Microbial communities associated with some harmful dinoflagellates from Malaysian waters revealed by culture-independent and culturedependent approaches

Muhd Danish-Daniel, Asmat Ahmad, Gires Usup

Research output: Contribution to journalArticle

Abstract

Diversity of bacteria associated with toxic dinoflagellates Alexandrium minutum, Alexandrium tamiyavanichii and Pyrodinium bahamense var compressum were assessed using culture-dependent and -independent approaches. Total DNA from the dinoflagellate cultures as well as those of culturable bacteria was extracted and used as templates for PCR amplification of the 16S rDNA. The PCR products from directly extracted genomics were analysed by denaturing gradient gel electrophoresis (DGGE) and direct sequencing. A total of 15 culturable isolates were obtained, of which 4 were from A. minutum culture, 7 were from A. tamiyavanichii culture and 4 from P. bahamense culture. DGGE analysis produced a total of 25 bands of which 6 were from A. minutum culture, 9 were from A. tamiyavanichii culture and 10 were from P. bahamense culture. Fourteen of the bands were unique. Sequence analysis of the unique bands and culturable isolates showed that 15 phylotypes belonged to the α-Proteobacteria, 1 belonged to β-Proteobacteria, 4 belonged to the γ-Proteobacteria, 9 belonged to Cytophaga-Flavobacterium-Bacteroides (CFB) and 1 belonged to Firmicutes. Only 3 of the 14 sequences obtained from the DGGE analysis had matches to known genera in Genbank. In this study, both approaches are important as not all bacteria could be solely detected.

Original languageEnglish
Pages (from-to)976-984
Number of pages9
JournalAACL Bioflux
Volume9
Issue number5
Publication statusPublished - 2016

Fingerprint

Proteobacteria
denaturing gradient gel electrophoresis
dinoflagellate
microbial communities
microbial community
bacteria
Cytophaga
Flavobacterium
Bacteroides
Firmicutes
Alexandrium
electrokinesis
gel
water
sequence analysis
bacterium
genomics
DNA
Miozoa
Alexandrium minutum

Keywords

  • 16S rDNA sequence analysis
  • Bacterial communties
  • DGGE analysis
  • Toxic dinoflagellates

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Aquatic Science
  • Water Science and Technology
  • Management, Monitoring, Policy and Law

Cite this

Microbial communities associated with some harmful dinoflagellates from Malaysian waters revealed by culture-independent and culturedependent approaches. / Danish-Daniel, Muhd; Ahmad, Asmat; Usup, Gires.

In: AACL Bioflux, Vol. 9, No. 5, 2016, p. 976-984.

Research output: Contribution to journalArticle

@article{f926f604d838413d952a37e55e09a303,
title = "Microbial communities associated with some harmful dinoflagellates from Malaysian waters revealed by culture-independent and culturedependent approaches",
abstract = "Diversity of bacteria associated with toxic dinoflagellates Alexandrium minutum, Alexandrium tamiyavanichii and Pyrodinium bahamense var compressum were assessed using culture-dependent and -independent approaches. Total DNA from the dinoflagellate cultures as well as those of culturable bacteria was extracted and used as templates for PCR amplification of the 16S rDNA. The PCR products from directly extracted genomics were analysed by denaturing gradient gel electrophoresis (DGGE) and direct sequencing. A total of 15 culturable isolates were obtained, of which 4 were from A. minutum culture, 7 were from A. tamiyavanichii culture and 4 from P. bahamense culture. DGGE analysis produced a total of 25 bands of which 6 were from A. minutum culture, 9 were from A. tamiyavanichii culture and 10 were from P. bahamense culture. Fourteen of the bands were unique. Sequence analysis of the unique bands and culturable isolates showed that 15 phylotypes belonged to the α-Proteobacteria, 1 belonged to β-Proteobacteria, 4 belonged to the γ-Proteobacteria, 9 belonged to Cytophaga-Flavobacterium-Bacteroides (CFB) and 1 belonged to Firmicutes. Only 3 of the 14 sequences obtained from the DGGE analysis had matches to known genera in Genbank. In this study, both approaches are important as not all bacteria could be solely detected.",
keywords = "16S rDNA sequence analysis, Bacterial communties, DGGE analysis, Toxic dinoflagellates",
author = "Muhd Danish-Daniel and Asmat Ahmad and Gires Usup",
year = "2016",
language = "English",
volume = "9",
pages = "976--984",
journal = "AACL Bioflux",
issn = "1844-8143",
publisher = "Bioflux Publishing House",
number = "5",

