain more insight into these observations, we studied the competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea and the heterotrophic species Arthrobacter globiformis in the presence of Nitrobacter winogradskyi with soil columns containing calcareous sandy soil. The soil columns were percolated continuously at a dilution rate of 0.007 h, based on liquid volumes, with medium containing 5 mM ammonium and different amounts of glucose ranging from 0 to 12 mM.A. globiformis was the most competitive organism for limiting amounts of ammonium. The numbers of N. europaea and N. winogradskyi cells were lower at higher glucose concentrations, and the potential ammonium-oxidizing activities in the uppermost 3 cm of the soil columns were nonexistent when at least 10 mM glucose was present in the reservoir, although 10 nitrifying cells per g of dry soil were still present. This result demonstrated that there was no correlation between the numbers of nitrifying bacteria and their activities. The numbers and activities of N. winogradskyi cells decreased less than those of N. europaea cells in all layers of the soil columns, probably because of heterotrophic growth of the nitrite-oxidizing bacteria on organic substrates excreted by the heterotrophic bacteria or because of nitrate reduction at reduced oxygen concentrations by the nitrite-oxidizing bacteria. Our conclusion was that the nitrifying bacteria were less competitive than the heterotrophic bacteria for ammonium in soil columns but that they survived as viable inactive cells. Inactive nitrifying bacteria may also be found in the rhizosphere of grassland plants, which is rich in organic carbon. They are possibly reactivated during periods of net mineralization.
Collapse
Affiliation(s)
- F J Verhagen
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
| | | | | |
Collapse
|
7
|
Campbell L, Carpenter EJ, Iacono VJ. Identification and enumeration of marine chroococcoid cyanobacteria by immunofluorescence. Appl Environ Microbiol 2010; 46:553-9. [PMID: 16346382 PMCID: PMC239315 DOI: 10.1128/aem.46.3.553-559.1983] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used an indirect immunofluorescence technique to permit the identification and enumeration of individual or closely related strains of chroococcoid cyanobacteria of the general Synechococcus and Synechocystis in natural seawater samples. Antisera directed against each of five strains (two phycoerythrin-containing Synechococcus strains, two phycocyanin-containing Synechococcus strains, and one Synechocystis strain) were produced and tested for cross-reactions with cultures of a variety of cyanobacteria and representatives of other algae and bacteria. Each antiserum was relatively specific. The observed cross-reactions occurred between strains that were isolated from similar oceanic environments. We were able, therefore, to apply this technique to field samples. Preliminary results for April to December 1982 in Great South Bay, New York, show that Synechocystis populations are present only during spring and summer, phycocyanin-containing Synechococcus strains are only a minor component in the spring and summer, and phycoerythrin-containing Synechococcus populations become significant in summer and remain so until late fall or winter.
Collapse
Affiliation(s)
- L Campbell
- Marine Sciences Research Center and Department of Periodontics, State University of New York at Stony Brook, Stony Brook, New York 11794
| | | | | |
Collapse
|
8
|
Dahle AB, Laake M. Diversity dynamics of marine bacteria studied by immunofluorescent staining on membrane filters. Appl Environ Microbiol 2010; 43:169-76. [PMID: 16345920 PMCID: PMC241797 DOI: 10.1128/aem.43.1.169-176.1982] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Of 34 strains of marine bacteria isolated on a general seawater medium, 5 were selected for detailed studies of their population dynamics in the plankton. The isolates were characterized as Aeromonas sp., Chromobacterium cf. lividum, Vibrio sp., and two Pseudomonas spp. Specific antibodies were produced by immunization of rabbits, and bacterial cells were stained on black Uni-Pore membrane filters by an indirect immunofluorescent staining procedure. The method proved to be very specific and practical for use in a large-scale field sampling program. Growth of all five isolates was stimulated by high values for net primary production, chlorophyll a, and dissolved organic carbon. Calculation of a diversity index based on specific and total counts is proposed as a way of characterizing the dynamics of organotrophic bacterial populations in the sea.
