COASTAL BACTERIAL COMMUNITIES: THEIR POTENTIAL ROLES IN DIMETHYLSULPHIDE (DMS) PRODUCTION AND CORAL DEFENCE By FELICITY KUEK WEN IK A thesis submitted in partial fulfilment of the requirements for the degree of Masters of Science (by Research) Faculty of Engineering, Computing and Science Swinburne University of Technology (Sarawak campus) 2014
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COASTAL BACTERIAL COMMUNITIES:
THEIR POTENTIAL ROLES IN
DIMETHYLSULPHIDE (DMS)
PRODUCTION AND CORAL DEFENCE
By
FELICITY KUEK WEN IK
A thesis submitted in partial fulfilment of
the requirements for the degree of
Masters of Science (by Research)
Faculty of Engineering, Computing and Science
Swinburne University of Technology (Sarawak campus)
2014
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Abstract
Little is known about the microbial communities in the South China Sea, especially
the eastern region and this study aims to expand our knowledge on the diversity of
culturable bacterial communities in this area. The Talang-Satang region is situated
off the coast of Sematan and is especially important as it is one of the most diverse
ecosystems found off Sarawak. Complex microbial communities are known to have
significant influence over coral reef ecosystems. Through isolation and
identification (16S rDNA) of native microbes from the open ocean, coral surface
mucus layer (SML), as well as the surrounding sediment and waters, we were able
to determine the species composition and abundance of the culturable bacteria in
the South China Sea (Kuching and Kota Kinabalu), the Celebes Sea (Semporna) and
the coral reef ecosystem (Talang-talang reef). Comparisons were made with
regards to physico-chemical parameters and bacterial communities. The diversity
of bacterial communities in these marine environments were analysed through
isolation and identification (16S rDNA) of culturable bacteria, as well as
preparation of clone libraries and subsequent restriction fragment length
polymorphism (RFLP). It was observed that although the majority of bacteria in
Kuching, Kota Kinabalu and Semporna are members of the Proteobacteria group,
the composition of bacterial communities in these three areas did vary
significantly, and the changes were also mirrored in physico-chemical differences.
There is also a clear distinction between the different species found in the different
parts of the reef system. Isolates found attached to the coral were mostly related to
Vibrio spp., presumably attached to the mucus from the water column and
surrounding sediment.
Cultures that were isolated from the SML are found to be closely related to
antibiotic producers with tolerance towards elevated temperatures and heavy
metal contamination. This specialized microbiota may be important for protecting
the corals from pathogens by occupying entry niches and/or through the
production of secondary metabolites (i.e. antibiotics). The role of the mucus-
associated bacteria for the defence of the coral was highlighted by the fact that
isolates related to pathogenic Vibrio spp. and Bacillus spp. were dominant amongst
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the samples from the water column and sediment, and isolates with closest
matches to the known coral pathogens Vibrio coralliilyticus and Vibrio shiloi were
obtained from the SML and sediment samples respectively. The ability of isolates
living in the SML (associated) to inhibit isolates loosely attached to the SML
(attached) and vice versa was assessed at varying temperatures. All isolates were
also screened (using specific sets of primers) for the presence of type I modular
polyketides synthase (PKS) genes responsible for macrolide polyketides
production and non-ribosomal peptide synthetase (NRPS) genes with the ability to
produce immunosuppressants and other antibiotics. Our results indicate that the
mucus-associated bacteria display maximum efficacy to ward off other bacteria at
28 °C, however the inhibitory abilities of mucus-associated bacteria became less
effective as temperatures increased.
One major and globally important role of surface bacteria is their involvement in
the breakdown or osmoregulation of dimethylsulphoniopropionate (DMSP) to
dimethylsulfide (DMS) or methanethiol (MeSH). Using genomic-based studies,
enzymes responsible for DMSP degradation within the microbial community can
be identified and over 200 culturable bacteria were screened for the existence of
two key genes (dmdA, dddP) which are involved in competing, enzymatically
mediated DMSP degradation pathways. Roseobacter spp. which are mainly
responsible for the degradation of DMSP – a major source of oceans’ organic
sulphur – into MeSH were also successfully isolated from the SML. Bacterial DMSP
degraders may also contribute significantly to DMS production when temperatures
are elevated. This is to our knowledge the first comprehensive study looking at
culturable bacteria in the eastern South China Sea and their potential roles in coral
defence and the DMS(P) cycle.
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Acknowledgements
For since the creation of the world God’s invisible qualities – his eternal power and divine nature –
have been clearly seen, being understood from what has been made, so that people are without excuse.
(Romans 1:20)
Foremost, I would like to express my sincere gratitude to my principal
coordinating supervisor, Dr. Moritz Müller for his continuous support of my MSc
study and research, for his patience, motivation, enthusiasm, and immense
knowledge. Thank you for giving me the chance to explore this field, allowing me
freedom and space to make mistakes and for believing in me. I would also like to
extend my appreciation to my co-supervisors: Dr. Aazani Mujahid, Assoc. Prof. Dr.
Lim Po Teen, and Dr. Leaw Chui Pin, for their encouragements, insightful
comments, hard questions, as well as access to laboratories and facilities in
Universiti Malaysia Sarawak (UNIMAS).
Heartfelt thanks also to the Biotechnology laboratory officers and technicians:
Chua Jia Ni, Dyg. Rafika Atiqah and Nurul Arina, for allowing me to use the labs
past office hours and weekends, and for loaning me apparatus and experiment
materials when I needed them. Without your help, this project may not have been
completed on time.
A big thank you to my fellow lab mates and student helpers: Onn May Ling, Jessica
Fong, Lim Li Fang, and Ngu Lin Hui, for the stimulating discussions, the company
during long hours in the lab, the support during various existential crises and for
all the fun we have had in the last two years.
Last but not least, I would like to thank my family, especially my mother, for
encouraging me to take up this M.Sc. opportunity and for having my back
throughout every circumstance in the past two years.
I am grateful to the Sarawak Foundation for providing me with funding via the
Tunku Abdul Rahman Scholarship which enabled me to pursue this postgraduate
study.
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Declaration
I hereby declare that this research entitled “Coastal Bacterial Communities: Their
Potential Roles in Dimethylsulphide (DMS) Production and Coral Defence” is
original and contains no material which has been accepted for the award to the
candidate of any other degree or diploma, except where due reference is made in
the text of the examinable outcome; to the best of my knowledge contains no
material previously published or written by another person except where due
reference is made in the text of the examinable outcome; and where work is based
on joint research or publications, discloses the relative contributions of the
respective workers or authors.
(FELICITY KUEK WEN IK)
Date: 9th September 2014
In my capacity as the Principal Coordinating Supervisor of the candidate’s thesis, I
certify that the above statements are true to the best of my knowledge.
(MORITZ MÜLLER)
Date: 9th September 2014.
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Publications Arising from this Thesis
The work described in this thesis has been submitted as described in the following:
Kuek F.W.I., Mujahid A., Lim P.T., Leaw C.P. & Müller M. ‘Diversity and DMS(P)-
related genes in culturable bacterial communities in Malaysian coastal
waters’. Systematic and Applied Microbiology (Manuscript ID:).
Kuek F.W.I., Lim L.F., Ngu L.H., Mujahid A., Lim P.T., Leaw C.P. & Müller M. ‘The
potential roles of bacterial communities in coral defence: a case study at
Table 3.3: Indices used to quantify the diversity of bacterial communities at
Kuching, Kota Kinabalu and Semporna.
Genus Kuching Kota Kinabalu Semporna
Total isolates (N) 89 39 48 Total genus (S) 14 15 14 Margalef index (DMg) 2.90 3.82 3.36 Shannon index (H’) 1.60 2.42 2.18 Shannon evenness (J’) 0.61 0.89 0.83 Smith and Wilson evenness (Evar) 0.49 0.69 0.59
*Formulae of diversity indices are from Margalef (1958), Shannon & Weaver (1963)
and Smith & Wilson (1996).
The Margalef index (DMg) measures species richness and is highly sensitive to
sample size (Magurran 2004). DMg is a more accurate index when it comes to
sample richness as it utilises absolute numbers compared to a density data matrix
(Gamito 2010). The commonly used Shanon index (H’) considers proportions,
ensuring no differences when using either data set (Gamito 2010). However,
calculated H’ values can be underestimations due to incomplete coverage as it
gives more weight to rare than to common species (S), making it more sensitive to
absolute (but not relative) changes in their abundance (Hill et al. 2003). Values for
both indices indicate that the bacterial community in Kota Kinabalu is the most
diverse with a greater number of genuses within the community, followed by the
communities in Semporna and Kuching.
The Shannon evenness index (J’) is derived from H’ which therefore makes it
sensitive to changes in evenness of rare species, thereby possibly overestimating
its true value (Hill et al. 2003). The Smith and Wilson evenness index (Evar),
however, is known to show greater resolution in reflecting true values (Blackwood
et al. 2007). The evenness values from both J’ and Evar show that not only does the
bacterial community in Kota Kinabalu have a greater amount of genuses present,
but the individuals in the community are distributed most equitably among these
genuses, and this corelation is replicated in the results from Semporna and
Kuching.
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Figure 3.7: 16S rRNA gene-based phylogenetic tree representing bacterial
sequences found in Kuching 1611. The phylogenetic tree was generated with
distance methods, and sequence distances were estimated with the neighbour-
joining method. Bootstrap values ≥50 are shown and the scale bar represents a
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difference of 0.05 substitution per site. Accession numbers for the reference
sequences are indicated.
Figure 3.8: 16S rRNA gene-based phylogenetic tree representing bacterial
sequences found in Kuching 1911. The phylogenetic tree was generated with
distance methods, and sequence distances were estimated with the neighbour-
joining method. Bootstrap values ≥50 are shown and the scale bar represents a
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difference of 0.1 substitution per site. Accession numbers for the reference
sequences are indicated.
Figure 3.9: 16S rRNA gene-based phylogenetic tree representing bacterial
sequences found in Kota Kinabalu. The phylogenetic tree was generated with
distance methods, and sequence distances were estimated with the neighbour-
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joining method. Bootstrap values ≥50 are shown and the scale bar represents a
difference of 0.05 substitution per site. Accession numbers for the reference
sequences are indicated.
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Figure 3.10: 16S rRNA gene-based phylogenetic tree representing bacterial
sequences found in Semporna. The phylogenetic tree was generated with distance
methods, and sequence distances were estimated with the neighbour-joining
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method. Bootstrap values ≥50 are shown and the scale bar represents a difference
of 0.1 substitution per site. Accession numbers for the reference sequences are
indicated.
Gammaproteobacteria are the dominant phylogenetic group at all three locations
and at all sampling depths, followed by Alphaproteobacteria (see Figure 3.5).
Betaproteobacteria were only found at Semporna at 1m depth (see Figure 3.6).
These results correlate with existing records of microbial communities found in
coastal and open-ocean environments (Bernard et al. 2000) although samples from
Kuching have some riverine influence. The percentage of bacterial culturability is
2% (Button et al. 1993), thus, giving the possibility that although some groups may
be present in low numbers in cultures, they may still occupy a significant portion
of the bacterial community. However, to better understand their physiology and
ecology, the isolation of bacteria in pure culture remains an essential step in
microbial ecology (Bernard et al. 2000).
In the following, we discuss some highlights of the diversity found within the major
bacterial groups and also try and establish differences between the three different
sampling sites.
The cultured Alphaproteobacteria group consisted of representatives from the
Caulobacteraceae, Phyllobacteriaceae, Rhodobacteraceae and Rhodospirillaceae.
