51
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Massieux B, Boivin MEY, Van Den Ende FP, Langenskiöld J, Marvan P, Barranguet C, Admiraal W, Laanbroek HJ, Zwart G. Analysis of structural and physiological profiles to assess the effects of Cu on biofilm microbial communities. Appl Environ Microbiol 2004; 70:4512-21. [PMID: 15294780 PMCID: PMC492431 DOI: 10.1128/aem.70.8.4512-4521.2004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the effects of copper on the structure and physiology of freshwater biofilm microbial communities. For this purpose, biofilms that were grown during 4 weeks in a shallow, slightly polluted ditch were exposed, in aquaria in our laboratory, to a range of copper concentrations (0, 1, 3, and 10 microM). Denaturing gradient gel electrophoresis (DGGE) revealed changes in the bacterial community in all aquaria. The extent of change was related to the concentration of copper applied, indicating that copper directly or indirectly caused the effects. Concomitantly with these changes in structure, changes in the metabolic potential of the heterotrophic bacterial community were apparent from changes in substrate use profiles as assessed on Biolog plates. The structure of the phototrophic community also changed during the experiment, as observed by microscopic analysis in combination with DGGE analysis of eukaryotic microorganisms and cyanobacteria. However, the extent of community change, as observed by DGGE, was not significantly greater in the copper treatments than in the control. Yet microscopic analysis showed a development toward a greater proportion of cyanobacteria in the treatments with the highest copper concentrations. Furthermore, copper did affect the physiology of the phototrophic community, as evidenced by the fact that a decrease in photosynthetic capacity was detected in the treatment with the highest copper concentration. Therefore, we conclude that copper affected the physiology of the biofilm and had an effect on the structure of the communities composing this biofilm.
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52
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Wrage N, Velthof GL, Oenema O, Laanbroek HJ. Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale. FEMS Microbiol Ecol 2004; 47:13-8. [DOI: 10.1016/s0168-6496(03)00220-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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53
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Bollmann A, Bär-Gilissen MJ, Laanbroek HJ. Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria. Appl Environ Microbiol 2002; 68:4751-7. [PMID: 12324316 PMCID: PMC126422 DOI: 10.1128/aem.68.10.4751-4757.2002] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 micro M ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.
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54
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Bie MJ, Starink M, Boschker HT, Peene JJ, Laanbroek HJ. Nitrification in the Schelde estuary: methodological aspects and factors influencing its activity. FEMS Microbiol Ecol 2002; 42:99-107. [DOI: 10.1111/j.1574-6941.2002.tb00999.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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55
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Laanbroek HJ, Bär-Gilissen MJ, Hoogveld HL. Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea. Appl Environ Microbiol 2002; 68:1454-7. [PMID: 11872501 PMCID: PMC123751 DOI: 10.1128/aem.68.3.1454-1457.2002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2001] [Accepted: 12/13/2001] [Indexed: 11/20/2022] Open
Abstract
Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite accumulates and may subsequently inhibit ammonia oxidation. The maintenance of a high ammonia-oxidizing capacity during starvation is then nullified. In this study we demonstrated that cells of N. europaea starved for ammonia were not sensitive to nitrite, either when they were starved in the presence of nitrite or when nitrite was supplied simultaneously with fresh ammonium. In the latter case, the initial ammonia-oxidizing activity of starved cells was stimulated at least fivefold.
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56
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Laanbroek HJ, Bär-Gilissen MJ. Weakened Activity of Starved Ammonia-oxidizing Bacteria by the Presence of Pre-activated Nitrobacter winogradskyi. Microbes Environ 2002. [DOI: 10.1264/jsme2.17.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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57
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Bollmann A, Laanbroek HJ. Continuous culture enrichments of ammonia-oxidizing bacteria at low ammonium concentrations. FEMS Microbiol Ecol 2001. [DOI: 10.1111/j.1574-6941.2001.tb00868.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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58
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Speksnijder AG, Kowalchuk GA, De Jong S, Kline E, Stephen JR, Laanbroek HJ. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 2001; 67:469-72. [PMID: 11133483 PMCID: PMC92603 DOI: 10.1128/aem.67.1.469-472.2001] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a mutational hot spot, and cloning of heteroduplexes and chimeras. These data may partially explain the high degree of microheterogeneity typical of sequence clusters detected in environmental clone libraries.
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59
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van Hannen EJ, Mooij W, van Agterveld MP, Gons HJ, Laanbroek HJ. Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 1999; 65:2478-84. [PMID: 10347030 PMCID: PMC91365 DOI: 10.1128/aem.65.6.2478-2484.1999] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the "microbial loop." To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.