Collapse
Affiliation(s)
- A B Dahle
- Institute of Microbiology and Plant Physiology, University of Bergen, Bergen, Norway
| | | |
Collapse
|
9
|
Ward BB, Carlucci AF. Marine ammonia- and nitrite-oxidizing bacteria: serological diversity determined by immunofluorescence in culture and in the environment. Appl Environ Microbiol 2010; 50:194-201. [PMID: 16346845 PMCID: PMC238603 DOI: 10.1128/aem.50.2.194-201.1985] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Immunofluorescence assays for marine ammonium- and nitrite-oxidizing bacteria were used to assess the diversity of nitrifying bacteria isolated from marine environments. The antisera show relatively broad specificity, in that each reacts with several strains of the same physiological type as the strain to which the antiserum was prepared. The antisera do not, however, react with any strains of differing physiological type. Seventy percent of the 30 unidentified ammonium-oxidizing isolates tested reacted with one or both of the antisera produced to marine ammonium-oxidizing strains, and 8 of the 9 unidentified nitrite-oxidizing strains tested reacted with 1 or more of the 3 nitrite oxidizer antisera used. Ammonium- and nitrite-oxidizing bacteria were enumerated in samples taken in a depth profile (to 750 m) in the Southern California Bight by immunofluorescence assays for two ammonium oxidizers and two nitrite oxidizers. Average abundances of the two types of nitrifiers were 3.5 x 10 and 2.8 x 10 cells liter, respectively. Nitrifiers constitute 0.1 to 0.8% of the total bacterial population in these samples.
Collapse
Affiliation(s)
- B B Ward
- Institute of Marine Resources, A-018, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093
| | | |
Collapse
|
10
|
Saraswat N, Alleman JE, Smith TJ. Enzyme Immunoassay Detection of Nitrosomonas europaea. Appl Environ Microbiol 2010; 60:1969-73. [PMID: 16349287 PMCID: PMC201588 DOI: 10.1128/aem.60.6.1969-1973.1994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An exploratory effort to selectively detect the presence of a nitrifying bacterium, Nitrosomonas europaea, successfully demonstrated the fundamental utility of an enzyme-based immunoassay protocol. The applied polyclonal antibody test seemingly offered a marked improvement over the available analytical options, including plating, activity, and fluorescence immunoassay techniques. Following an initial purification step to enhance overall specificity, this procedure had an apparent lower limit of detection of approximately 5 x 10 cells per ml. Tests conducted with activated sludge samples exhibited a distinct difference between nitrifying and nonnitrifying mixed liquors, although the highest Nitrosomonas levels observed (i.e., at 1 to 2% of the overall viable cell density) were relatively close to the latter detection boundary.
Collapse
Affiliation(s)
- N Saraswat
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907
| | | | | |
Collapse
|
11
|
Boer SD. Enumeration of two competingErwinia carotovorapopulations in potato tubers by a membrane filter-immunofluorescence procedure. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1984.tb01418.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Ward BB, Martino DP, Diaz MC, Joye SB. Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences. Appl Environ Microbiol 2000; 66:2873-81. [PMID: 10877781 PMCID: PMC92086 DOI: 10.1128/aem.66.7.2873-2881.2000] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/1999] [Accepted: 05/02/2000] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples.
Collapse
Affiliation(s)
- B B Ward
- Institute of Marine Sciences, University of California, Santa Cruz, California, USA.
| | | | | | | |
Collapse
|
13
|
ARAKI N, YAZAWA K, HARADA H. Quantitative Monitoring of Ammonia Oxidizing Bacteria in PVA-immobilized Pellets by Fluorescent in situ Hybridization(FISH). ACTA ACUST UNITED AC 1999. [DOI: 10.2965/jswe.22.600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
14
|
Bauer-Kreisel P, Eisenbeis M, Scholz-Muramatsu H. Quantification of Dehalospirillum multivorans in Mixed-Culture Biofilms with an Enzyme-Linked Immunosorbent Assay. Appl Environ Microbiol 1996; 62:3050-2. [PMID: 16535389 PMCID: PMC1388927 DOI: 10.1128/aem.62.8.3050-3052.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fast, highly selective and sensitive method to quantify specific biomasses in mixed-culture biofilms is described. It consists of detachment of a biofilm from its support material, resolution of the detached biofilm flocs in order to separate the enclosed cells and antigens, and quantification of specific biomass by an enzyme-linked immunosorbent assay.