Caulobacteraceae were only found in Kota Kinabalu at 1 m depth with two isolates
related to Brevundimonas diminuta (see Figure 3.9). They are aerobic, non-
photosynthetic organisms which are widespread in natural bodies of water (Stove
Poindexter & Cohen-Bazire 1964). The closest related strains were Brevundimonas
diminuta strain c138 (GenBank accession number FJ950570; 99% similarity) and
Brevundimonas diminuta strain KSC_AK3a (GenBank accession number EF191247;
100% similarity), both of which have shown antibiotic resistance under extreme
conditions (La Duc et al. 2007; Li et al. 2010). Members of the family
Phyllobacteriaceae are part of a large variety of bacteria able to reduce nitrate to
nitrite or to molecular nitrogen (Zumft 1997; Labbé, Parent & Villemur 2004).
Isolates related to this family were grouped with Nitratireductor spp. and were
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found in Kota Kinabalu and Semporna, at depths of 5 and 10 m (see Figures 3.9 and
3.10). Isolates belonging to Rhodobacteraceae were related to Roseovarius
pacificus strain 81-2 (GenBank accession number NR_043564) and Rhodobacter
capsulatus strain PSB-06 (GenBank accession number FJ866784), with overlaps
across Kuching and Semporna at 1 and 5 m depth (see Figures 3.7, 3.8 and 3.10).
The property to reduce nitric oxide is not restricted to denitrifiers within
Phyllobacteriaceae as strains of Rhodobacter capsulatus have been shown to be
able to transform nitric oxide to nitrous oxide at a significant rate (Bell, Richardson
& Ferguson 1992) and are also able to convert nitrous oxide to nitrogen through
the involvement of cytochrome bc1 complex (Itoh, Matsuura & Satoh 1989;
Richardson et al. 1989). Roseovarius pacificus was previously isolated from deep-
sea sediment of the Western Pacific Ocean and displayed the ability to degrade
polycyclic aromatic hydrocarbons (Wang, Tan & Shao 2009). Rhodospirillaceae are
typically purple non-sulphur photosynthetic bacteria, possessing the adaptive
capacity to grow photosynthetically and by oxidative phosphorylation (Saunders
1978). Cultures from this family were related to Thalassospira spp. which generally
form opaque, unpigmented or slightly yellow colonies on agar (López-López et al.
2002) and are potential bioremediation agents as they have the ability to degrade
polycyclic aromatic hydrocarbons and diesel fuel (Liu et al. 2007; Kim & Kwon
2010; Lai & Shao 2012). Isolates related to the Alphaproteobacteria at all three
areas seem to be involved in the nitrogen cycle and possibly in the degradation of
hydrocarbons.
The sole Betaproteobacteria that was cultured was related to Alcaligenes faecalis
(GenBank accession number JF264463; 88% similarity) which was previously
isolated from a coastal aquaculture environment. The isolate was obtained from
Semporna (see Figure 3.10), an area that is surrounded with aquaculture and
seaweed farms. Alcaligenes faecalis have also been found in salt marsh and
estuarine waters (Ansede, Friedman & Yoch 2001). It has the potential to degrade
DMSP to DMS via acrylate metabolism through the induction of β-
2008) and suspected to be involved in a symbiotic relationship with zooxanthellae
(Raina et al. 2009). An antibiotic produced by Roseobacter, thiotropocin, is a
sulphur compound derived from DMSP metabolism (Wagner-Döbler et al. 2004).
4.4 CONCLUSION
The bacterial communities at the Talang-talang reef were different according to
the environment (coral SML, water column and reef sediment). The coral mucus
community is the most diverse with isolates playing potential roles in coral
defence, while the community from reef sediment is dominated by potentially
pathogenic Vibrio spp.. Two known coral pathogens, Vibrio coralliilyticus and Vibrio
shiloi were successfully cultured from the coral reef environment. While the corals
are healthy at the time of isolation, these opportunistic pathogens may pose a
problem at elevated temperatures.
The coral mucus community also showed high potential in the production of PKS
and NRPS compounds. The inhibitory results support the efficiency of PCR
screening using specific PKS and NRPS primers, whereby PKS and/or NRPS strains
exhibit substantial inhibition activity. Antimicrobial activities of mucus associated
bacteria decrease as temperature increase while mucus attached bacteria are most
effective at 30 °C. This study also confirms the coral mucus as a regulating media
capable of choosing associated communities exhibiting antibacterial properties
under optimum conditions.
The preliminary study on the potential role of coral SML bacterial communities in
the local sulphur cycle revealed that the presence of DMSP degrading genes in the
coral mucus bacterial groups mirrors the general bacterial community where the
majority of gene abundance are within the Gammaproteobacteria, indicating a
major role for the group. The majority of the SML isolates were observed to have
both dmdA and/or dddP genes, showing potential in undergoing both DMSP
degrading pathways depending on DMSP availability. Members of the Roseobacter
genus which is widely associated with corals and DMSP degrading capabilities
were successfully isolated from the coral SML, indicating possible roles (such as?)
in the biogeochemical cycling of sulphur within the mucus.
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Further in-depth characterization of these communities through a combination of
physical, chemical and molecular biological studies is however needed to improve
our understanding of the role of bacteria in coral defence and especially in DMS(P)
cycling.
4.5 ACKNOWLEDGEMENTS
The authors would like to thank the Sarawak Forestry Department for their kind
permission to conduct research at the Talang-Satang National Park (Permit No.
NCCD.907.4.4 (Jld.VI)-104 and Park Permit No. 54/2011). Kuek FWI is funded by
the Sarawak Foundation’s Tunku Abdul Rahman scholarship. The research leading
to these results has received funding from the European Union's Seventh
Framework Programme FP7/2007-2013 under grant agreement no. 226224 -
SHIVA.
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CHAPTER 5
Summary and Future Work
This study has presented (i) an overview of culturable bacterial communities in
waters of the South China Sea, Celebes Sea and a coral reef environment (Talang-
talang reef), (ii) the potential roles of these communities in the marine DMS(P)
cycle and (iii) the antimicrobial properties of cultured isolates from coral SML at
elevated temperatures and their potential role in coral defence.
The bacterial communities in the waters of Kuching and Kota Kinabalu (within the
South China Sea) and Semporna (within the Celebes Sea) are almost entirely
unknown and have not been sampled by either culture or culture-independent
techniques. Members of the Alphaproteobacteria, Gammaproteobacteria and
Firmicutes were successfully cultured from all three sampling locations while
isolates from Betaproteobacteria were only found in Semporna. Differences in
bacterial communities between the three areas can partly be explained by
differences in physico-chemical parameters. Kuching is dominated by potentially
pathogenic Vibrio spp. possibly due to higher nutrients and riverine input at the
sampling locations, while the community at Kota Kinabalu is more indicative of an
open ocean environment. Bacterial communities from Kota Kinabalu and
Semporna also show potential roles in bioremediation, nitrogen fixing and
sulphate reduction.
The bacterial communities at the Talang-talang reef also show variations between
environments (coral SML, water column and reef sediment). The isolated
community from coral mucus is the most diverse of the three, with members from
Actinobacteria, Alphaproteobacteria, Gammaproteobacteria and Firmicutes.
Isolates from the SML also indicate potential roles in coral defence with strains
related to antibiotic producers with tolerance towards elevated temperatures and
heavy metal contamination, while the community from reef sediment is dominated
by potentially pathogenic Vibrio spp..
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Isolates from the SML isolates also displayed a high potential in the production of
PKS and NRPS compounds. Strains that contained PKS and/or NRPS genes did
exhibit substantial inhibition activity in the well diffusion assay. Antimicrobial
properties of mucus associated bacteria were observed to decrease as temperature
increase while mucus attached bacteria were most effective at 30 °C. This is an
indication that different groups of coral mucus bacteria can dominate the SML
environment at different periods depending on temperature, and that
opportunistic pathogens can cause diseases which may lead to bleaching at
elevated temperatures.
Two known coral pathogens, Vibrio coralliilyticus and Vibrio shiloi were
successfully cultured from the coral reef environment, the latter showing
resistance against the antimicrobial properties of the mucus associated bacterial
community. While the corals are healthy at the time of isolation, these
opportunistic pathogens may pose a problem at elevated temperatures.
In both open water and coral reef environments studied, the cultured bacterial
communities displayed an abundance of DMSP degrading genes. Communities in
this study have either dmdA or dddP or both genes when screened, showing high
adaptability in DMS(P) utilisation which we believe is influenced by bacterial
carbon and sulphur demands and by DMSP availability.
5.1 Future research
Culturing and isolation of bacteria is necessary for detailed studies of physiology
and ecological function. Culture-based methods used in this study enables us to
further biochemically classify and analyse the bacterial portion of marine
environment. Further in-depth characterization of these communities through a
combination of physical, chemical and molecular biological studies is needed and
will improve our understanding of the role of bacteria in DMS(P), coral defence
and their impacts on climate change. Initial clone library from Kuching and Kota
Kinabalu showed that culture-independent and cultured bacterial communities are
very different, so further molecular-based studies are essential for a more
complete assessment of their diversity.
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The use of an assortment of media types and growth condition variables can aid in
increasing the diversity of microorganisms recovered by culturing and discovery of
other specific properties fundamental to the species. Studies by Vila-Costa et al.
2010 have successfully utilised DMSP enriched media to select for bacteria capable
of degrading DMSP into DMS from the natural environment. The approach used in
this study did uncover the existence of dmdA and dddP genes in species that were
previously involved in DMSP degradation (i.e. Alcaligenes faecalis), confirming
their potential role in our waters. However, our understanding of the role of the
genes in the various isolates (i.e. gene activity, conditions for ‘bacterial switch’) is
limited and further studies are needed to reveal their role in the sulphur cycle.
Partial sequencing of the 16S gene is insufficient for a thorough identification of
the bacterial isolates; therefore these isolates will require further genetic
delineation using gene specific primers.
After final identification it would also be of interest to see if the isolates that are
related to Vibrio coralliilyticus and Vibrio shiloi actually do cause diseases on
corals; if the disease symptoms differ or even why the corals in our reef are healthy
despite enhanced temperatures and existence of potentially pathogenic strains.
Furthermore, some of the isolates that have displayed enhanced antibiotic activity
at higher temperatures could be tested on corals and see if they develop diseases.
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References
Adam, A, Mohammad-Noor, N, Anton, A, Saleh, E, Saad, S & Muhd Shaleh, SR 2011, “Temporal and spatial distribution of harmful algal bloom (HAB) species in coastal waters of Kota Kinabalu, Sabah, Malaysia,” Harmful Algae, vol. 10, no. 5, pp. 495–502.
Aguirre, AA, Balazs, GH, Zimmerman, B & Spraker, TR 1994, “Evaluation of Hawaiian green turtles (Chelonia mydas) for potential pathogens associated with fibropapillomas,” Journal of Wildlife Diseases, vol. 30, no. 1, pp. 8–15.
Van Alstyne, K, Schupp, P & Slattery, M 2006, “The distribution of dimethylsulfoniopropionate in tropical Pacific coral reef invertebrates,” Coral Reefs, vol. 25, no. 3, Springer-Verlag, pp. 321–327.
Andreae, MO 1986, “The Ocean as a Source of Atmospheric Sulfur Compounds,” in P Buat-Ménard (ed.), The Role of Air-Sea Exchange in Geochemical Cycling SE - 14, Springer Netherlands, pp. 331–362.
Andreae, MO & Crutzen, PJ 1997, “Atmospheric Aerosols: Biogeochemical Sources and Role in Atmospheric Chemistry,” Science, vol. 276, no. 5315, pp. 1052–1058.
