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Microalgal communities on mangrove forest sediments of East Java,Indonesia(࢖ࣥࢻࢿࢩ࢔ᮾࢪࣕ࣡ࡢ࣐ࣥࢢ࣮ࣟࣈᯘᗏἾ࡟⏕ᜥࡍࡿᚤ⣽⸴ࢥ࣑ࣗࢽࢸ࢕ᗈᓥ኱Ꮫ኱Ꮫ㝔⏕≀ᅪ⛉Ꮫ◊✲⛉⎔ቃᚠ⎔⣔ไᚚᏛᑓᨷᏛ⏕␒ྕD171871
Ặྡ Ayu Lana Nafisyah

CHAPTER 1: General introduction
Indonesia is known as an archipelagic country that has been attributed as thethird longest coastline globally. Diverse coastal ecosystems of Indonesia areconsidered to be rich in biodiversity, and one of the vital ecosystems is themangrove forests, those accounting for 23% (3 million ha) of the worldwidemangrove areas. In this ecosystem, benthic or epiphytic microalgae (hereinabbreviated as MPB) have been regarded as the second largest carbon stocks after
the litterfall of mangrove trees; however, there has been still scanty knowledge
about MPB flora especially in the Indonesian waters. While MPB in mangrove
ecosystems were primarily composed of diatoms, other algal taxa occasionallyoccur in specific area or season. Dinoflagellates blooming were found at mangrove
estuary in Thailand during a period of scant occurrence of diatoms in dry season.
Actually, during the survey for MPBs in East Java coasts in this study, a harmful
raphydophycean alga was found on the mangrove sediments at Probolinggo.
This study was conducted aiming to increase an awareness and to provide
new insights on the importance of mangrove ecosystems in Indonesia, at where thehighest annual deforestation rate of mangrove forests in the world has been reported.
For this general purpose, the investigation on MPB in the sediment of mangroves
are of interests because their compositions are expected to be indices of fertility.
Also, there has been no research particularly for harmful algal species in theIndonesian mangrove areas.
CHAPTER 2: Cryptic occurrence of Chattonella marina var. marina inmangrove sediments in Probolinggo, East Java, Indonesia
During the MPB flora investigation on mangrove swamps of Probolinggo, a
mud sample unexpectedly included large numbers of a notorious fish killer,
Chattonella-like motile cells, and its resting cysts. These motile cells wereestablished as clonal cultures for further identification and physiological tests. Thecysts were examined through palynological and molecular biological techniques.
Based on light microscopy and ribosomal RNA gene sequences, these cells andcysts were identified as Chattonella marina var. marina. While the strains were
genetically identical to the temperate strains isolated from Japan and China,temperature experiments showed that the Indonesian strains possessed a highmaximum quantum yield of photosystem II even after exposure to 34 °C, atemperature at which the Japanese strain could not survive. Salinity experiments
showed adaptation of the strains to a salinity of 15. These findings, together withthe discovery of populations of cysts in the mangrove sediment, highlight the toughand unique nature of the Indonesian strains, which are likely adapted to wide
fluctuations of temperature and salinity in mangrove swamps, and pose a potential
risk to fisheries in Indonesia.
CHAPTER 3: Microphytobenthos florae in different mangrove sediments
along the East Java coast; Probolinggo, Situbondo, Banyuwangi
It has been reported that MPB composition tends to exhibit unique locality
and unique to adjacent environments. If so, those in the Indonesian mangrove
forests could be an indicator of the forests’ status, those now suffering intensive
activities by human. Therefore, for the first time in Indonesia, this study aims todetermine the taxonomic composition of MPB in the sediment of mangrove forests
those ranging in geographically and environmentally variations in the East Java.
The study locations were stretch along the northern coast of East Java, Probolinggo,
Situbondo and Banyuwangi, each representing artificially replanted forest, wellconserved forest and adjacent to shrimp ponds, respectively.
A total of 27 species were identified morphologically in the sediment
samples. The cell density and biovolume based on the cell length, width and heightmeasured under the microscope revealed the highest biovolume (183,495 x 10 3 ±66,965 x 103 μm3 cm−3) at Situbondo, followed by the replanted site, Probolinggo(107,092 x 103 ± 26,021 x 103 μm3 cm−3) and the nearby shrimp pond site,
Banyuwangi (66,962 x 10 3 ± 19,920 x 103 μm3 cm−3), insisting MPB assemblages
and their biomass might differ depend on the fertility status of mangrove
ecosystems.
CHAPTER 4: Microphytobenthos florae in mangrove sediments of Pang-Pang
Bay; a comparison between a conserved mangrove area and human-affectedswamps of the bay
Further field survey was conducted in the unique areas that is Pang-Pang
Bay, where the human-affected swamps and the well-conserved national forest(Alas Purwo National Park) are coexisting. At this bay, we aimed to clarify MPB
communities of both sides and further proof the above hypothesis stating MPB
assemblages might differ depend on the fertility status of mangrove ecosystems.
Also, in this study, the water columns during high tide were observed to furtherestimating the primary production rate of the bay that could be driven by suspended
MPB. A total of 56 species of MPB were observed in the sediment samples. Thehighest cell density (448,380 cells cm-3), as well as biovolume (1,666 x 106 μm3