Collapse
|
15
|
Zaccone R, Caruso G, Azzaro M. Detection of Nitrosococcus oceanus in a Mediterranean lagoon by immunofluorescence. THE JOURNAL OF APPLIED BACTERIOLOGY 1996; 80:611-6. [PMID: 8698662 DOI: 10.1111/j.1365-2672.1996.tb03265.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The autotrophic ammonium-oxidizing bacterium Nitrosococcus oceanus was studied in the brackish lake of Ganzirri by cultural and immunofluorescent methods. The preparation of the specific antiserum in rabbits is reported. The polyclonal antiserum for Nitrosococcus oceanus cross-reacted with other ammonia oxidizing strains, but not with other marine bacteria. Temporal changes were determined by taking monthly water samples from a station 6 m deep and the distribution in sediments was investigated in four stations. Isolation of a strain of Nitrosococcus sp. was obtained from a sediment sample collected in December. The abundance of Nitrosococcus spp. bacteria correlated positively with particulate organic carbon (POC), particulate organic nitrogen (PON), temperature and total bacteria, whereas there was a negative relationship with oxygen tension. No correlation was found between immunofluorescent and MPN counts of Nitrosococcus spp. bacteria.
Collapse
Affiliation(s)
- R Zaccone
- Istituto Sperimentale Talassografico-CNR, Messina, Italy
| | | | | |
Collapse
|
16
|
Voytek MA, Ward BB. Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR. Appl Environ Microbiol 1995; 61:1444-50. [PMID: 7538277 PMCID: PMC167402 DOI: 10.1128/aem.61.4.1444-1450.1995] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The PCR was used as the basis for the development of a sensitive and specific assay for the detection of ammonium-oxidizing bacteria belonging to the beta-subclass of the class Proteobacteria. PCR primers were selected on the basis of nucleic acid sequence data available for seven species of nitrifiers in this subclass. The specificity of the ammonium oxidizer primers was evaluated by testing known strains of nitrifiers, several serotyped environmental nitrifier isolates, and other members of the Proteobacteria, including four very closely related, nonnitrifying species (as determined by rRNA sequence analysis). DNA extracts from 19 bacterio-plankton samples collected from Lake Bonney, Antarctica, and the Southern California Bight were assayed for the presence of ammonium oxidizers. By using a two-stage amplification procedure, ammonium oxidizers were detected in samples collected from both sites. Chemical data collected simultaneously support the occurrence of nitrification and the presence of nitrifiers. This is the first report describing PCR primers specific for ammonium-oxidizing bacteria and the successful amplification of nitrifier genes coding for rRNA from DNA extracts from natural samples. This application of PCR is of particular importance for the detection and study of microbes, such as autotrophic nitrifiers, which are difficult or impossible to isolate from indigenous microbial communities.
Collapse
Affiliation(s)
- M A Voytek
- Marine Sciences Program, University of California, Santa Cruz 95064, USA
| | | |
Collapse
|
17
|
Wagner M, Rath G, Amann R, Koops HP, Schleifer KH. In situ Identification of Ammonia-oxidizing Bacteria. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80396-6] [Citation(s) in RCA: 371] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Verhagen FJ, Duyts H, Laanbroek HJ. Effects of Grazing by Flagellates on Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Soil Columns. Appl Environ Microbiol 1993; 59:2099-106. [PMID: 16348988 PMCID: PMC182242 DOI: 10.1128/aem.59.7.2099-2106.1993] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enhanced mineralization of immobilized nitrogen by bacteriophagous protozoa has been thought to favor the nitrification process in soils in which nitrifying bacteria must compete with heterotrophic bacteria for the available ammonium. To obtain more insight into this process, the influence of grazing by the flagellate
Adriamonas peritocrescens
on the competition for ammonium between the chemolithotrophic species
Nitrosomonas europaea
and the heterotrophic species
Arthrobacter globiformis
in the presence of
Nitrobacter winogradskyi
was studied in soil columns, which were continuously percolated with media containing 5 mM ammonium and different amounts of glucose at a dilution rate of 0.007 h
-1
(liquid volumes).