Andreae, MO & Raemdonck, H 1983, “Dimethyl Sulfide in the Surface Ocean and the Marine Atmosphere: A Global View,” Science, vol. 221, no. 4612, pp. 744–747.
Ansari, MZ, Yadav, G, Gokhale, RS & Mohanty, D 2004, “NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases,” Nucleic Acids Research, vol. 32, no. suppl 2, pp. W405–W413.
Ansede, JH, Friedman, R & Yoch, DC 2001, “Phylogenetic Analysis of Culturable Dimethyl Sulfide-Producing Bacteria from a Spartina-Dominated Salt Marsh and Estuarine Water,” Applied and Environmental Microbiology, vol. 67, no. 3, pp. 1210–1217.
Ansede, JH, Pellechia, PJ & Yoch, DC 1999, “Metabolism of Acrylate to β-Hydroxypropionate and Its Role in Dimethylsulfoniopropionate Lyase Induction by a Salt Marsh Sediment Bacterium, Alcaligenes faecalis M3A,” Applied and Environmental Microbiology, vol. 65, no. 11, pp. 5075–5081.
Anzai, Y, Kim, H, Park, JY, Wakabayashi, H & Oyaizu, H 2000, “Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence.,” International Journal of Systematic and Evolutionary Microbiology, vol. 50, no. 4, pp. 1563–1589.
Archer, SD, Ragni, M, Webster, R, Airs, RL & Geider, RJ 2010, “Dimethyl sulfoniopropionate and dimethyl sulfide production in response to
P a g e | 96
photoinhibition in Emiliania huxleyi,” Limnology and oceanography, vol. 55, no. 4, American Society of Limnology and Oceanography, pp. 1579–1589.
Arnon, S, Ronen, Z, Adar, E, Yakirevich, A & Nativ, R 2005, “Two-dimensional distribution of microbial activity and flow patterns within naturally fractured chalk,” Journal of Contaminant Hydrology, vol. 79, no. 3–4, pp. 165–186.
Arrigo, KR 2005, “Marine microorganisms and global nutrient cycles,” Nature, vol. 437, no. 7057, pp. 349–355.
Awang, D, Moshidi, MZ & Muda, AA 2003, “Living coral reef resources of Sarawak, with special reference Kuching area,” fri.gov.my, pp. 1–13.
Ayuso-Sacido, a & Genilloud, O 2005, “New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups.,” Microbial ecology, vol. 49, no. 1, pp. 10–24.
Baker, AC, Glynn, PW & Riegl, B 2008, “Climate change and coral reef bleaching: An ecological assessment of long-term impacts, recovery trends and future outlook,” Estuarine, Coastal and Shelf Science, vol. 80, no. 4, Elsevier Ltd, pp. 435–471.
Banin, E, Ben-Haim, Y, Israely, T, Loya, Y & Rosenberg, E 2000, “Effect of the Environment on the Bacterial Bleaching of Corals,” Water, Air, and Soil Pollution, vol. 123, no. 1-4, Kluwer Academic Publishers, pp. 337–352.
Banin, E, Israely, T, Kushmaro, A, Loya, Y, Orr, E & Rosenberg, E 2000, “Penetration of the Coral-Bleaching Bacterium Vibrio shiloi into Oculina patagonica,” Applied and Environmental Microbiology, vol. 66, no. 7, pp. 3031–3036.
Banin, E, Vassilakos, D, Orr, E, Martinez, RJ & Rosenberg, E 2003, “Superoxide dismutase is a virulence factor produced by the coral bleaching pathogen Vibrio shiloi.,” Current microbiology, vol. 46, no. 6, pp. 418–22.
Barneah, O, Ben-Dov, E, Kramarsky-Winter, E & Kushmaro, A 2007, “Characterization of black band disease in Red Sea stony corals.,” Environmental microbiology, vol. 9, no. 8, pp. 1995–2006.
Baticados, MCL, Lavilla-Pitogo, CR, Cruz-Lacierda, ER, de la Peña, LD & Suñaz, NA 1990, “Studies on the chemical control of luminous bacteria Vibrio harveyi and V splendidus solated from diseased Penaeus monodon arvae and rearing water.,” Diseases of Aquatic Organisms, vol. 9, no. 2, Inter Research, pp. 133–139.
Bell, LC, Richardson, DJ & Ferguson, SJ 1992, “Identification of nitric oxide reductase activity in Rhodobacter capsulatus: the electron transport pathway can either use or bypass both cytochrome c2 and the cytochrome bc1 complex,” Journal of General Microbiology, vol. 138, no. 3, pp. 437–443.
P a g e | 97
Ben-Haim, Y, Banim, E, Kushmaro, a, Loya, Y & Rosenberg, E 1999, “Inhibition of photosynthesis and bleaching of zooxanthellae by the coral pathogen Vibrio shiloi.,” Environmental microbiology, vol. 1, no. 3, pp. 223–9.
Ben-Haim, Y & Rosenberg, E 2002, “A novel Vibrio sp. pathogen of the coral Pocillopora damicornis,” Marine Biology, vol. 141, no. 1, Springer-Verlag, pp. 47–55.
Ben-Haim, Y, Thompson, FL, Thompson, CC, Cnockaert, MC, Hoste, B, Swings, J & Rosenberg, E 2003, “Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis,” International Journal of Systematic and Evolutionary Microbiology, vol. 53, no. 1, pp. 309–315.
Ben-Haim, Y, Zicherman-Keren, M & Rosenberg, E 2003, “Temperature-Regulated Bleaching and Lysis of the Coral Pocillopora damicornis by the Novel Pathogen Vibrio coralliilyticus,” Applied and Environmental Microbiology, vol. 69, no. 7, pp. 4236–4242.
Bernard, L, Schäfer, H, Joux, F, Courties, C, Muyzer, G & Lebaron, P 2000, “Genetic diversity of total, active and culturable marine bacteria in coastal seawater,” Aquatic Microbial Ecology, vol. 23, no. 1, pp. 1–11.
Bidle, KD & Fletcher, M 1995, “Comparison of free-living and particle-associated bacterial communities in the chesapeake bay by stable low-molecular-weight RNA analysis.,” Applied and Environmental Microbiology, vol. 61, no. 3, pp. 944–952.
Birnboim, HC & Doly, J 1979, “A rapid alkaline extraction procedure for screening recombinant plasmid DNA,” Nucleic Acids Research, vol. 7, no. 6, pp. 1513–1523.
Blackwood, CB, Hudleston, D, Zak, DR & Buyer, JS 2007, “Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities,” Applied and Environmental Microbiology, vol. 73, no. 16, pp. 5276–5283.
Bourne, D, Iida, Y, Uthicke, S & Smith-Keune, C 2008, “Changes in coral-associated microbial communities during a bleaching event.,” The ISME journal, vol. 2, no. 4, pp. 350–63.
Bourne, DG, Garren, M, Work, TM, Rosenberg, E, Smith, GW & Harvell, CD 2009, “Microbial disease and the coral holobiont.,” Trends in microbiology, vol. 17, no. 12, pp. 554–62.
Bourne, DG & Munn, CB 2005, “Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef,” Environmental Microbiology, vol. 7, no. 8, Blackwell Science Ltd, pp. 1162–1174.
P a g e | 98
Boyle, VJ, Fancher, ME & Ross, RW 1973, “Rapid, Modified Kirby-Bauer Susceptibility Test with Single, High-Concentration Antimicrobial Disks,” Antimicrobial Agents and Chemotherapy, vol. 3, no. 3, pp. 418–424.
Brink, A, van Straten, A & van Rensburg, A 1995, “Shewanella (Pseudomonas) putrefaciens Bacteremia,” Clinical Infectious Diseases, vol. 20, no. 5, pp. 1327–1332.
Broadbent, AD & Jones, GB 2004, “DMS and DMSP in mucus ropes, coral mucus, surface films and sediment pore waters from coral reefs in the Great Barrier Reef,” Marine and Freshwater Research, pp. 849–855.
Broadbent, AD, Jones, GB & Jones, RJ 2002, “DMSP in Corals and Benthic Algae from the Great Barrier Reef,” Estuarine, Coastal and Shelf Science, vol. 55, no. 4, pp. 547–555.
Broadbent, P, Baker, KF & Waterworth, Y 1977, “Effect of Bacillus spp. on increased growth of seedlings in steamed and non-treated soil,” Phytopathology, vol. 67, pp. 1027–1034.
Buddemeier, RW, Kleypas, JA & Aronson, RB 2004, Coral reefs & global climate change: potential contributions of climate change to stresses on coral reef ecosystems, Pew Center on Global Climate Change.
Button, DK, Schut, F, Quang, P, Martin, R & Robertson, BR 1993, “Viability and Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results,” Applied and Environmental Microbiology, vol. 59, no. 3, pp. 881–891.
Cabral, R, Cruz-Trinidad, A, Geronimo, R, Napitupulu, L, Lokani, P, Boso, D, Casal, CM, Ahmad Fatan, N & Aliño, P 2013, “Crisis sentinel indicators: Averting a potential meltdown in the Coral Triangle,” Marine Policy, vol. 39, no. 0, pp. 241–247.
Cane, DE 1997, “Introduction: Polyketide and nonribosomal polypeptide biosynthesis. From collie to coli,” Chemical Reviews, vol. 97, no. 7, ACS Publications, pp. 2463–2464.
Cervino, JM, Thompson, FL, Gomez-Gil, B, Lorence, E a, Goreau, TJ, Hayes, RL, Winiarski-Cervino, KB, Smith, GW, Hughen, K & Bartels, E 2008, “The Vibrio core group induces yellow band disease in Caribbean and Indo-Pacific reef-building corals.,” Journal of applied microbiology, vol. 105, no. 5, pp. 1658–71.
Chang, JC, Ossoff, SF, Lobe, DC, Dorfman, MH, Dumais, CM, Qualls, RG & Johnson, JD 1985, “UV inactivation of pathogenic and indicator microorganisms.,” Applied and Environmental Microbiology, vol. 49, no. 6, pp. 1361–1365.
P a g e | 99
Charlson, RJ, Lovelock, JE, Andreae, MO & Warren, SG 1987, “Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate,” Nature, vol. 326, no. 6114, pp. 655–661.
Collins, MD, Martinez-Murcia, AJ & Cai, J 1993, “Aeromonas enteropelogenes and Aeromonas ichthiosmia Are Identical to Aeromonas trota and Aeromonas veronii, Respectively, as Revealed by Small-Subunit rRNA Sequence Analysis,” International Journal of Systematic Bacteriology, vol. 43, no. 4, pp. 855–856.
Colwell, RR 1996, “Global Climate and Infectious Disease: The Cholera Paradigm*,” Science, vol. 274, no. 5295, pp. 2025–2031.
Colwell, RR, Macdonell, MT & De Ley, J 1986, “Proposal to Recognize the Family Aeromonadaceae fam. nov.,” International Journal of Systematic Bacteriology, vol. 36, no. 3, pp. 473–477.
Corbett, JJ, Fischbeck, PS & Pandis, SN 1999, “Global nitrogen and sulfur inventories for oceangoing ships,” Journal of Geophysical Research: Atmospheres, vol. 104, no. D3, pp. 3457–3470.
Crump, BC, Armbrust, EV & Baross, JA 1999, “Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean,” Applied and Environmental Microbiology, vol. 65, no. 7, pp. 3192–3204.
