Bacterial communities associated with aquatic organisms in the floodwater of a Japanese paddy field estimated by RFLP pattern analysis

Niswati, Ainin; Yamazaki, Masatsugu; Ikenaga, Makoto; Kimura, Makoto

doi:10.1080/00380768.2002.10409190

Cited by 9 publications

(10 citation statements)

References 30 publications

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“…(Fig. 2), which coincided with the larger number of RFLP bands (Niswati et al 2002(Niswati et al , 2003. Taniguchi et al (1997a) also reported a sparser colonization of microorganisms on Tanycypris sp.…”

Section: Discussionmentioning

confidence: 90%

“…DNA was extracted from the microcrustacean samples at a high temperature according to the lysis method based on salt and sodium dodecyl sulfate (SDS) (Zhou et al 1996) with slight modifications (Niswati et al 2002). The DNA samples were stored at 4°C for immediate use or at -20°C for prolonged storage.…”

Section: Sampling Of Microcrustaceansmentioning

confidence: 99%

“…Not only individual epibionts but also the community structure seemed to be specific for each microcrustacean in the floodwater. Niswati et al (2002Niswati et al ( , 2003 compared the community structure of bacteria (epibiotic and intestinal bacteria) among microcrustaceans in the floodwater of a paddy soil microcosm based on the PCR (polymerase chain reaction)-RFLP (restriction fragment length polymorphism) pattern analysis, and revealed the presence of statistical differences in the bacterial communities associated with a cladoceran (Moina sp. ), a cyclopoid (Mesocyclops sp.…”

mentioning

confidence: 99%

“…in the floodwater of a paddy field microcosm and to determine the phylogenetic position of bacterial associates specific to the respective microcrustaceans for confirming the specific association of eubacteria with microcrustaceans phylogenetically. We first performed a PCR-DGGE pattern analysis of the bacterial communities associated with microcrustaceans in the floodwater of a paddy soil microcosm to determine the specific community structure of the bacteria for the respective microcrustaceans that had been estimated based on the PCR-RFLP pattern analysis (Niswati et al 2002(Niswati et al , 2003. Then, the DGGE bands that were common to every microcrustacean and specific to each microcrustacean were sequenced to determine their phylogenetic positions.…”

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confidence: 99%

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Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Niswati

Murase

Kimura

2005

Soil Science and Plant Nutrition

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Bacterial communities associated with five kinds of microcrustaceans (Tanycypris sp., Moina sp., Mesocyclops sp., Cypretta sp. and Heterocypris sp.) from the floodwater of a paddy field microcosm were examined by the application of denaturing gradient gel electrophoresis (DGGE) to PCR‐amplified 16S rDNA products with universal bacterial primers and by sequencing of characteristic DGGE bands. The number of DGGE bands of the associated bacteria was small, indicating the association of specific bacterial members with the microcrustaceans studied, among which Tanycypris sp. showed the smallest number of bands. Principal component analysis (PCA) demonstrated that the community structure of the associated bacteria could be divided into three groups: Podocopida (Tanycypris sp., Cypretta sp. and Heterocypris sp.), Moina sp. and Mesocyclops sp., and further analysis separated Tanycypris sp. and Heterocypris sp. into different clusters. The duration of the incubation period affected the bacteria associated with Tanycypris sp., Moina sp. and Cypretta sp. only. Nearly all of the associated bacteria belonged to Gram‐negative bacteria, especially the Cytophaga‐Flavobacterium‐Bacteroides (CFB) group. Closest relatives of the DGGE bands common to three Podocopida and Mesocyclops sp. belonged to an invertebrate endosymbiont.

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Section: Discussionmentioning

confidence: 90%

Section: Sampling Of Microcrustaceansmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Niswati

Murase

Kimura

2005

Soil Science and Plant Nutrition

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“…DNA was extracted from the microcrustacean samples using a high temperature, salt and sodium dodecyl sulfate (SDS)-based lysis method (Zhou et al 1996) with slight modifications for the extraction of a small volume of Moina sp. samples (Niswati et al 2002). The DNA extracts were stored at 4°C for immediate use or at -20°C for long storage.…”

Section: Methodsmentioning

confidence: 99%

Effect of Application of Rice Straw and Compost on the Bacterial Communities Associated withMoinasp. in the Floodwater of a Paddy Soil Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Niswati

Murase

Kimura

2005

Soil Science and Plant Nutrition

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Bacterial communities associated with Moina sp. in the floodwater of a paddy field microcosm were examined by denaturing gradient gel electrophoresis (DGGE) of PCR‐amplified 16S rDNA. Eighteen out of 20 eubacterial DGGE bands were sequenced. The associated eubacterial communities mainly consisted of the Cytophaga‐Flavobacterium‐Bacteroides group and α‐, β‐, and γ‐Proteobacterial groups, irrespective of the application of rice straw and rice straw compost. The effect of the application of rice straw and compost on the communities was not appreciable, compared with host specificity. An uncultured Cytophagales bacterium was estimated to be specifically associated with Moina sp. Presence of bacteria that are specific to rice straw treatment was also estimated.

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Storage of Carotenoids in Crustaceans as an Adaptation to Modulate Immunopathology and Optimize Immunological and Life‐History Strategies

2019

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Why do some invertebrates store so much carotenoids in their tissues? Storage of carotenoids may not simply be passive and dependent on their environmental availability, as storage variation exists at various taxonomic scales, including among individuals within species. While the strong antioxidant and sometimes immune-stimulating properties of carotenoids may be beneficial enough to cause the evolution of features improving their assimilation and storage, they may also have fitness downsides explaining why massive carotenoid storage is not universal. Here, the functional and ecological implications of carotenoid storage for the evolution of invertebrate innate immune defenses are examined, especially in crustaceans, which massively store carotenoids for unclear reasons. Three testable hypotheses about the role of carotenoid storage in immunological (resistance and tolerance) and life-history strategies (with a focus on aging) are proposed, which may ultimately explain the storage of large amounts of these pigments in a context of host-pathogen interactions.

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Bacterial communities associated with aquatic organisms in the floodwater of a Japanese paddy field estimated by RFLP pattern analysis

Cited by 9 publications

References 30 publications

Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Comparison of Bacterial Communities Associated with Microcrustaceans from the Floodwater of a Paddy Field Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Effect of Application of Rice Straw and Compost on the Bacterial Communities Associated withMoinasp. in the Floodwater of a Paddy Soil Microcosm: Estimation Based on DGGE Pattern and Sequence Analyses

Storage of Carotenoids in Crustaceans as an Adaptation to Modulate Immunopathology and Optimize Immunological and Life‐History Strategies

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