A. globiformis
won the competition for ammonium. The grazing activities of the flagellates had two prominent effects on the competition between
N. europaea
and
A. globiformis
. First, the distribution of ammonium over the profile of the soil columns was more uniform in the presence of flagellates than in their absence. In the absence of flagellates, relatively high amounts of ammonium accumulated in the upper layer (0 to 3 cm), whereas in the underlying layers the ammonium concentrations were low. In the presence of flagellates, however, considerable amounts of ammonium were found in the lower layers, whereas less ammonium accumulated in the upper layer. Second, the potential ammonium-oxidizing activity of
N. europaea
was stimulated in the presence of flagellates. The numbers of
N. europaea
at different glucose concentrations in the presence of flagellates were comparable to those in the absence of protozoa. However, in the presence of flagellates, the potential ammonium-oxidizing activities were four to five times greater than those in the absence of protozoa.
Collapse
Affiliation(s)
- F J Verhagen
- Department of Soil Biology, Centre for Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 40, 6666 ZG Heteren, The Netherlands
| | | | | |
Collapse
|
19
|
Ward BB, Cockcroft AR. Immunofluorescence detection of the denitrifying strain Pseudomonas stutzeri (ATCC 14405) in seawater and intertidal sediment environments. MICROBIAL ECOLOGY 1993; 25:233-246. [PMID: 24189920 DOI: 10.1007/bf00171890] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/1992] [Revised: 01/19/1993] [Indexed: 06/02/2023]
Abstract
A strain-specific immunofluorescence assay for enumeration of a marine denitrifying bacterium was developed and applied in the marine environment. The polyclonal antiserum for Pseudomonas stutzeri (ATCC 14405) did not react with other pseudomonads, other heterotrophs, or autotrophic nitrifying strains. The abundance of P. stutzeri in the shallow water column of Monterey Bay was less than 0.1% of the total bacterial abundance and decreased with depth, whereas the total bacterial abundance was variable and nearly constant with depth. P. stutzeri was also detected in the sediments of a microbial mat from Tomales Bay. The relatively low contribution of P. stutzeri to the total bacterial abundance in both environments implies that it is not a major component of the heterotrophic assemblage. This conclusion appears to hold for most other strains for which specific assays have been applied in the marine environment. The isolation of several different denitrifying strains from local marine environments implies that the culturable population is quite diverse, even in the absence of different selective enrichment media. Thus, strain specific immunofluorescence is of limited use in quantifying functional groups of bacteria. Conversely, they provide specific information on the diversity of natural populations and their relation to culturable strains.
Collapse
Affiliation(s)
- B B Ward
- Institute of Marine Sciences, University of California, 95064, Santa Cruz, California, USA
| | | |
Collapse
|
20
|
Verhagen FJ, Laanbroek HJ. Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats. Appl Environ Microbiol 1991; 57:3255-63. [PMID: 16348588 PMCID: PMC183957 DOI: 10.1128/aem.57.11.3255-3263.1991] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The absence of nitrification in soils rich in organic matter has often been reported. Therefore, competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species
Nitrosomonas europaea
and the heterotrophic species
Arthrobacter globiformis
was studied in the presence of
Nitrobacter winogradskyi
in continuous cultures at dilution rates of 0.004 and 0.01 h
−1
. Ammonium limitation of
A. globiformis
was achieved by increasing the glucose concentration in the reservoir stepwise from 0 to 5 mM while maintaining the ammonium concentration at 2 mM. The numbers of
N. europaea
and
N. winogradskyi
cells decreased as the numbers of heterotrophic bacteria rose with increasing glucose concentrations for both dilution rates. Critical carbon-to-nitrogen ratios of 11.6 and 9.6 were determined for the dilution rates of 0.004 and 0.01 h
−1
, respectively. Below these critical values, coexistence of the competing species was found in steady-state situations. Although the numbers were strongly reduced, the nitrifying bacteria were not fully outcompeted by the heterotrophic bacteria above the critical carbon-to-nitrogen ratios. Nitrifying bacteria could probably maintain themselves in the system above the critical carbon-to-nitrogen ratios because they are attached to the glass wall of the culture vessels. The numbers of
N. europaea
decreased more than did those of
N. winogradskyi
. This was assumed to be due to heterotrophic growth of the latter species on organic substrates excreted by the heterotrophic bacteria.