Curson, ARJ, Fowler, EK, Dickens, S, Johnston, AWB & Todd, JD 2011, “Multiple DMSP lyases in the γ-proteobacterium Oceanimonas doudoroffii,” Biogeochemistry, vol. 110, no. 1-3, pp. 109–119.
Curson, ARJ, Rogers, R, Todd, JD, Brearley, CA & Johnston, AWB 2008, “Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides.,” Environmental microbiology, vol. 10, no. 3, pp. 757–67.
Curson, ARJ, Sullivan, MJ, Todd, JD & Johnston, AWB 2011, “DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria,” ISME J, vol. 5, no. 7, International Society for Microbial Ecology, pp. 1191–1200.
DeLong, EF 2009, “The microbial ocean from genomes to biomes,” Nature, vol. 459, no. 7244, Nature Publishing Group, pp. 200–206.
Donadio, S, Monciardini, P & Sosio, M 2007, “Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics.,” Natural product reports, vol. 24, no. 5, pp. 1073–109.
P a g e | 100
Du, L, Sánchez, C & Shen, B 2001, “Hybrid Peptide–Polyketide Natural Products: Biosynthesis and Prospects toward Engineering Novel Molecules,” Metabolic Engineering, vol. 3, no. 1, pp. 78–95.
La Duc, MT, Dekas, A, Osman, S, Moissl, C, Newcombe, D & Venkateswaran, K 2007, “Isolation and Characterization of Bacteria Capable of Tolerating the Extreme Conditions of Clean Room Environments,” Applied and Environmental Microbiology, vol. 73, no. 8, pp. 2600–2611.
Ducklow, H & Mitchell, R 1979, “Composition of mucus released by coral reef coelenterates,” Limnol. Oceanogr, vol. 24, no. 4, pp. 706–714.
Dugdale, RC, Wilkerson, FP & Minas, HJ 1995, “The role of a silicate pump in driving new production,” Deep Sea Research Part I: Oceanographic Research Papers, vol. 42, no. 5, pp. 697–719.
Van Duyl, FC, Gieskes, WWC, Kop, AJ & Lewis, WE 1998, “Biological control of short-term variations in the concentration of DMSP and DMS during a Phaeocystis spring bloom,” Journal of Sea Research, vol. 40, no. 3–4, pp. 221–231.
Eden, PA, Schmidt, TM, Blakemore, RP & Pace, NR 1991, “Phylogenetic Analysis of Aquaspirillum magnetotacticum Using Polymerase Chain Reaction-Amplified 16S rRNA-Specific DNA,” International Journal of Systematic Bacteriology, vol. 41, no. 2, pp. 324–325.
Eghtesadi-Araghi, P 2011, “Coral reefs in the Persian Gulf and Oman Sea: an integrated perspective on some important stressors,” J Fish Aquat Sci, vol. 6, pp. 48–56.
Eilers, H, Pernthaler, J, Glöckner, FO & Amann, R 2000, “Culturability and In Situ Abundance of Pelagic Bacteria from the North Sea,” Applied and Environmental Microbiology, vol. 66, no. 7, pp. 3044–3051.
Feltham, RKA, Power, AK, Pell, PA & Sneath, PHA 1978, “A Simple Method for Storage of Bacteria at — 76°C,” Journal of Applied Microbiology, vol. 44, no. 2, Blackwell Publishing Ltd, pp. 313–316.
Fiedler, H-P, Bruntner, C, Bull, AT, Ward, A, Goodfellow, M, Potterat, O, Puder, C & Mihm, G 2005, “Marine actinomycetes as a source of novel secondary metabolites,” Antonie van Leeuwenhoek, vol. 87, no. 1, Kluwer Academic Publishers, pp. 37–42.
Fierer, N & Jackson, RB 2006, “The diversity and biogeography of soil bacterial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 3, pp. 626–631.
Fitt, W, Brown, B, Warner, M & Dunne, R 2001, “Coral bleaching: interpretation of thermal tolerance limits and thermal thresholds in tropical corals,” Coral Reefs, vol. 20, no. 1, Springer-Verlag, pp. 51–65.
Fogelqvist, E 1991, “Dimethylsulphide (DMS) in the Weddell Sea surface and bottom water,” Marine Chemistry, vol. 35, no. 1–4, pp. 169–177.
Frias-Lopez, J, Zerkle, AL, Bonheyo, GT & Fouke, BW 2002, “Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces,” Applied and Environmental Microbiology, vol. 68, no. 5, pp. 2214–2228.
Fujii, I, Watanabe, A, Sankawa, U & Ebizuka, Y 2001, “Identification of Claisen cyclase domain in fungal polyketide synthase WA, a naphthopyrone synthase of Aspergillus nidulans,” Chemistry & Biology, vol. 8, no. 2, pp. 189–197.
Gamito, S 2010, “Caution is needed when applying Margalef diversity index,” Ecological Indicators, vol. 10, no. 2, pp. 550–551.
Gomare, S, Jadhav, J & Govindwar, S 2008, “Degradation of sulfonated azo dyes by the purified lignin peroxidase from Brevibacillus laterosporus MTCC 2298,” Biotechnology and Bioprocess Engineering, vol. 13, no. 2, The Korean Society for Biotechnology and Bioengineering, pp. 136–143.
González, JM, Covert, JS, Whitman, WB, Henriksen, JR, Mayer, F, Scharf, B, Schmitt, R, Buchan, A, Fuhrman, JA, Kiene, RP & Moran, MA 2003, “Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments,” International Journal of Systematic and Evolutionary Microbiology, vol. 53, no. 5, pp. 1261–1269.
González, JM, Kiene, RP & Moran, MA 1999, “Transformation of Sulfur Compounds by an Abundant Lineage of Marine Bacteria in the α-Subclass of the ClassProteobacteria,” Applied and Environmental Microbiology, vol. 65, no. 9, pp. 3810–3819.
González, JM, Simó, R, Massana, R, Covert, JS, Casamayor, EO, Pedrós-Alió, C & Moran, MA 2000, “Bacterial Community Structure Associated with a Dimethylsulfoniopropionate-Producing North Atlantic Algal Bloom,” Applied and Environmental Microbiology, vol. 66, no. 10, pp. 4237–4246.
Goreau, TJ & Hayes, RL 2008, “Effects of rising seawater temperature on coral reefs,” Encyclopedia of Life Support Systems (EOLSS), Eolss Publishers, Oxford, UK.
Grover, JP 2000, “Resource competition and community structure in aquatic micro-organisms: experimental studies of algae and bacteria along a gradient of organic carbon to inorganic phosphorus supply,” Journal of Plankton Research, vol. 22, no. 8, pp. 1591–1610.
P a g e | 102
Harborne, A, Fenner, D, Barnes, A, Beger, M, Harding, S & Roxburgh, T 2000, “Status report on the coral reefs of the east coast of Peninsula Malaysia,” Report Prepared to Department of Fisheries Malaysia, Kuala Lumpur, Malaysia.
Harvell, CD, Mitchell, CE, Ward, JR, Altizer, S, Dobson, AP, Ostfeld, RS & Samuel, MD 2002, “Climate Warming and Disease Risks for Terrestrial and Marine Biota,” Science, vol. 296, no. 5576, pp. 2158–2162.
Heath, RJ & Rock, CO 2002, “The Claisen condensation in biology,” Natural Product Reports, vol. 19, no. 5, The Royal Society of Chemistry, pp. 581–596.
Hedlund, BP & Staley, JT 2001, “Vibrio cyclotrophicus sp. nov., a polycyclic aromatic hydrocarbon (PAH)-degrading marine bacterium.,” International Journal of Systematic and Evolutionary Microbiology, vol. 51, no. 1, pp. 61–66.
Hill, RW, Dacey, JWH & Krupp, DA 1995, “Dimethylsulfoniopropionate in Reef Corals,” Bulletin of Marine Science, pp. 489–494.
Hill, RW, White, BA & Cottrell, MT 1998, “Virus-mediated total release of dimethylsulfoniopropionate from marine phytoplankton: a potential climate process,” Aquatic Microbial Ecology, vol. 14, no. 1, pp. 1–6.
Hill, TCJ, Walsh, KA, Harris, JA & Moffett, BF 2003, “Using ecological diversity measures with bacterial communities,” FEMS Microbiology Ecology, vol. 43, no. 1, Blackwell Publishing Ltd, pp. 1–11.
Hjelm, M, Bergh, Ø, Riaza, A, Nielsen, J, Melchiorsen, J, Jensen, S, Duncan, H, Ahrens, P, Birkbeck, H & Gram, L 2004, “Selection and Identification of Autochthonous Potential Probiotic Bacteria from Turbot Larvae (Scophthalmus maximus) Rearing Units,” Systematic and Applied Microbiology, vol. 27, no. 3, pp. 360–371.
Hoegh-Guldberg, O 1999, “Climate change, coral bleaching and the future of the world’s coral reefs,” Marine and freshwater research.
Hoegh-Guldberg, O 2004, “Coral Reefs and Projections of Future Change,” in E Rosenberg & Y Loya (eds), Coral Health and Disease SE - 26, Springer Berlin Heidelberg, pp. 463–484.
Howard, EC, Sun, S, Biers, EJ & Moran, MA 2008, “Abundant and diverse bacteria involved in DMSP degradation in marine surface waters.,” Environmental microbiology, vol. 10, no. 9, pp. 2397–410.
Huppert, A & Stone, L 1998, “Chaos in the Pacific’s coral reef bleaching cycle,” The American Naturalist, vol. 152, no. 3, pp. 447–459.
Iijima, S, Washio, K, Okahara, R & Morikawa, M 2009, “Biofilm formation and proteolytic activities of Pseudoalteromonas bacteria that were isolated from
P a g e | 103
fish farm sediments,” Microbial Biotechnology, vol. 2, no. 3, Blackwell Publishing Ltd, pp. 361–369.
Itoh, M, Matsuura, K & Satoh, T 1989, “Involvement of cytochrome bc1 complex in the electron transfer pathway for N2O reduction in a photodenitrifier, Rhodobacter sphaeroides f. s. denitrificans,” FEBS Letters, vol. 251, no. 1–2, pp. 104–108.
Ivanova, EP, Flavier, S & Christen, R 2004, “Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferri,” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 5, pp. 1773–1788.
Ivanova, EP, Onyshchenko, OM, Christen, R, Zhukova, N V, Lysenko, AM, Shevchenko, LS, Buljan, V, Hambly, B & Kiprianova, EA 2005, “Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea,” Systematic and Applied Microbiology, vol. 28, no. 2, pp. 131–136.
Ivanova, EP, Shevchenko, LS, Sawabe, T, Lysenko, AM, Svetashev, VI, Gorshkova, NM, Satomi, M, Christen, R & Mikhailov, V V 2002, “Pseudoalteromonas maricaloris sp. nov., isolated from an Australian sponge, and reclassification of [Pseudoalteromonas aurantia] NCIMB 2033 as Pseudoalteromonas flavipulchra sp. nov.,” International Journal of Systematic and Evolutionary Microbiology, vol. 52, no. 1, pp. 263–271.
Jensen, PR & Fenical, W 1994, “Strategies for the discovery of secondary metabolites from marine bacteria: ecological perspectives.,” Annual review of microbiology, vol. 48, Annual Reviews 4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA, pp. 559–84.
Jensen, PR, Mincer, TJ, Williams, PG & Fenical, W 2005, “Marine actinomycete diversity and natural product discovery,” Antonie van Leeuwenhoek, vol. 87, no. 1, Kluwer Academic Publishers, pp. 43–48.