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60
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Nold SC, Boschker HT, Pel R, Laanbroek HJ. Ammonium addition inhibits 13C-methane incorporation into methanotroph membrane lipids in a freshwater sediment. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00600.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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61
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van Hannen EJ, Zwart G, van Agterveld MP, Gons HJ, Ebert J, Laanbroek HJ. Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ Microbiol 1999; 65:795-801. [PMID: 9925618 PMCID: PMC91097 DOI: 10.1128/aem.65.2.795-801.1999] [Citation(s) in RCA: 214] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.
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62
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Kowalchuk GA, Bodelier PL, Heilig GJ, Stephen JR, Laanbroek HJ. Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00550.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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63
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Zwart G, Hiorns WD, Methé BA, van Agterveld MP, Huismans R, Nold SC, Zehr JP, Laanbroek HJ. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 1998; 21:546-56. [PMID: 9924823 DOI: 10.1016/s0723-2020(98)80067-2] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity < 90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments.
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64
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Gerards S, Duyts H, Laanbroek HJ. Ammonium-induced inhibition of ammonium-starved Nitrosomonas europaea cells in soil and sand slurries. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00511.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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65
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Nijburg JW, Gerards S, Laanbroek HJ. Competition for nitrate and glucose between Pseudomonas fluorescens and Bacillus licheniformis under continuous or fluctuating anoxic conditions. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00519.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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66
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Speksnijder AG, Kowalchuk GA, Roest K, Laanbroek HJ. Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Syst Appl Microbiol 1998; 21:321-30. [PMID: 9704117 DOI: 10.1016/s0723-2020(98)80040-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to study the diversity of ammonia-oxidising bacteria in freshwater habitats, including sediments, a molecular approach focused on the sequencing of 16S rDNA was adopted. 16S rDNA sequences showing affinity with the beta-subgroup of ammonia-oxidising bacteria were recovered by specific PCR of directly isolated DNA from freshwater samples, and samples from brackish water and Glyceria maxima rhizosphere were included in the analysis for comparison. The ammonia oxidiser-like sequences recovered from several locations, which exhibit differences in the composition of their total microbial communities as indicated by denaturing gradient gel electrophoresis, formed a strong monophyletic cluster including Nitrosomonas ureae. This is the first report presenting sequences from an apparently dominant group of Nitrosomonas-like organisms among the beta-subdivision of ammonia-oxidising bacteria in freshwater environments. This group of sequences extends the known diversity within the beta-subgroup of ammonia-oxidisers. The new sequences related to Nitrosomonas ureae do not match with some published primers and probes designed for the detection of Nitrosomonas species, which may explain why these sequences have not previously been detected in freshwater habitats. The sequence diversity detected within this group of sequences was minimal across the environments examined, and no patterns of distribution were indicated with respect to environmental factors such as sediment depth or location.
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67
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Zwart G, Huismans R, Agterveld MP, Peer Y, Rijk P, Eenhoorn H, Muyzer G, Hannen EJ, Gons HJ, Laanbroek HJ. Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00469.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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68
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Bodelier PL, Duyts H, Blom CW, Laanbroek HJ. Interactions between nitrifying and denitrifying bacteria in gnotobiotic microcosms planted with the emergent macrophyte Glyceria maxima. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00460.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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69
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Nijburg JW, Laanbroek HJ. The Fate of 15N-Nitrate in Healthy and Declining Phragmites australis Stands. MICROBIAL ECOLOGY 1997; 34:254-262. [PMID: 9337421 DOI: 10.1007/s002489900055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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70
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Bodelier PLE, Laanbroek HJ. Oxygen uptake kinetics of Pseudomonas chlororaphis grown in glucose- or glutamate-limited continuous cultures. Arch Microbiol 1997. [DOI: 10.1007/s002030050460] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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71
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Kester RA, Boer W, Laanbroek HJ. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples1. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00310.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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72
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Laanbroek HJ, Bodelier PLE, Gerards S. Oxygen consumption kinetics of Nitrosomonas europaea and Nitrobacter hamburgensis grown in mixed continuous cultures at different oxygen concentrations. Arch Microbiol 1994. [DOI: 10.1007/bf00276477] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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73
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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.