Collapse
Affiliation(s)
- F J Verhagen
- Institute for Ecological Research, P.O. Box 40, 6666 ZG Heteren, The Netherlands
| | | |
Collapse
|
21
|
Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry. Appl Environ Microbiol 1990; 56:2430-5. [PMID: 2403253 PMCID: PMC184745 DOI: 10.1128/aem.56.8.2430-2435.1990] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Two different serotypes of the genus Nitrosomonas were isolated from samples of the sewage plant Heidelberg. These nitrifiers were enumerated in activated sludge of various other sewage plants after immunofluorescent labeling and staining with propidium iodide by flow cytometry. The concentrations of these serotypes of Nitrosomonas spp. were in the range of 0.1 to 2%. Also, a test for the determination of the activity of ammonia-oxidizing bacteria was developed. Nitrite-oxidizing bacteria were specifically inhibited with sodium chlorate, and the activity of ammonia-oxidizing bacteria could be calculated from the increase of nitrite. Concentrations and activities of ammonia oxidizers were measured for a period of 6 months in the sewage plant Heidelberg. With one exception, activities and concentrations of ammonia-oxidizing bacteria decreased and increased in parallel.
Collapse
|
22
|
Desmonts C, Minet J, Colwell R, Cormier M. Fluorescent-antibody method useful for detecting viable but nonculturable Salmonella spp. in chlorinated wastewater. Appl Environ Microbiol 1990; 56:1448-52. [PMID: 2187414 PMCID: PMC184427 DOI: 10.1128/aem.56.5.1448-1452.1990] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An indirect fluorescent-antibody (IFA) technique, which employed adsorbed Behring polyvalent I O antiserum, was used to detect Salmonella spp. in environmental water systems. The IFA method used in this study detected 95% of Salmonella serotypes encountered in human infections in France, with a sensitivity threshold of 7.5 x 10(3) bacteria per ml of wastewater. Specificity was assessed by testing IFA against Salmonella-free seawater and a variety of bacteria other than Salmonella spp. When used to examine raw and chlorinated wastewater over a 2-month period, the IFA method was successful in detecting Salmonella spp. in all 12 of the samples examined, with total numbers determined to be 4.5 x 10(5) to 3.3 x 10(7) salmonellae per 100 ml. In comparison, for the same samples, enumeration by culture, using the most-probable-number technique, was effective in detecting Salmonella spp. in only four of eight raw-water samples and one of four chlorinated water samples tested. Three samples were further tested by using the direct viable count procedure combined with IFA and results showed that 5 to 31.5% of the Salmonella spp. enumerated by this method in chlorinated water were substrate responsive.
Collapse
Affiliation(s)
- C Desmonts
- Laboratoire de Microbiologie Pharmaceutique, Université de Rennes I, France
| | | | | | | |
Collapse
|
23
|
Abstract
Flow cytometry/cell sorting in aquatic sciences has been driven in two directions. The frontier directions are on shipboard and shore-based. On the one hand, the rapid analytical technique has been taken on shipboard to provide a real-time assessment of the particles and phytoplankton in water masses. These data also give information on the amount of vertical mixing and advection, and denote fronts between two or more water masses. There is an optical characterization (based on sizes, numbers, and pigment groups) of the individual primary producers, as well as detritus and suspended sediments. An optical-closure question is being addressed: "Does the total optical signal equal the sum of the parts?" Additionally, associations with chemical and physical oceanographic features are readily accomplished. A "census" of thousands of phytoplankton cells is obtained and can be mapped. Scientists are able to identify "who is where?" Such data are critical to understand the optical-feedback loop or the so-called photon-budget-in-the-sea, which in turn controls the rates at which growth processes occur in nature. On the other hand, an in-depth understanding is sought as to how particle size, shape, refractive index, nutritional status (nutrient and/or light limitation), growth dynamics, and cell cycle combine to control the optics (light scatter and fluorescence at the moment, and ideally absorption as well) or the photon-budget-of-the-cell. For this purpose, a shore-based facility associated with a diverse collection of phytoplankton is ideal. The development at Bigelow Laboratory of the Jane J. MacIsaac Facility is to provide services for the oceanographic community. Association and co-location with the Provasoli-Guillard Center for Culture of Marine Phytoplankton is key. Visitors are trained and given access to state-of-the-art instrumentation. Visiting investigators have available "the tropical, temperate, and polar seas" in concentrated form, as marine phytoplankton isolated worldwide and maintained as living clonal cultures. In this way, frontline cell biology questions can be addressed. The relentless exploration of standards and controls appropriate for the aquatic community must be continued. An intercalibration effort is a vital step. It is only with the widespread acceptance of particular reference materials and uniform optical filters among research groups utilizing FCM that comparable data sets describing aquatic particle distributions will be possible. For a global science, this strategy is imperative.