Jiang, H, Dong, H, Ji, S, Ye, Y & Wu, N 2007, “Microbial Diversity in the Deep Marine Sediments from the Qiongdongnan Basin in South China Sea,” Geomicrobiology Journal, vol. 24, no. 6, Taylor & Francis, pp. 505–517.
Johnston, AWB, Todd, JD, Sun, L, Nikolaidou-Katsaridou, MN, Curson, ARJ & Rogers, R 2008, “Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses.,” Journal of experimental botany, vol. 59, no. 5, pp. 1059–67.
Jokiel, PL & Brown, EK 2004, “Global warming, regional trends and inshore environmental conditions influence coral bleaching in Hawaii,” Global Change Biology, vol. 10, no. 10, Blackwell Science Ltd, pp. 1627–1641.
P a g e | 104
Jones, RJ, Hoegh-Guldberg, O, Larkum, AWD & Schreiber, U 1998, “Temperature-induced bleaching of corals begins with impairment of the CO2 fixation mechanism in zooxanthellae,” Plant, Cell & Environment, vol. 21, no. 12, Blackwell Publishing Ltd, pp. 1219–1230.
Jordan, DC, McNicol, PJ & Marshall, MR 1978, “Biological nitrogen fixation in the terrestrial environment of a high Arctic ecosystem (Truelove Lowland, Devon Island, N.W.T.),” Canadian Journal of Microbiology, vol. 24, no. 6, NRC Research Press, pp. 643–649.
Jørgensen, B 2006, “Bacteria and Marine Biogeochemistry,” in H Schulz & M Zabel (eds), Marine Geochemistry SE - 5, Springer Berlin Heidelberg, pp. 169–206.
Juíz-Río, S, Osorio, CR, de Lorenzo, V & Lemos, ML 2005, “Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element,” Microbiology, vol. 151, no. 8, pp. 2659–2669.
Kajimura, Y 1995, “Bacillopeptins, new cyclic lipopeptide antibiotics from Bacillus subtilis FR-2,” J. Antibiotics, vol. 48, pp. 1095–1103.
Karl, DM 2002, “Nutrient dynamics in the deep blue sea,” Trends in Microbiology, vol. 10, no. 9, pp. 410–418.
Kiene, RP 1996a, “Production of methanethiol from dimethylsulfoniopropionate in marine surface waters,” Marine Chemistry, vol. 54, no. 1–2, pp. 69–83.
Kiene, RP 1996b, “Turnover of Dissolved DMSP in Estuarine and Shelf Waters of the Northern Gulf of Mexico,” in R Kiene, P Visscher, M Keller & G Kirst (eds), Biological and Environmental Chemistry of DMSP and Related Sulfonium Compounds SE - 29, Springer US, pp. 337–349.
Kiene, RP, Linn, LJ & Bruton, J a. 2000, “New and important roles for DMSP in marine microbial communities,” Journal of Sea Research, vol. 43, no. 3-4, pp. 209–224.
Kim, D, Baik, KS, Kim, MS, Jung, B-M, Shin, T-S, Chung, G-H, Rhee, MS & Seong, CN 2007, “Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai,” International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 12, pp. 2926–2931.
Kim, S-J & Kwon, KK 2010, “Marine, Hydrocarbon-Degrading Alphaproteobacteria,” in K Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology SE - 120, Springer Berlin Heidelberg, pp. 1707–1714.
Kirchmann, DL 2000, “Microbial ecology of the oceans,” Wiley Series in Ecological and Applied Microbiology.
P a g e | 105
Kirkwood, M, Le Brun, NE, Todd, JD & Johnston, AWB 2010, “The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide,” Microbiology, vol. 156, no. 6, pp. 1900–1906.
Kirst, GO, Thiel, C, Wolff, H, Nothnagel, J, Wanzek, M & Ulmke, R 1991, “Dimethylsulfoniopropionate (DMSP) in icealgae and its possible biological role,” Marine Chemistry, vol. 35, no. 1–4, pp. 381–388.
Kleinkauf, H & Von Döhren, H 1996, “A Nonribosomal System of Peptide Biosynthesis,” European Journal of Biochemistry, vol. 236, no. 2, Blackwell Science Ltd, pp. 335–351.
Koh, EGL 1997, “Do Scleractinian Corals Engage in Chemical Warfare Against Microbes?,” Journal of Chemical Ecology, vol. 23, no. 2, pp. 379–398.
Kooperman, N, Ben-Dov, E, Kramarsky-Winter, E, Barak, Z & Kushmaro, A 2007, “Coral mucus-associated bacterial communities from natural and aquarium environments,” FEMS Microbiology Letters, vol. 276, no. 1, Blackwell Publishing Ltd, pp. 106–113.
Koren, O & Rosenberg, E 2006, “Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter.,” Applied and environmental microbiology, vol. 72, no. 8, pp. 5254–9.
Kushmaro, A, Banin, E, Loya, Y, Stackebrandt, E & Rosenberg, E 2001, “Vibrio shiloi sp. nov., the causative agent of bleaching of the coral Oculina patagonica.,” International journal of systematic and evolutionary microbiology, vol. 51, no. Pt 4, pp. 1383–8.
Kushmaro, A, Loya, Y, Fine, M & Rosenberg, E 1996, “Bacterial infection and coral bleaching,” Nature, vol. 380, no. 6573, p. 396.
Kushmaro, A, Rosenberg, E, Fine, M & Loya, Y 1997, “Bleaching of the coral Oculina patagonica by Vibrio AK-1,” Marine ecology progress …, vol. 147, pp. 159–165.
Kusuda, R & Kawai, K 1998, “Bacterial diseases of cultured marine fish in Japan,” Fish Pathology, vol. 33, no. 4, pp. 221–227.
Labbé, N, Parent, S & Villemur, R 2004, “Nitratireductor aquibiodomus gen. nov., sp. nov., a novel α-proteobacterium from the marine denitrification system of the Montreal Biodome (Canada),” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 1, pp. 269–273.
Lai, Q & Shao, Z 2012, “Genome Sequence of Thalassospira xiamenensis Type Strain M-5,” Journal of Bacteriology, vol. 194, no. 24, p. 6957.
P a g e | 106
Lalucat, J, Bennasar, A, Bosch, R, García-Valdés, E & Palleroni, NJ 2006, “Biology of Pseudomonas stutzeri,” Microbiology and Molecular Biology Reviews, vol. 70, no. 2, pp. 510–547.
Lamberti, GA & Resh, VH 1983, “Geothermal Effects on Stream Benthos: Separate Influences of Thermal and Chemical Components on Periphyton and Macroinvertebrates,” Canadian Journal of Fisheries and Aquatic Sciences, vol. 40, no. 11, NRC Research Press, pp. 1995–2009.
Lampert, Y, Kelman, D, Nitzan, Y, Dubinsky, Z, Behar, A & Hill, RT 2008, “Phylogenetic diversity of bacteria associated with the mucus of Red Sea corals,” FEMS Microbiology Ecology, vol. 64, no. 2, Blackwell Publishing Ltd, pp. 187–198.
Lane, DJ, Pace, B, Olsen, GJ, Stahl, DA, Sogin, ML & Pace, NR 1985, “Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses,” Proceedings of the National Academy of Sciences, vol. 82, no. 20, pp. 6955–6959.
Ledyard, K, DeLong, E & Dacey, JH 1993, “Characterization of a DMSP-degrading bacterial isolate from the Sargasso Sea,” Archives of Microbiology, vol. 160, no. 4, Springer-Verlag, pp. 312–318.
Ledyard, KM, Dacey, JWH & Dacey, JWH 1996, “Microbial cycling of DMSP and DMS in coastal and oligotrophic seawater,” Limnology and oceanography, vol. 41, no. 1, pp. 33–40.
Lee, JN & Mohamed, CAR 2009, “Trace Metal Contents in the Porites Corals of PeninsularMalaysia,” International Journal of Environmental Research, vol. 3, no. 1, pp. 85–94.
Lee, K-H & Ruby, EG 1994, “Effect of the Squid Host on the Abundance and Distribution of Symbiotic Vibrio fischeri in Nature,” Applied and Environmental Microbiology, vol. 60, no. 5, pp. 1565–1571.
Lee, M & Chandler, AC 1941, “A Study of the Nature, Growth and Control of Bacteria in Cutting Compounds,” Journal of Bacteriology, vol. 41, no. 3, pp. 373–386.
Lesser, MP, Bythell, JC, Gates, RD, Johnstone, RW & Hoegh-Guldberg, O 2007, “Are infectious diseases really killing corals? Alternative interpretations of the experimental and ecological data,” Journal of Experimental Marine Biology and Ecology, vol. 346, no. 1-2, pp. 36–44.
Levasseur, M, Gosselin, M & Michaud, S 1994, “A new source of dimethylsulfide (DMS) for the arctic atmosphere: ice diatoms,” Marine Biology, vol. 121, no. 2, Springer-Verlag, pp. 381–387.
P a g e | 107
Levine, NM, Varaljay, V a, Toole, D a, Dacey, JWH, Doney, SC & Moran, MA 2012, “Environmental, biochemical and genetic drivers of DMSP degradation and DMS production in the Sargasso Sea.,” Environmental microbiology, vol. 14, no. 5, pp. 1210–23.
Li, D, Yu, T, Zhang, Y, Yang, M, Li, Z, Liu, M & Qi, R 2010, “Antibiotic Resistance Characteristics of Environmental Bacteria from an Oxytetracycline Production Wastewater Treatment Plant and the Receiving River,” Applied and Environmental Microbiology, vol. 76, no. 11, pp. 3444–3451.
Li, Z-Y, He, L-M, Wu, J & Jiang, Q 2006, “Bacterial community diversity associated with four marine sponges from the South China Sea based on 16S rDNA-DGGE fingerprinting,” Journal of Experimental Marine Biology and Ecology, vol. 329, no. 1, pp. 75–85.
Lin, Z, Kumagai, K, Baba, K, Mekalanos, JJ & Nishibuchi, M 1993, “Vibrio parahaemolyticus has a homolog of the Vibrio cholerae toxRS operon that mediates environmentally induced regulation of the thermostable direct hemolysin gene.,” Journal of Bacteriology, vol. 175, no. 12, pp. 3844–3855.
Lipp, EK, Huq, A & Colwell, RR 2002, “Effects of global climate on infectious disease: the cholera model,” Clinical microbiology reviews, vol. 15, no. 4.
Liu, C, Wu, Y, Li, L, Ma, Y & Shao, Z 2007, “Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.,” International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 2, pp. 316–320.
López-López, A, Pujalte, MJ, Benlloch, S, Mata-Roig, M, Rosselló-Mora, R, Garay, E & Rodríguez-Valera, F 2002, “Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the alpha-Proteobacteria.,” International Journal of Systematic and Evolutionary Microbiology, vol. 52, no. 4, pp. 1277–1283.
Lovelock, JE, Maggs, RJ & Rasmussen, RA 1972, “Atmospheric Dimethyl Sulphide and the Natural Sulphur Cycle,” Nature, vol. 237, no. 5356, pp. 452–453.
Magarvey, NA, Keller, JM, Bernan, V, Dworkin, M & Sherman, DH 2004, “Isolation and Characterization of Novel Marine-Derived Actinomycete Taxa Rich in Bioactive Metabolites,” Applied and Environmental Microbiology, vol. 70, no. 12, pp. 7520–7529.
Malin, G & Erst, GO 1997, “Algal Production of Dimethyl Sulfide and its Atmospheric Role,” Journal of Phycology, vol. 33, no. 6, Blackwell Publishing Ltd, pp. 889–896.