}

TY - JOUR

T1 - Microbial communities associated with some harmful dinoflagellates from Malaysian waters revealed by culture-independent and culturedependent approaches

AU - Danish-Daniel, Muhd

AU - Ahmad, Asmat

AU - Usup, Gires

PY - 2016

Y1 - 2016

N2 - Diversity of bacteria associated with toxic dinoflagellates Alexandrium minutum, Alexandrium tamiyavanichii and Pyrodinium bahamense var compressum were assessed using culture-dependent and -independent approaches. Total DNA from the dinoflagellate cultures as well as those of culturable bacteria was extracted and used as templates for PCR amplification of the 16S rDNA. The PCR products from directly extracted genomics were analysed by denaturing gradient gel electrophoresis (DGGE) and direct sequencing. A total of 15 culturable isolates were obtained, of which 4 were from A. minutum culture, 7 were from A. tamiyavanichii culture and 4 from P. bahamense culture. DGGE analysis produced a total of 25 bands of which 6 were from A. minutum culture, 9 were from A. tamiyavanichii culture and 10 were from P. bahamense culture. Fourteen of the bands were unique. Sequence analysis of the unique bands and culturable isolates showed that 15 phylotypes belonged to the α-Proteobacteria, 1 belonged to β-Proteobacteria, 4 belonged to the γ-Proteobacteria, 9 belonged to Cytophaga-Flavobacterium-Bacteroides (CFB) and 1 belonged to Firmicutes. Only 3 of the 14 sequences obtained from the DGGE analysis had matches to known genera in Genbank. In this study, both approaches are important as not all bacteria could be solely detected.

AB - Diversity of bacteria associated with toxic dinoflagellates Alexandrium minutum, Alexandrium tamiyavanichii and Pyrodinium bahamense var compressum were assessed using culture-dependent and -independent approaches. Total DNA from the dinoflagellate cultures as well as those of culturable bacteria was extracted and used as templates for PCR amplification of the 16S rDNA. The PCR products from directly extracted genomics were analysed by denaturing gradient gel electrophoresis (DGGE) and direct sequencing. A total of 15 culturable isolates were obtained, of which 4 were from A. minutum culture, 7 were from A. tamiyavanichii culture and 4 from P. bahamense culture. DGGE analysis produced a total of 25 bands of which 6 were from A. minutum culture, 9 were from A. tamiyavanichii culture and 10 were from P. bahamense culture. Fourteen of the bands were unique. Sequence analysis of the unique bands and culturable isolates showed that 15 phylotypes belonged to the α-Proteobacteria, 1 belonged to β-Proteobacteria, 4 belonged to the γ-Proteobacteria, 9 belonged to Cytophaga-Flavobacterium-Bacteroides (CFB) and 1 belonged to Firmicutes. Only 3 of the 14 sequences obtained from the DGGE analysis had matches to known genera in Genbank. In this study, both approaches are important as not all bacteria could be solely detected.

KW - 16S rDNA sequence analysis

KW - Bacterial communties

KW - DGGE analysis

KW - Toxic dinoflagellates

UR - http://www.scopus.com/inward/record.url?scp=84989208887&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84989208887&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:84989208887

VL - 9

SP - 976

EP - 984

JO - AACL Bioflux

JF - AACL Bioflux

SN - 1844-8143

IS - 5

ER -