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74
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Brunel B, Janse JD, Laanbroek HJ, Woldendorp JW. Effect of transient oxic conditions on the composition of the nitrate-reducing community from the rhizosphere of Typha angustifolia. MICROBIAL ECOLOGY 1992; 24:51-61. [PMID: 24193039 DOI: 10.1007/bf00171970] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/1991] [Accepted: 02/07/1992] [Indexed: 06/02/2023]
Abstract
Within a nitrate-reducing bacterial community, a niche differentiation between denitrifying and nitrate ammonifying bacteria may be determinated by a complex of environmental parameters, such as the availability of carbon, nitrate, and oxygen. Hence, oxygen- and carbon-releasing aerenchymatous plants may affect the composition of the nitrate-reducing community in waterlogged sediment. The composition of the nitrate-reducing community in the rhizosphere of the aerenchymatous plant species Typha angustifolia was compared with the community in nonrhizospheric sediment. All three functional groups (NO2 (-) accumulators, N2O producers, and presumed NH4 (+) producers) were present at both sites with an ratio of 36:45:12 and 43:22:18 for nonrhizospheric and rhizospheric sediments, respectively. Most of the isolated were gram-negative, and approximately 50% of these strains demonstrated an obligatory oxidative metabolism.In the absence of nitrate, Enterobacteriaceae (belonging to the NO2 (-) accumulating group) became dominant during enrichment of bacteria from the rhizosphere of T. angustifolia in a chemostat with glycerol (20 mM) as substrate, both under strictly anoxic and transient oxic conditions. Addition of nitrate to the chemostats led to the predominance of denitrifying pseudomonads, irrespective of the presence or absence of oxygen. However, in the presence of nitrate under anoxic conditions, enterobacteria persisted in the medium together with pseudomonads.It was concluded that oxidative bacteria such as pseudomonads are the better competitors for limiting amounts of glycerol, provided oxygen or nitrate is present. In the absence of these electron acceptors, fermentative bacteria become dominant.
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75
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Both GJ, Gerards S, Laanbroek HJ. Kinetics of nitrite oxidation in two Nitrobacter species grown in nitrite-limited chemostats. Arch Microbiol 1992. [DOI: 10.1007/bf00249101] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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76
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Frijlink MJ, Abee T, Laanbroek HJ, de Boer W, Konings WN. Secondary transport of amino acids in Nitrosomonas europaea. Arch Microbiol 1992. [DOI: 10.1007/bf00248686] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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77
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Both GJ, Gerards S, Laanbroek HJ. The occurrence of chemolitho-autotrophic nitrifiers in water-saturated grassland soils. MICROBIAL ECOLOGY 1992; 23:15-26. [PMID: 24192826 DOI: 10.1007/bf00165904] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/1991] [Revised: 10/10/1991] [Indexed: 06/02/2023]
Abstract
Relatively high most probable number (MPN) counts of chemolithotrophic nitrite oxidizers were present in water-saturated soils compared with MPNs and activity of ammonia oxidizers. These high numbers of nitrite oxidizers were confirmed by fluorescent antibody counts and potential activity measurements. Application of different nitrite concentrations in the MPN procedure discriminated within the community of nitrite oxidizers and revealed a large number of nitrite-sensitive nitrite oxidizers and a subcommunity of nitrite-insensitive nitrite oxidizers. The size of this subcommunity was small but corresponded with the low numbers of ammonium oxidizers. Numbers of nitrite-sensitive nitrite oxidizers outnumbered the ammonia oxidizing bacteria by 2-4 orders of magnitude in these soils. The possibility is discussed that the fraction of the nitrite-insensitive cells was active as aerobic nitrite oxidizers, whereas the nitrite-sensitive cells represented an inactive group of nitrite oxidizers growing as heterotrophs or as anaerobes reducing nitrite. In this situation, both MPN enumerations at a low nitrite concentration and activity measurements could give false information about the size of the in situ nitrite-oxidizing community.
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78
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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.
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79
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Laanbroek HJ, Blok JP, Steenhuis L. Variability in fermentation patterns of sugar-utilizing bacteria isolated from anaerobic, intertidal sediments. MICROBIAL ECOLOGY 1985; 11:117-125. [PMID: 24221300 DOI: 10.1007/bf02010484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Three dominant types of sugar-fermenting bacteria were isolated from the anaerobic, intertidal sediments of the Eems-Dollard estuary by applying techniques involving anaerobic agar shake tubes. One of the isolated types was tentatively identified as aStreptococcus species, the other two asBacteroides species. All types were versatile with respect to the utilization of sugars. The fermentation patterns of two types were dependent upon conditions of cultivation. In glucose-limited cultures ofStreptococcus strain NS.G52, the production of lactate was suppressed in favor of formate, acetate, and ethanol. In glucose-limited syntrophic cultures withMethanospirillum hungatei, Bacteroides strain NS.G42 was forced to produce acetate and hydrogen at the expense of ethanol. The fermentation pattern ofBacteroides strain NS.S42, which consisted of acetate, propionate, and succinate, was not affected by conditions of cultivation.