Malmstrom, RR, Kiene, RP & Kirchman, DL 2004, “Identification and enumeration of bacteria assimilating dimethylsulfoniopropionate (DMSP) in the North
P a g e | 108
Atlantic and Gulf of Mexico,” Limnology and Oceanography, vol. 49, no. 2, pp. 597–606.
Marahiel, MA, Stachelhaus, T & Mootz, HD 1997, “Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis,” Chemical Reviews, vol. 97, no. 7, American Chemical Society, pp. 2651–2674.
Margalef, DR 1958, “Information theory in ecology,” General Systems, vol. 3, Society for General Systems Research, pp. 36–71.
Maruyama, A, Honda, D, Yamamoto, H, Kitamura, K & Higashihara, T 2000, “Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov.,” International Journal of Systematic and Evolutionary Microbiology, vol. 50, no. 2, pp. 835–846.
Matu, EN, Kirira, PG, Kigondu, EVM, Moindi, EM & Amugune, BA 2012, “Antimicrobial activity of organic total extracts of three Kenyan medicinal plants,” African Journal of Pharmacology and Therapeutics.
Mayer, FW & Wild, C 2010, “Coral mucus release and following particle trapping contribute to rapid nutrient recycling in a Northern Red Sea fringing reef,” Marine and Freshwater Research, pp. 1006–1014.
McCarter, L 1999, “The multiple identities of Vibrio parahaemolyticus,” Journal of molecular microbiology and biotechnology, vol. 1, no. 1, p. 51.
McKnight, TL & Hess, D 2000, “Climate zones and types: the Köppen system,” Physical Geography: A Landscape Appreciation. Upper Saddle River, NJ: Prentice Hall.
McLeod, E, Moffitt, R, Timmermann, A, Salm, R, Menviel, L, Palmer, MJ, Selig, ER, Casey, KS & Bruno, JF 2010, “Warming Seas in the Coral Triangle: Coral Reef Vulnerability and Management Implications,” Coastal Management, vol. 38, no. 5, Taylor & Francis, pp. 518–539.
Meier, JL & Burkart, MD 2009, “The chemical biology of modular biosynthetic enzymes,” Chemical Society Reviews, vol. 38, no. 7, The Royal Society of Chemistry, pp. 2012–2045.
Millero, FJ, Lee, K & Roche, M 1998, “Distribution of alkalinity in the surface waters of the major oceans,” Marine Chemistry, vol. 60, no. 1–2, pp. 111–130.
Mincer, TJ, Fenical, W & Jensen, PR 2005, “Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora,” Applied and Environmental Microbiology, vol. 71, no. 11, pp. 7019–7028.
P a g e | 109
Mincer, TJ, Jensen, PR, Kauffman, CA & Fenical, W 2002, “Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments,” Applied and Environmental Microbiology, vol. 68, no. 10, pp. 5005–5011.
Moberg, F & Folke, C 1999, “Ecological goods and services of coral reef ecosystems,” Ecological Economics, vol. 29, no. 2, pp. 215–233.
Moran, M, Belas, R, Schell, M, González, J, Sun, F, Sun, S, Binder, B, Edmonds, J, Ye, W, Orcutt, B, Howard, E, Meile, C, Palefsky, W, Goesmann, A, Ren, Q, Paulsen, I, Ulrich, L, Thompson, L, Saunders, E & Buchan, A 2007, “Ecological genomics of marine Roseobacters.,” Applied and environmental microbiology, vol. 73, no. 14, pp. 4559–69.
Morton, B & Blackmore, G 2001, “South China Sea,” Marine Pollution Bulletin, vol. 42, no. 12, pp. 1236–1263.
Muhling, M, Woolven-Allen, J, Murrell, JC & Joint, I 2008, “Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities,” ISME J, vol. 2, no. 4, International Society for Microbial Ecology, pp. 379–392.
Nagasawa, S & Terazaki, M 1987, “Bacterial epibionts of the deep-sea copepod calanus-cristatus kroyer,” Oceanologica acta, vol. 10, no. 4, Gauthier-Villars, pp. 475–479.
Ndyetabura, T, Lyantagaye, SL & Mshandete, AM 2010, “Antimicrobial activity of ethyl acetate extracts from edible tanzanian Coprinus cinereus (schaeff) s. Gray s. lat. Cultivated on grasses supplemented with cow dung manure,” Arpn. J. Agric. Biol. Sci, vol. 5, no. 5.
Neilan, BA, Dittmann, E, Rouhiainen, L, Bass, RA, Schaub, V, Sivonen, K & Börner, T 1999, “Nonribosomal Peptide Synthesis and Toxigenicity of Cyanobacteria,” Journal of Bacteriology, vol. 181, no. 13, pp. 4089–4097.
Neu, HC & Gootz, TD 1996, “Antimicrobial chemotherapy,” Medical Microbiology. 4th ed.
Ni, Y-Y, Kim, DY, Chung, MG, Lee, SH, Park, H-Y & Rhee, YH 2010, “Biosynthesis of medium-chain-length poly(3-hydroxyalkanoates) by volatile aromatic hydrocarbons-degrading Pseudomonas fulva TY16,” Bioresource Technology, vol. 101, no. 21, pp. 8485–8488.
Nishimori, E, Kita-Tsukamoto, K & Wakabayashi, H 2000, “Pseudomonas plecoglossicida sp. nov., the causative agent of bacterial haemorrhagic ascites of ayu, Plecoglossus altivelis.,” International Journal of Systematic and Evolutionary Microbiology, vol. 50, no. 1, pp. 83–89.
P a g e | 110
Nithyanand, P & Pandian, SK 2009, “Phylogenetic characterization of culturable bacterial diversity associated with the mucus and tissue of the coral Acropora digitifera from the Gulf of Mannar,” FEMS Microbiology Ecology, vol. 69, no. 3, Blackwell Publishing Ltd, pp. 384–394.
Noble, RC & Overman, SB 1994, “Pseudomonas stutzeri infection a review of hospital isolates and a review of the literature,” Diagnostic Microbiology and Infectious Disease, vol. 19, no. 1, pp. 51–56.
Nold, S & Zwart, G 1998, “Patterns and governing forces in aquatic microbial communities,” Aquatic Ecology, vol. 32, no. 1, Kluwer Academic Publishers, pp. 17–35.
Okuda, J, Nakai, T, Chang, PS, Oh, T, Nishino, T, Koitabashi, T & Nishibuchi, M 2001, “The toxR Gene of Vibrio(Listonella) anguillarum Controls Expression of the Major Outer Membrane Proteins but Not Virulence in a Natural Host Model,” Infection and Immunity, vol. 69, no. 10, pp. 6091–6101.
De Oliveira, EJ, Rabinovitch, L, Monnerat, RG, Passos, LKJ & Zahner, V 2004, “Molecular Characterization of Brevibacillus laterosporus and Its Potential Use in Biological Control,” Applied and Environmental Microbiology, vol. 70, no. 11, pp. 6657–6664.
Patz, J, Epstein, P, Burke, T & Balbus, J 1996, “Global climate change and emerging infectious diseases,” JAMA, vol. 275, no. 3, pp. 217–223.
Petrosino, JF, Highlander, S, Luna, RA, Gibbs, R a & Versalovic, J 2009, “Metagenomic pyrosequencing and microbial identification.,” Clinical chemistry, vol. 55, no. 5, pp. 856–66.
Piel, J 2002, “A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 22, pp. 14002–7.
Pilcher, N & Cabanban, A 2000a, “The status of coral reefs in Eastern Malaysia,” Global Coral Reef Monitoring Network (GCRMN) Report. Australia Institute of Marine Science, Townsville.
Pilcher, N & Cabanban, A 2000b, “The status of coral reefs in Sabah, Labuan and Sarawak, East Malaysia,” Australian Institute of Marine Sciences, Townsville.
Praveena, SM, Siraj, SS & Aris, AZ 2012, “Coral reefs studies and threats in Malaysia: a mini review,” Reviews in Environmental Science and Biotechnology, vol. 11, no. 1, pp. 27–39.
Prayitno, SB & Latchford, JW 1995, “Experimental infections of crustaceans with luminous bacteria related to Photobacterium and Vibrio. Effect of salinity and pH on infectiosity,” Aquaculture, vol. 132, no. 1–2, pp. 105–112.
P a g e | 111
Radjasa, OK & Sabdono, A 2003, “Screening of secondary metabolite-producing bacteria associated with corals using 16S rDNA-based approach,” Journal of Coastal Development, vol. 7, no. 1, pp. 11–19.
Raguénès, G, Christen, R, Guezennec, J, Pignet, P & Barbier, G 1997, “Vibrio diabolicus sp. nov., a New Polysaccharide-Secreting Organism Isolated from a Deep-Sea Hydrothermal Vent Polychaete Annelid, Alvinella pompejana,” International Journal of Systematic Bacteriology, vol. 47, no. 4, pp. 989–995.
Raina, J-B, Dinsdale, EA, Willis, BL & Bourne, DG 2010, “Do the organic sulfur compounds DMSP and DMS drive coral microbial associations?,” Trends in microbiology, vol. 18, no. 3, Elsevier Ltd, pp. 101–8.
Raina, J-B, Tapiolas, D, Willis, BL & Bourne, DG 2009, “Coral-associated bacteria and their role in the biogeochemical cycling of sulfur.,” Applied and environmental microbiology, vol. 75, no. 11, pp. 3492–501.
Rajendhran, J & Gunasekaran, P 2011, “Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond,” Microbiological Research, vol. 166, no. 2, pp. 99–110.
Ramaiah, N, Hill, RT, Chun, J, Ravel, J, Matte, MH, Straube, WL & Colwell, RR 2000, “Use of a chiA probe for detection of chitinase genes in bacteria from the Chesapeake Bay1,” FEMS Microbiology Ecology, vol. 34, no. 1, Blackwell Publishing Ltd, pp. 63–71.
Rappé, MS & Giovannoni, SJ 2003, “The uncultured microbial majority.,” Annual review of microbiology, vol. 57, Annual Reviews 4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA, pp. 369–94.
Raven, J, Caldeira, K, Elderfield, H, Hoegh-Guldberg, O, Liss, P, Riebesell, U, Shepherd, J, Turley, C & Watson, A 2005, “Ocean acidification due to increasing atmospheric carbon dioxide,” The Royal Society.
Rehnstam, A-S, Bäckman, S, Smith, DC, Azam, F & Hagström, Å 1993, “Blooms of sequence-specific culturable bacteria in the sea,” FEMS Microbiology Letters, vol. 102, no. 3–4, pp. 161–166.
Reisch, CR, Moran, MA & Whitman, WB 2011, “Bacterial catabolism of dimethylsulfoniopropionate (DMSP),” Frontiers in microbiology, vol. 2, Frontiers Media SA.
Reshef, L, Koren, O, Loya, Y, Zilber-Rosenberg, I & Rosenberg, E 2006, “The coral probiotic hypothesis.,” Environmental microbiology, vol. 8, no. 12, pp. 2068–73.
Richardson, DJ, McEwan, AG, Jackson, JB & Ferguson, SJ 1989, “Electron transport pathways to nitrous oxide in Rhodobacter species,” European Journal of Biochemistry, vol. 185, no. 3, Blackwell Publishing Ltd, pp. 659–669.
P a g e | 112
Ritchie, K, Dennis, J, McGrath, T & Smith, G 1994, “Bacterial Asociated with Bleached and Nonbleached Areas of Montastrea Annularis,” Proceedings of the 5th Symposium on the Natural History of The Bahamas, vol. 5, pp. 75–80.
