bacteria recovered from aquaculture in oman, with emphasis on aeromonas spp.

213 Pages·2015·3.12 MB·English

BACTERIA RECOVERED FROM
AQUACULTURE IN OMAN, WITH
EMPHASIS ON AEROMONAS SPP.

THESIS SUMITTED TO THE UNIVERSITY OF STIRLING
FOR THE DEGREE OF DOCTOR OF PHILOSOPHY
BY
ALYA SALIM AL-GHABSHI
APRIL 2015

INSTITUTE OF AQUACULTURE
DECLARATION

I hereby declare that the work and results presented in this thesis were conducted by me at
the Institute of Aquaculture, University of Stirling, Scotland. The work presented in this
thesis has not been previously submitted for any other degree or qualification. The litera-
ture consulted has been cited and where appropriate, collaborative assistance has been
acknowledged.

Signature: ________________________________________

Signature of Principal Supervisor: ________________________________________

Signature of Supervisor: ________________________________________

Date: ________________________________________

I
In loving memory of my mother
To my husband Hamood Al-Ghabshi and My lovely sons Yousuf and Mohammed
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Acknowledgements

ACKNOWLEDGEMENTS

First of all, I would like to thank the almighty Allah for helping me to finish my study
successfully.
I would like to express my warmest gratitude to my supervisor’s and mentors Professor
Brian Austin and Dr. Mags Crumlish, who has introduced me to the world of science.
Their support and guidance gave me to find out the way to continue my research in the
field and laboratory. During writing up this thesis, their valuable comments, suggestions,
excellent proofreading skills and encouragement helped me to complete this work with
the incredible optimism.
I am also extremely grateful for the assistance and guidance from Dr. Ponnerassery S.
Sudheesh and from staff members at the Institute of Aquaculture (stirling) particularly,
Mrs. Debbie Faichney, Mrs. Jan Seggie, Dr. John Taggart, Mrs. Jacquie Ireland, Mr. Niall
Auchinachie, Dr. Amaya Albalat, Professor Randolph Richards. Without their training,
perseverance and patience I would never have learned the techniques required to finish
this project.
I am also thankfull Amal Al- Maashari , Umm kulthum Al Kindi, Nasser Al-Aboudi, Wa-
heeda Al-Amri, Mr. Denny Conway, Mochamad Syaifudin , Greta Carmona-Antonanzas ,
Gil Ha Yoon and Dr. Andy Shinn for their kind help in my research.
Special thanks to my dear friends Olga Rubio Mejia, Taslima Khanam and to all my good
friends in Stirling who helped me to find a home abroad.
My special thanks to my sisters, nieces and nephews for they endless love that encour-
aged me a lot. I’m deeply grateful to my husband Hamood Al-Ghabshi, for his endless
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Acknowledgements

love and support that helped me to keep going, especially during the time I was very

much frustrated.
I also wish to thank my lovely sons Yousuf and Mohammed for doing their best to under-

stand their mother who had to be confined to her study for such a long time.
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Abstract

ABSTRACT

Aquaculture is being seriously considered as a promising sustainable industry in the Sul-
tanate of Oman. Fish farming commenced in Oman in 1986, but it was only in 2011 that it
became a more commercially driven sector. While worldwide aquaculture production is
expected to rise to meet the shortage in capture fisheries, there is a parallel requirement to
identify potential threats to the health and welfare of existing aquatic farmed stocks and to
take appropriate steps to mitigate them.

As aquaculture in Oman is in an early stage of development, it is important to acquire
baseline data on the existence and prevalence of aquatic diseases and pathogens to help
the Government make policy decisions to develop health management regimes applicable
for Omani aquaculture. Therefore, this study was conducted to evaluate current farming
practices of tilapia in Oman, to investigate the bacterial species composition and distribu-
tion from different sites in some of the economically important fish species, and to study
the characteristics and pathogenicity of Aeromonas species.

The current practices were studied for 9 Nile tilapia (Oreochromis niloticus) farms from
four areas (Al Batinah, Ad Dhahirah, Ad Dakhiliyah and Ash Sharqiyah North) during the
period of September to November 2012 by using questionnaires and interviews with the
farm owners and staff.