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Laanbroek HJ, Geerligs HJ, Peijnenburg AA, Siesling J. Competition for L-lactate betweenDesulfovibrio, Veillonella, andAcetobacterium species isolated from anaerobic intertidal sediments. MICROBIAL ECOLOGY 1983; 9:341-354. [PMID: 24221822 DOI: 10.1007/bf02019023] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Almost equal numbers ofDesulfovibrio, Veillonella, andAcetobacterium species were found in agar shake dilutions of anaerobic intertidal brackish sediments applying L-lactate as the only energy source and sulfate as electron acceptor. Pure cultures of these bacteria were studied in more detail in batch cultures as well as in L-lactate-limited chemostats. The maximal specific growth rates on L-lactate were determined in washout experiments and amounted to 0.16, 0.30, and 0.06 h(-1) forDesulfovibrio baculatus H.L21,Veillonella alcalescens NS.L49, andAcetobacterium NS.L40, respectively. Competition for L-lactate was studied in energy-limited chemostats at a dilution rate of 0.02 h(-1).D. baculatus H.L21 turned out to be the best competitor at low L-lactate concentrations provided that sufficient sulfate and iron were present.V. alcalescens NS.L49 was favored by the absence of sulfate and iron. Coexistence ofD. baculatus H.L21 andV. alcalescens NS.L49 was observed in a L-lactate-limited chemostat with additional sulfate and citrate. Syntrophic growth ofV. alcalescens NS.L49 andAcetobacterium NS.L40 occurred in a L-lactate-limited chemostat in the absence of sulfate. No coexistence betweenD. baculatus H.L21 andAcetobacterium NS.L40 was observed in a L-lactate-limited chemostat without sulfate. Addition of calcium-saturated illite to an energy-limited mixed culture ofV. alcalescens NS.L49 andAcetobacterium NS.L40 induced iron limitation and subsequent washout of theAcetobacterium species. Finally, the ecological niches of the 3 species in relation to the consumption of lactate were discussed.
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Laanbroek HJ, Geerligs HJ. Influence of clay particles (Illite) on substrate utilization by sulfate-reducing bacteria. Arch Microbiol 1983. [DOI: 10.1007/bf00407951] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Laanbroek HJ, Veldkamp H. Microbial interactions in sediment communities. Philos Trans R Soc Lond B Biol Sci 1982; 297:533-50. [PMID: 6125961 DOI: 10.1098/rstb.1982.0059] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mineralization of organic matter in aquatic ecosystems with shallow waters occurs to a large extent in their sediments under anoxic conditions. This is achieved by a community of bacteria, which are the catalysts in a sequence of processes. Of the two possible terminal processes, methanogenesis and sulphate reduction, the first usually dominates in freshwater systems, whereas in estuarine and marine sediments electrons are mainly channelled to sulphate. Interactions between sulphate-reducing and methanogenic bacteria are described. Sulphate-reducing bacteria also show interactions with fermentative bacteria. After a brief description of properties of sulphate-reducing and fermentative bacteria occurring in sediments, examples are given of interactions between them. This is followed by the presentation of some results obtained from studies on competition for L-lactate between organisms belonging to both groups. It is shown that sulphate-reducing bacteria could successfully compete for L-lactate when this was available in growth-limiting amounts with sufficient sulphate and iron. Finally, a brief discussion is given of ecological niches of sulphide-oxidizing bacteria thriving in the upper sediment layers.
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Laanbroek HJ, Abee T, Voogd IL. Alcohol conversion by Desulfobulbus propionicus Lindhorst in the presence and absence of sulfate and hydrogen. Arch Microbiol 1982. [DOI: 10.1007/bf00414998] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Laanbroek HJ, Pfennig N. Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments. Arch Microbiol 1981; 128:330-5. [PMID: 7212933 DOI: 10.1007/bf00422540] [Citation(s) in RCA: 175] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Colony counts of acetate-, propionate- and L-lactate-oxidizing sulfate-reducing bacteria in marine sediments were made. The vertical distribution of these organisms were equal for the three types considered. The highest numbers were found just beneath the border of aerobic and anaerobic layers. Anaerobic mineralization of acetate, propionate and L-lactate was studied in the presence and in the absence of sulfate. In freshwater and in marine sediments, acetate and propionate were oxidized completely with concomitant reduction of sulfate. L-Lactate was always fermented. Lactate-oxidizing, sulfate-reducing bacteria could only be isolated from marine sediments, they belonged to the genus Desulfobacter and oxidized only acetate and ethanol by sulfate reduction. Propionate-oxidizing, sulfate-reducing bacteria belonged to the genus Desulfobulbus. They were isolated from freshwater as well as from marine sediments and showed a relatively large range of usable substrates: hydrogen, formate, propionate, L-lactate and ethanol were oxidized with concomitant sulfate reduction. L-Lactate and pyruvate could be fermented by most of the isolated strains.