Ritchie, K & Smith, G 2004, “Microbial Communities of Coral Surface Mucopolysaccharide Layers,” in E Rosenberg & Y Loya (eds), Coral Health and Disease SE - 13, Springer Berlin Heidelberg, pp. 259–264.
Ritchie, KB 2006, “Regulation of microbial populations by coral surface mucus and mucus-associated bacteria,” Marine Ecology Progress Series, vol. 322, pp. 1–14.
Ritchie, KB & Smith, GW 1995a, “Carbon-source utilization patterns of coral-associated marine heterotrophs,” Journal of marine biotechnology, vol. 3, no. 1, pp. 105–107.
Ritchie, KB & Smith, GW 1995b, “Preferential carbon utilization by surface bacterial communities from water mass, normal, and white-band diseased Acropora cervicornis,” Molecular Marine Biology and Biotechnology, vol. 4, no. 4, pp. 345–352.
Rohwer, F, Seguritan, V, Azam, F & Knowlton, N 2002, “Diversity and distribution of coral-associated bacteria,” Marine Ecology Progress Series, vol. 243, pp. 1–10.
Rosenberg, E 2004, “The Bacterial Disease Hypothesis of Coral Bleaching,” in E Rosenberg & Y Loya (eds), Coral Health and Disease SE - 25, Springer Berlin Heidelberg, pp. 445–461.
Rosenberg, E & Ben-Haim, Y 2002, “Microbial diseases of corals and global warming,” Environmental Microbiology, vol. 4, no. 6, Blackwell Science Ltd, pp. 318–326.
Rosenberg, E & Falkovitz, L 2004, “The Vibrio shiloi/Oculina patogonica Model System of Coral Bleaching,” Annual Review of Microbiology, vol. 58, no. 1, Annual Reviews, pp. 143–159.
Rosenberg, E, Koren, O, Reshef, L, Efrony, R & Zilber-Rosenberg, I 2007, “The role of microorganisms in coral health, disease and evolution,” Nature reviews. Microbiology, vol. 5, no. 5, pp. 355–62.
Rosenberg, E, Kushmaro, A, Kramarsky-Winter, E, Banin, E & Yossi, L 2009, “The role of microorganisms in coral bleaching,” The ISME journal, vol. 3, no. 2, pp. 139–46.
Saha, R, Spröer, C, Beck, B & Bagley, S 2010, “Pseudomonas oleovorans subsp. lubricantis subsp. nov., and Reclassification of Pseudomonas pseudoalcaligenes ATCC 17440T as Later Synonym of Pseudomonas oleovorans ATCC 8062T,” Current Microbiology, vol. 60, no. 4, Springer-Verlag, pp. 294–300.
P a g e | 113
Sanger, F, Nicklen, S & Coulson, AR 1977, “DNA sequencing with chain-terminating inhibitors,” Proceedings of the National Academy of Sciences, vol. 74, no. 12, pp. 5463–5467.
Satomi, M, Vogel, BF, Gram, L & Venkateswaran, K 2006, “Shewanella hafniensis sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea,” International Journal of Systematic and Evolutionary Microbiology, vol. 56, no. 1, pp. 243–249.
Saunders, VA 1978, “Genetics of Rhodospirillaceae.,” Microbiological reviews, vol. 42, no. 2, pp. 357–84.
Saville Waid, J 1999, “Does soil biodiversity depend upon metabiotic activity and influences?,” Applied Soil Ecology, vol. 13, no. 2, pp. 151–158.
Sayeh, R, Birrien, J, Alain, K, Barbier, G, Hamdi, M & Prieur, D 2010, “Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches,” Extremophiles, vol. 14, no. 6, Springer Japan, pp. 501–514.
Scarratt, M, Cantin, G, Levasseur, M & Michaud, S 2000, “Particle size-fractionated kinetics of DMS production: where does DMSP cleavage occur at the microscale?,” Journal of Sea Research, vol. 43, no. 3–4, pp. 245–252.
Schut, F, Prins, R & Gottschal, J 1997, “Oligotrophy and pelagic marine bacteria: facts and fiction,” Aquatic Microbial Ecology, vol. 12, no. 2, pp. 177–202.
Schut, F, de Vries, EJ, Gottschal, JC, Robertson, BR, Harder, W, Prins, RA & Button, DK 1993, “Isolation of Typical Marine Bacteria by Dilution Culture: Growth, Maintenance, and Characteristics of Isolates under Laboratory Conditions,” Applied and Environmental Microbiology, vol. 59, no. 7, pp. 2150–2160.
Sekiguchi, H, Watanabe, M, Nakahara, T, Xu, B & Uchiyama, H 2002, “Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis,” Applied and Environmental Microbiology, vol. 68, no. 10, pp. 5142–5150.
Shannon, CE & Weaver, W 1963, Mathematical theory of communication, University Illinois Press, p. 117.
Sharon, G & Rosenberg, E 2008, “Bacterial growth on coral mucus,” Current microbiology, vol. 56, no. 5, pp. 481–8.
Shaw, G 1983, “Bio-controlled thermostasis involving the sulfur cycle,” Climatic Change, vol. 5, no. 3, Kluwer Academic Publishers, pp. 297–303.
Shivaji, S, Suresh, K, Chaturvedi, P, Dube, S & Sengupta, S 2005, “Bacillus arsenicus sp. nov., an arsenic-resistant bacterium isolated from a siderite concretion in
P a g e | 114
West Bengal, India,” International Journal of Systematic and Evolutionary Microbiology, vol. 55, no. 3, pp. 1123–1127.
Shnit-Orland, M & Kushmaro, A 2008, “Coral mucus bacteria as a source for antibacterial activity,” Proceedings of the 11th International Coral Reef Symposium, no. 8, pp. 257–259.
Shnit-Orland, M & Kushmaro, A 2009, “Coral mucus-associated bacteria: a possible first line of defense,” FEMS microbiology ecology, vol. 67, no. 3, pp. 371–80.
Sievert, SM, Kiene, RP & Schultz-Vogt, HN 2007, “The sulfur cycle,” Oceanography, vol. 20, no. 2, Oceanography Society, pp. 117–123.
Silakowski, B, Kunze, B & Müller, R 2001, “Multiple hybrid polyketide synthase/non-ribosomal peptide synthetase gene clusters in the myxobacterium Stigmatella aurantiaca,” Gene, vol. 275, no. 2, pp. 233–240.
Simó, R 2001, “Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links,” Trends in Ecology & Evolution, vol. 16, no. 6, pp. 287–294.
Singh, BK 2010, “Exploring microbial diversity for biotechnology: the way forward,” Trends in Biotechnology, vol. 28, no. 3, pp. 111–116.
Slezak, D & Brugger, A 2001, “Impact of solar radiation on the biological removal of dimethylsulfoniopropionate and dimethylsulfide in marine surface waters,” Aquatic Microbial Ecology, vol. 25, no. 1, pp. 87–97.
Smith, B & Wilson, JB 1996, “A consumer’s guide to evenness indices,” Oikos, JSTOR, pp. 70–82.
Sogin, ML, Morrison, HG, Huber, JA, Welch, DM, Huse, SM, Neal, PR, Arrieta, JM & Herndl, GJ 2006, “Microbial diversity in the deep sea and the underexplored ‘rare biosphere,’” Proceedings of the National Academy of Sciences, vol. 103, no. 32, pp. 12115–12120.
De Souza, MP & Yoch, DC 1995, “Comparative Physiology of Dimethyl Sulfide Production by Dimethylsulfoniopropionate Lyase in Pseudomonas doudoroffii and Alcaligenes sp. Strain M3A.,” Applied and Environmental Microbiology, vol. 61, no. 11, pp. 3986–3991.
De Souza, MP, Yoch, DC & Souza, M 1996, “N-Terminal Amino Acid Sequences and Comparison of DMSP Lyases from Pseudomonas Doudoroffii and Alcagenes Strain M3A,” in R Kiene, P Visscher, M Keller & G Kirst (eds), Biological and environmental chemistry of DMSP and related sulfonium compounds, Springer, pp. 293–304.
P a g e | 115
Stefels, J 2000, “Physiological aspects of the production and conversion of DMSP in marine algae and higher plants,” Journal of Sea Research, vol. 43, no. 3–4, pp. 183–197.
Stelma, GN, Reyes, AL, Peeler, JT, Johnson, CH & Spaulding, PL 1992, “Virulence characteristics of clinical and environmental isolates of Vibrio vulnificus.,” Applied and Environmental Microbiology, vol. 58, no. 9, pp. 2776–2782.
Stevens, H & Brinkhoff, T 2005, “Composition of free-living, aggregate-associated and sediment surface-associated bacterial communities in the German Wadden Sea,” Aquatic Microbial Ecology, vol. 38, no. 1, pp. 15–30.
Stove Poindexter, JL & Cohen-Bazire, G 1964, “The Fine Structure of Stalked Bacteria Belonging to the Family Caulobacteraceae,” The Journal of Cell Biology, vol. 23, no. 3, pp. 587–607.
Stover, CK, Pham, XQ, Erwin, AL, Mizoguchi, SD, Warrener, P, Hickey, MJ, Brinkman, FSL, Hufnagle, WO, Kowalik, DJ, Lagrou, M, Garber, RL, Goltry, L, Tolentino, E, Westbrock-Wadman, S, Yuan, Y, Brody, LL, Coulter, SN, Folger, KR, Kas, A, Larbig, K, Lim, R, Smith, K, Spencer, D, Wong, GK-S, Wu, Z, Paulsen, IT, Reizer, J, Saier, MH, Hancock, REW, Lory, S & Olson, M V 2000, “Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen,” Nature, vol. 406, no. 6799, pp. 959–964.
Strom, SL 2008, “Microbial Ecology of Ocean Biogeochemistry: A Community Perspective,” Science, vol. 320, no. 5879, pp. 1043–1045.
Sucharita, K, Sasikala, C, Park, SC, Baik, KS, Seong, CN & Ramana, C V 2009, “Shewanella chilikensis sp. nov., a moderately alkaliphilic gammaproteobacterium isolated from a lagoon,” International Journal of Systematic and Evolutionary Microbiology, vol. 59, no. 12, pp. 3111–3115.
Sunagawa, S, DeSantis, TZ, Piceno, YM, Brodie, EL, DeSalvo, MK, Voolstra, CR, Weil, E, Andersen, GL & Medina, M 2009, “Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata,” ISME J, vol. 3, no. 5, International Society for Microbial Ecology, pp. 512–521.
Sunda, W, Kieber, DJ, Kiene, RP & Huntsman, S 2002, “An antioxidant function for DMSP and DMS in marine algae,” Nature, vol. 418, no. 6895, Macmillian Magazines Ltd., pp. 317–320.
Sussman, M, Mieog, JC, Doyle, J, Victor, S, Willis, BL & Bourne, DG 2009, “Vibrio zinc-metalloprotease causes photoinactivation of coral endosymbionts and coral tissue lesions.,” PloS one, vol. 4, no. 2, p. e4511.
Sutherland, KP, Porter, JW & Torres, C 2004, “Disease and immunity in Caribbean and Indo-Pacific zooxanthellate corals,” Marine ecology. Progress series, vol. 266, Inter-Research, pp. 273–302.
P a g e | 116
Suzuki, MT, Rappé, MS, Haimberger, ZW, Winfield, H, Adair, N, Ströbel, J & Giovannoni, SJ 1997, “Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.,” Applied and Environmental Microbiology, vol. 63, no. 3, pp. 983–989.