In total 417 fish representing 5 target species were chosen on the basis of the commercial
importance and their potential for aquaculture in Oman, including red spot emperor (Le-
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Abstract

thrinus lentjan), king soldier bream (Argyrops spinifer), white spotted rabbit fish (Siganus
canaliculatus), abalone (Haliotis mariae) and tilapia (Oreochromis niloticus). The fish
were collected from 5 main sampling areas in Oman (Muscat, Mudhaibi, Manah, Sohar
and Salalah) based on the Atlas of suitable sites for aquaculture in Oman to investigate
the bacterial species composition and distribution. The animals were examined for clini-
cal signs of disease prior to routine bacteriology. Bacterial isolates were recovered using
traditional methods and identified to species level using phenotypic and molecular ap-
proaches using 16S rDNA, 16S rDNA RFLP and 16S rDNA sequencing. Experimental
fish challenge studies were also conducted using both live bacterial cells and ECP protein
to investigate the pathogenicity of Aeromonas isolates. In addition, the presence of some
virulence factors was investigated using both phenotypic and genotypic methods.

The results of this study showed that, the most farms in the Oman follow very similar
farming practices. The major proportion of the tilapia is consumed within the local com-
munities. A number of farmers have experienced mortalities, which were considered to be
attributable to poor water quality, overcrowding or due to excessive feeding. Farmers fac-
ing fish mortalities tended not to record the problems due to a lack of understanding of
the concept of fish farm management. There is a regulation about aquaculture and related
quality control, but it has not yet been implemented in an appropriate manner in Oman.

From the diverse group of bacteria recovered from wild and farmed fish, 83% of the total
isolates comprised Gram negative, rod-shaped bacteria. The most frequently isolated
groups from marine and cultured fish were Aeromonas spp., Vibrio spp., Sphingobacte-
rium spp., Micrococcus spp. and Staphylococcus spp., with Aeromonas spp. being the
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Abstract

predominant group representing 25% of the isolates recovered in this study. Identification
of the Aeromonas spp. showed 57% agreement between the results of phenotypic and
genotypic methodologies, and determined 6 species as the dominant organisms, i.e. A.
veronii, A. jandaei, A. caviae, A. trota, A. encheleia and A. salmonicida. 65% of the iso-
lates shared 99% 16S rDNA sequence similarity with the closest sequences in GenBank,
and the dominant species was A. veronii.
In conclusion, the Aeromonas isolates recovered from fish with clinical signs of disease
showed heterogeneity in their identification profiles and their pathogenicity.
VII
List of attendance conference and published articles

LIST OF ATTENDANCE CONFERENCE AND PUBLISHED ARTICLES

Presentation
 Alya AL-Ghabshi, Brian Austin and Mags Crumlish (18-2-2015). Aeromonas spe-
cies diversity in the aquatic environment of Oman. PhD Research Conference on
sustainable aquaculture 2015 (Stirling University).
Article
 Alya AL-Ghabshi. (March 2015). Disease data in young industry. fish farmer,
www.fishamer-magazine.com ,38,P.49

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Table of contents

TABLE OF CONTENTS

DECLARATION ................................................................................................................ I
ACKNOWLEDGEMENTS ............................................................................................III
ABSTRACT ...................................................................................................................... V
LIST OF ATTENDANCE CONFERENCE AND PUBLISHED ARTICLES ....... VIII
TABLE OF CONTENTS ............................................................................................. VIII
LIST OF FIGURES ...................................................................................................... XVI
chapter 1 . General introduction ...................................................................................... 1
1.1 Background ................................................................................................................ 1
1.2 Fish and fisheries in Oman ......................................................................................... 2
1.3 Fish pathogens ........................................................................................................... 5
1.4 Aeromonas ................................................................................................................. 7
1.4.1 Disease distribution and clinical signs associated with Aeromonas infections ....... 9
1.4.2 Clinical signs of disease .......................................................................................... 10
1.4.3 Geographical distribution ....................................................................................... 13
1.4.4 Diagnostic methods for the detection and characterization of Aeromonas spp. .. 13
1.4.5 Pathogenicity and virulence factors ....................................................................... 16
1.5 Research objectives ................................................................................................. 26
1.6 References................................................................................................................ 27
chapter 2 . Current Status of Aquaculture in Oman .................................................... 46
2.1 Introduction ............................................................................................................. 46
2.1.1 History of aquaculture in the region ...................................................................... 46
2.1.2 Current situation of aquaculture in Oman ............................................................. 47
2.1.3 Commercial aquaculture production in Oman ...................................................... 51
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