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Laanbroek HJ, Smit AJ, Nulend GK, Veldkamp H. Competition for L-glutamate between specialised and versatile Clostridium species. Arch Microbiol 1979; 120:61-6. [PMID: 426599 DOI: 10.1007/bf00413275] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clostridium cochlearium could be reproducibly enriched in an L-aspartate- and L-glutamate-limited, anaerobic chemostat inoculated with anaerobic sludge. L-glutamate, L-glutamine and L-histidine were the only fermentable substrates. Less specialised clostridia of the C. tetanomorphum type could only be isolated from batch enrichments with L-glutamate and L-aspartate as energy sources. Competition experiments with C. cochlearium and C. tetanomorphum in a L-glutamate-limited chemostat resulted in the selective elimination of the latter species. Addition of glucose to the medium resulted in coexistence of both species. The molar growth yields for L-glutamate at different dilution rates at 30 degrees C were determined for both species. The maximum specific growth rates on L-glutamate were 0.55 h-1 for C. cochlearium and 0.35 h-1 for C. tetanomorphum.
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Laanbroek HJ, Veldkamp H. Growth yield and energy generation in anaerobically-grown Campylobacter spec. Arch Microbiol 1979; 120:47-51. [PMID: 426598 DOI: 10.1007/bf00413272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An anaerobic continuous culture study was made with Campylobacter spec. to determine growth yields under various growth conditions. The growth media contained 0.1% (w/v) yeast extract as carbon source. When grown in an aspartate-limited culture Ymaxasp was 4.6. Inclusion of formate in the culture medium hardly affected the true growth yield. The number of ATP equivalents generated in the fumarate-reductase system was 0.66 and the YmaxATP was 7.0. In the nitrate reduction with formate 1.7 ATP equivalents were generated, and a YmaxNO3- of 12.2 was observed. The true growth yield obtained with a mixture of lactate and aspartate was lower than that found with aspartate alone.
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Laanbroek HJ, Stal LH, Veldkamp H. Utilization of hydrogen and formate by Campylobacter spec. under aerobic and anaerobic conditions. Arch Microbiol 1978; 119:99-102. [PMID: 718373 DOI: 10.1007/bf00407935] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A free-living aspartate-fermenting Campylobacter spec. was shown to utilize hydrogen produced in mixed culture by Clostridium cochlearium from glutamate. Resting cells of Campylobacter were shown to reduce aspartate, fumarate and malate as well as nitrate, nitrite, hydroxylamine, sulphite, thiosulphate and elemental sulphur with molecular hydrogen. Growth of Campylobacter spec. was demonstrated with formate as electron donor and nitrate, thiosulphate, elemental sulphur or oxygen as electron acceptor in the presence of acetate as carbon source.
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Barents JW, Dankert J, Ilic P, Laanbroek HJ, de Vries H. [The indwelling catheter in gynecology and the development of bacteriuria; a comparative study of patients with the transurethral and the suprapubic catheter]. NEDERLANDS TIJDSCHRIFT VOOR GENEESKUNDE 1978; 122:1321-7. [PMID: 567753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Laanbroek HJ, Lambers JT, de Vos WM, Veldkamp H. L-Aspartate fermentation by a free-living Campylobacter species. Arch Microbiol 1978; 117:109-14. [PMID: 678010 DOI: 10.1007/bf00689359] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the fermentation of L-aspartate by a free-living Campylobacter spec., the products formed were acetate, succinate, carbon dioxide and ammonia. The oxidative part of the fermentation pathway yielded acetate, succinate, carbon dioxide and ammonia, and the reductive part gave rise to the formation of succinate and ammonia. When grown anaerobically with aspartate, cells contained cytochromes b and c as well as menaquinone. Reduced cytochrome b, but not reduced cytochrome c could be reoxidized by fumarate. In the presence of nitrate, 90% of the available electrons were transferred to nitrate, which was reduced to nitrite; the remainder was transported via the fumarate reductase system. Cells grown with aspartate and excess of formate converted aspartate quantitatively to succinate.
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