Tamura, K, Peterson, D, Peterson, N, Stecher, G, Nei, M & Kumar, S 2011, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.,” Molecular biology and evolution, vol. 28, no. 10, pp. 2731–9.
Tamura, K, Stecher, G, Peterson, D, Filipski, A & Kumar, S 2013, “MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0,” Molecular Biology and Evolution, vol. 30, no. 12, pp. 2725–2729.
Tan, CH & Heron, SF 2011, “First observed severe mass bleaching in Malaysia, Greater Coral Triangle,” Galaxea, Journal of Coral Reef Studies, vol. 13, no. 1, pp. 27–28.
Tao, L, Peng, W & Pinxian, W 2008, “Microbial diversity in surface sediments of the Xisha Trough, the South China Sea,” Acta Ecologica Sinica, vol. 28, no. 3, pp. 1166–1173.
Taylor, BF 1993, “Bacterial Transformations of Organic Sulfur Compounds in Marine Environments,” in R Oremland (ed.), Biogeochemistry of Global Change SE - 40, Springer US, pp. 745–781.
Tian, B, Yang, J, Lian, L, Wang, C, Li, N & Zhang, K-Q 2007, “Role of an extracellular neutral protease in infection against nematodes by Brevibacillus laterosporus strain G4,” Applied Microbiology and Biotechnology, vol. 74, no. 2, Springer-Verlag, pp. 372–380.
Todd, JD, Curson, ARJ, Dupont, CL, Nicholson, P & Johnston, AWB 2009, “The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi.,” Environmental microbiology, vol. 11, no. 6, pp. 1376–85.
Todd, JD, Curson, ARJ, Kirkwood, M, Sullivan, MJ, Green, RT & Johnston, AWB 2011, “DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria,” Environmental Microbiology, vol. 13, no. 2, Blackwell Publishing Ltd, pp. 427–438.
Todd, JD, Curson, ARJ, Sullivan, MJ, Kirkwood, M & Johnston, AWB 2012, “The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate.,” PloS one, vol. 7, no. 4, p. e35947.
Todd, JD, Kirkwood, M, Newton-Payne, S & Johnston, AWB 2012, “DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi
P a g e | 117
DSS-3,” ISME J, vol. 6, no. 1, International Society for Microbial Ecology, pp. 223–226.
Todd, JD, Rogers, R, Li, YG, Wexler, M, Bond, PL, Sun, L, Curson, ARJ, Malin, G, Steinke, M & Johnston, AWB 2007, “Structural and Regulatory Genes Required to Make the Gas Dimethyl Sulfide in Bacteria,” Science, vol. 315, no. 5812, pp. 666–669.
Toole, DA, Slezak, D, Kiene, RP, Kieber, DJ & Siegel, DA 2006, “Effects of solar radiation on dimethylsulfide cycling in the western Atlantic Ocean,” Deep Sea Research Part I: Oceanographic Research Papers, vol. 53, no. 1, pp. 136–153.
Trevena, AJ, Jones, GB, Wright, SW & van den Enden, RL 2003, “Profiles of dimethylsulphoniopropionate (DMSP), algal pigments, nutrients, and salinity in the fast ice of Prydz Bay, Antarctica,” Journal of Geophysical Research: Oceans, vol. 108, no. C5, p. 3145.
Trevena, AJ, Jones, GB, Wright, SW & van den Enden, RL 2000, “Profiles of DMSP, algal pigments, nutrients and salinity in pack ice from eastern Antarctica,” Journal of Sea Research, vol. 43, no. 3–4, pp. 265–273.
Tun, K, Chou, LM, Low, J, Yeemin, T, Phongsuwan, N, Setiasih, N, Wilson, J, Amri, AY, Adzis, KAA, Lane, D, van Bochove, JW, Kluskens, B, Long, N Van, Tuan, VS & Gomez, E 2010, “A Regional overview on the 2010 coral bleaching event in Southeast Asia,” Status of Coral Reefs in East Asian Seas Region: 2010, Ministry of the Environment, Japan, pp. 1–27.
Turner, JT & Backman, PA 1991, “Factors relating to peanut yield increases after seed treatment with Bacillus subtilis,” Plant disease, vol. 75, no. 4, American Phytopathological Society, pp. 347–353.
Uchino, M, Shida, O, Uchimura, T & Komagata, K 2001, “Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov.,” The Journal of General and Applied Microbiology, vol. 47, no. 5, pp. 247–261.
Del Valle, D, Kiene, R & Karl, D 2012, “Effect of visible light on dimethylsulfoniopropionate assimilation and conversion to dimethylsulfide in the North Pacific Subtropical Gyre,” Aquatic Microbial Ecology, vol. 66, no. 1, pp. 47–62.
Vallina, SM & Simó, R 2007, “Strong Relationship Between DMS and the Solar Radiation Dose over the Global Surface Ocean,” Science, vol. 315, no. 5811, pp. 506–508.
Varaljay, VA, Gifford, SM, Wilson, ST, Sharma, S, Karl, DM & Moran, MA 2012, “Bacterial dimethylsulfoniopropionate degradation genes in the oligotrophic north pacific subtropical gyre.,” Applied and environmental microbiology, vol. 78, no. 8, pp. 2775–82.
P a g e | 118
Varaljay, VA, Howard, EC, Sun, S & Moran, MA 2010, “Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data.,” Applied and environmental microbiology, vol. 76, no. 2, pp. 609–17.
Veron, J, Devantier, LM, Turak, E, Green, AL, Kininmonth, S, Stafford-Smith, M & Peterson, N 2009, “Delineating the Coral Triangle,” Galaxea, Journal of Coral Reef Studies, vol. 11, no. 2, pp. 91–100.
Veron, JEN & Stafford-Smith, M 2000, Corals of the World.
Vila-Costa, M, Rinta-Kanto, JM, Sun, S, Sharma, S, Poretsky, R & Moran, MA 2010, “Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate,” ISME J, vol. 4, no. 11, International Society for Microbial Ecology, pp. 1410–1420.
Vishnivetskaya, T, Kathariou, S & Tiedje, J 2009, “The Exiguobacterium genus: biodiversity and biogeography,” Extremophiles, vol. 13, no. 3, Springer Japan, pp. 541–555.
Vizcaino, MI, Johnson, WR, Kimes, NE, Williams, K, Torralba, M, Nelson, KE, Smith, GW, Weil, E, Moeller, PDR & Morris, PJ 2010, “Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral.,” Microbial ecology, vol. 59, no. 4, pp. 646–57.
Wagner-Döbler, I, Rheims, H, Felske, A, El-Ghezal, A, Flade-Schröder, D, Laatsch, H, Lang, S, Pukall, R & Tindall, BJ 2004, “Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites,” International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 4, pp. 1177–1184.
Wang, B, Tan, T & Shao, Z 2009, “Roseovarius pacificus sp. nov., isolated from deep-sea sediment,” International Journal of Systematic and Evolutionary Microbiology, vol. 59, no. 5, pp. 1116–1121.
Ward, DM, Weller, R & Bateson, MM 1990, “16S rRNA sequences reveal numerous uncultured microorganisms in a natural community,” Nature, vol. 345, no. 6270, pp. 63–65.
Watanabe, A & Ebizuka, Y 2004, “Unprecedented Mechanism of Chain Length Determination in Fungal Aromatic Polyketide Synthases,” Chemistry & Biology, vol. 11, no. 8, pp. 1101–1106.
Webster, NS, Wilson, KJ, Blackall, LL & Hill, RT 2001, “Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeides odorabile,” Applied and Environmental Microbiology, vol. 67, no. 1, pp. 434–444.
P a g e | 119
Welsh, DT 2000, “Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate,” FEMS Microbiology Reviews, vol. 24, no. 3, Blackwell Publishing Ltd, pp. 263–290.
Wiese, J, Thiel, V, Nagel, K, Staufenberger, T & Imhoff, J 2009, “Diversity of Antibiotic-Active Bacteria Associated with the Brown Alga Laminaria saccharina from the Baltic Sea,” Marine Biotechnology, vol. 11, no. 2, Springer-Verlag, pp. 287–300.
Wilkinson, CR 1999, “Global and local threats to coral reef functioning and existence: review and predictions,” Marine and Freshwater Research, vol. 50, no. 8, pp. 867–878.
Wilkinson, CR & Buddemeier, RW 1994, Global Climate Change and Coral Reefs: Implications for People and Reefs: Report of the UNEP-IOC-ASPEI-IUCN Global Task Team on the Implications of Climate Change on Coral Reefs, IUCN.
Wilson, B, Aeby, GS, Work, TM & Bourne, DG 2012, “Bacterial communities associated with healthy and Acropora white syndrome-affected corals from American Samoa,” FEMS Microbiology Ecology, vol. 80, no. 2, pp. 509–520.
Wipat, A & Harwood, CR 1999, “The Bacillus subtilis genome sequence: the molecular blueprint of a soil bacterium,” FEMS Microbiology Ecology, vol. 28, no. 1, Blackwell Publishing Ltd, pp. 1–9.
Xu, X-W, Wu, Y-H, Wang, C-S, Gao, X-H, Wang, X-G & Wu, M 2010, “Pseudoalteromonas lipolytica sp. nov., isolated from the Yangtze River estuary,” International Journal of Systematic and Evolutionary Microbiology, vol. 60, no. 9, pp. 2176–2181.
Yahya, NK, Hassan, R & Husaini, AASA 2012, “Molecular Phylogeny of Sarawak Green Sea Turtle (Chelonia mydas) inferred by the D-loop region and 16S rRNA gene.,” Borneo Journal of Resource Science and Technology, vol. 2, no. 1, pp. 20–27.
Yaman, ARBG n.d., “Coral Reefs in the Coastal Waters of the South China Sea.”
Yoch, DC 2002, “Dimethylsulfoniopropionate: Its Sources, Role in the Marine Food Web, and Biological Degradation to Dimethylsulfide,” Applied and Environmental Microbiology, vol. 68, no. 12, pp. 5804–5815.
Yoch, DC, Ansede, JH & Rabinowitz, KS 1997, “Evidence for Intracellular and Extracellular Dimethylsulfoniopropionate (DMSP) Lyases and DMSP Uptake Sites in Two Species of Marine Bacteria.,” Applied and Environmental Microbiology, vol. 63, no. 8, pp. 3182–3188.
Yoshida, A, Nishimura, M & Kogure, K 2007, “Bacterial community structure in the Sulu Sea and adjacent areas,” Deep Sea Research Part II: Topical Studies in Oceanography, vol. 54, no. 1–2, pp. 103–113.
P a g e | 120
Zahner, V, Rabinovitch, L, Suffys, P & Momen, H 1999, “Genotypic Diversity among Brevibacillus laterosporus Strains,” Applied and Environmental Microbiology, vol. 65, no. 11, pp. 5182–5185.
Zhang, Z, Schwartz, S, Wagner, L & Miller, W 2000, “A greedy algorithm for aligning DNA sequences,” Journal of Computational biology, vol. 7, no. 1-2, Mary Ann Liebert, Inc., pp. 203–214.
Ziemke, F, Höfle, MG, Lalucat, J & Rossellö-Mora, R 1998, “Reclassification of Shewanella putrefaciens Owen’s genomic group II as Shewanella baltica sp. nov.,” International Journal of Systematic Bacteriology, vol. 48, no. 1, pp. 179–186.
Zumft, WG 1997, “Cell biology and molecular basis of denitrification.,” Microbiology and Molecular Biology Reviews, vol. 61, no. 4, pp. 533–616.
P a g e | 121
APPENDIX
Table A.1: 16S rRNA gene sequence analysis of bacterial cultures from Kuching