Collapse
Affiliation(s)
- C M Yentsch
- J.J. MacIsaac Flow Cytometry/Sorting Facility, Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine 04575
| |
Collapse
|
24
|
Legendre L, Yentsch CM. Overview of flow cytometry and image analysis in biological oceanography and limnology. CYTOMETRY 1989; 10:501-10. [PMID: 2776566 DOI: 10.1002/cyto.990100505] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- L Legendre
- GIROQ, Département de Biologie, Universite Laval, Quebec, Canada
| | | |
Collapse
|
25
|
|
26
|
|
27
|
|
28
|
Chemistry of the dissolved and particulate phases in the water column. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
29
|
Nutrient cycling and food web dynamics in the Southern California Bight: The microbial food web. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
30
|
Automated Individual Cell Analysis in Aquatic Research. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/s0074-7696(08)61064-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
31
|
Jackson GA. Physical oceanography of the Southern California Bight. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
32
|
Beers JR. Organisms and the food web. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
33
|
Introduction to the Southern California Bight. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
34
|
Eppley RW, Holm-Hansen O. Primary production in the Southern California Bight. ACTA ACUST UNITED AC 1986. [DOI: 10.1029/ln015p00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
35
|
Mullin MM. Spatial and temporal scales and patterns. PLANKTON DYNAMICS OF THE SOUTHERN CALIFORNIA BIGHT 1986. [DOI: 10.1029/ln015p00216] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
36
|
Detection, enumeration, and sizing of planktonic bacteria by image-analyzed epifluorescence microscopy. Appl Environ Microbiol 1985; 49:799-810. [PMID: 2408564 PMCID: PMC238449 DOI: 10.1128/aem.49.4.799-810.1985] [Citation(s) in RCA: 137] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epifluorescence microscopy is now being widely used to characterize planktonic procaryote populations. The tedium and subjectivity of visual enumeration and sizing have been largely alleviated by our use of an image analysis system consisting of a modified Artek 810 image analyzer and an Olympus BHT-F epifluorescence microscope. This system digitizes the video image of autofluorescing or fluorochrome-stained cells in a microscope field. The digitized image can then be stored, edited, and analyzed for total count or individual cell size and shape parameters. Results can be printed as raw data, statistical summaries, or histograms. By using a stain concentration of 5 micrograms of 4'6-diamidino-2-phenylindole per ml of sample and the optimal sensitivity level and mode, counts by image analysis of natural bacterial populations from a variety of habitats were found to be statistically equal to standard visual counts. Although the time required to prepare slides, focus, and change fields is the same for visual and image analysis methods, the time and effort required for counting is eliminated since image analysis is instantaneous. The system has been satisfactorily tested at sea. Histograms of cell silhouette areas indicate that rapid and accurate estimates of bacterial biovolume and biomass will be possible with this system.
Collapse
|
37
|
Zambon JJ, Huber PS, Meyer AE, Slots J, Fornalik MS, Baier RE. In situ identification of bacterial species in marine microfouling films by using an immunofluorescence technique. Appl Environ Microbiol 1984; 48:1214-20. [PMID: 6393875 PMCID: PMC241712 DOI: 10.1128/aem.48.6.1214-1220.1984] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An immunofluorescence technique was developed for the in situ identification of specific bacteria in marine microfouling films. Microorganisms adherent to glass plates after 30 days of immersion in a synthetic seawater system were cultured and classified by biochemical tests, flagellar arrangement, and the API 20E system. All isolates were gram-negative aerobic or facultative motile rods, predominantly Pseudomonas spp. Rabbit antisera to the five dominant organisms including Achromobacter spp., Comamonas terrigena, P. putrefaciens, a yellow-pigmented Pseudomonas sp., and Vibrio alginolyticus were prepared. These antisera were shown to be species specific in indirect immunofluorescence assays against a battery of 26 marine isolates from 14 bacterial species, with the exception of antisera to the Pseudomonas spp, which cross-reacted with each other but not with test bacteria of other genera. These immunofluorescent reagents enabled the in situ identification of all five bacterial species in microfouling films. Low-surface-energy test plates had smaller numbers of adherent bacteria in microfouling films than medium-surface-energy test plates, suggesting that the degree of microfouling may be influenced by the surface energy. In addition, the reagents could identify up to 39% of the attached bacteria in microfouling films spontaneously formed on steel plates in flow cells deployed in different areas of the Atlantic Ocean. The microbial composition of the ocean-formed films varied with the geographical area of their formation. The present results indicate that immunofluorescence techniques may provide a rapid and reliable means to identify, in situ, specific bacteria in marine microfouling films.
Collapse
|
38
|
Karl DM, Knauer GA, Martin JH, Ward BB. Bacterial chemolithotrophy in the ocean is associated with sinking particles. Nature 1984. [DOI: 10.1038/309054a0] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
39
|
Xu HS, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR. Survival and viability of nonculturableEscherichia coli andVibrio cholerae in the estuarine and marine environment. MICROBIAL ECOLOGY 1982; 8:313-23. [PMID: 24226049 DOI: 10.1007/bf02010671] [Citation(s) in RCA: 593] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Plating methods for estimating survival of indicator organisms, such asEscherichia coli, and water-borne pathogens includingVibrio cholerae, have severe limitations when used to estimate viable populations of these organisms in the aquatic environment. By combining the methods of immunofluorescent microscopy, acridine orange direct counting, and direct viable counting, with culture methods such as indirect enumeration by most probable number (MPN) estimation and direct plating, it was shown that bothE. coli andV. cholerae undergo a "nonrecoverable" stage of existence, but remain viable. Following 2-week incubations in saltwater (5-25%o NaCl) microcosms, total counts, measured by direct microscopic examination of fluorescent antibody and acridine orange stained cells, remained unchanged, whereas MPN estimates and plate counts exhibited rapid decline. Results of direct viable counting, a procedure permitting estimate of substrate-responsive viable cells by microscopic examination, revealed that a significant proportion of the nonculturable cells were, indeed, viable. Thus, survival of pathogens in the aquatic environment must be re-assessed. The "die-off" or "decay" concept may not be completely valid. Furthermore, the usefulness of the coliform and fecal coliform indices for evaluating water quality for public health purposes may be seriously compromised, in the light of the finding reported here.
Collapse
Affiliation(s)
- H S Xu
- Department of Marine Biology, Shandong College of Oceanography, Qingdao, PRC
| | | | | | | | | | | |
Collapse
|
40
|
Ward B, Olson RJ, Perry MJ. Microbial nitrification rates in the primary nitrite maximum off southern California. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0198-0149(82)90112-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Geesey GG, Morita RY. Relationship of Cell Envelope Stability to Substrate Capture in a Marine Psychrophilic Bacterium. Appl Environ Microbiol 1981; 42:533-40. [PMID: 16345849 PMCID: PMC244049 DOI: 10.1128/aem.42.3.533-540.1981] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells of a psychrophilic marine bacterium were found to take up a variety of amino acids from seawater. Some of the amino acids that were taken up were released when the cells were exposed to a hypotonic salt solution. The proportion that was released varied according to the amino acid. A pool of the amino acid arginine that was formed during very short periods of exposure of cells to the exogenously supplied amino acid was particularly sensitive to reductions in salinity. In general, exposure to hypotonic salt solutions also resulted in reduced amino acid uptake by the cells. Complete removal of seawater salts (SE treatment) produced obvious structural alterations in the cell envelope, resulting in an even greater reduction in amino acid uptake. Under these conditions, amino acid-binding components were released by the cells. Differential centrifugation and fluorescent antibody studies indicated that arginine-binding components are located on or near the surface of intact cells. The data suggest that substrate receptors were sensitive to reductions in seawater salt concentrations and that lesions at this level affected the organism's substrate uptake and retention capabilities.
Collapse
Affiliation(s)
- G G Geesey
- Department of Microbiology, California State University, Long Beach, California 90840
| | | |
Collapse
|