cm−3) was found at St 1 that located in the conserved side at the east. A dendrogramusing the cell density data of each station showed an interesting result where two
major clusters determined with ca. 48-50% similarities separated the west (humanaffected swamps) and east side (well-conserved swamps). During high tidesampling, about half of microalgal community in the water was consisted of MPB
species, including Navicula agnita (124 x 106 μm3 cm−3) that was also dominant insediment samples during low tide sampling. An estimation of primary production in
Pang-Pang Bay resulting the highest value of 1.28 gC m −2 day−1 at the offshore
waters (St E).

CHAPTER 5: Physiological responses of microphytobenthos towards
environmental changes
Benthic communities of intertidal area, including mangrove swamps, usually
suffered to harsh environmental drifts, e.g. drastic salinity and temperature changes
within a single day, exposure to direct sunlight at low tide, etc. The unique
physiological responses of MPB have been reported to enable them to tolerate theseharsh environmental conditions. In this study, the physiological characters of thecandidate MPB species were tested against some environmental fluctuations; i.e.
extremely high temperature, wide fluctuation of salinity and intensive light
exposure those are characteristic environments of the sites. Tryblionella
cocconeiformis, Navicula gregaria, N. agnita and Nitzschia sigma were selected as
the candidate Indonesian strains. For the comparison, two planktonic strains weresubjected, Biddulphia sp. (Myanmar strain) and Melosira sp. (Japan strain). Against
the rises of temperature, Fv/Fm values of N. sigma was recognized to be highest
even under the highest temperature (36 °C). Among other strains, Indonesian strains
was also able to grow in the broader range of salinity (10 to 30 PSU) with N. sigma
as the most tolerate species with 1.43 ± 0.14 division day⁻ 1 at the lowest salinity of10. The photosynthetic parameters, ΦPSII, NPQ, and qP, were measured toinvestigate the tolerances on repeated alteration between low light and high light.
During the exposure of high light, the ability to quench an excess energy as heat(NPQ) was limiting among the Indonesian strains, especially in T. cocconeiformis
and Navicula species. Even without this dissipating function, at least N. agnita
could utilize high light without photoinhibition, as indicated by higher
photochemical quenching (qP) during high light, indicating the species could adapt
high light exposure on the sediments.

CHAPTER 6: General discussion
The ultimate goal of this study is to provide new insights on the importanceof mangrove ecosystems, particularly in Indonesia, where the wide mangrove forest
is existing but at the same time facing the highest annual deforestation rate. For thispurpose, investigation of microalgal communities on mangrove forest sedimentswas done revealing their abundance and diversity which was indicating the fertilityof mangrove forests in East Java, Indonesia. Beside MPB that primarily consisted ofdiatoms, Chattonella marina var. marina was also found in this study, wherein
when they bloom, it can cause severe economic losses in fisheries production for
adjacent waters.
This study reported a linear regression between the chlorophyll a ofsediment surface and biovolume of the MPB which showed almost all MPB florae
consisted of benthic diatom species. Such linear regression was also obtained in
Chapter 4 (Fig. 4-13) which further showed the Fv/Fm values and the species
diversity index were correlated, which implied environments suitable for thediatoms’ photosynthetic performance led high MPB diversity and biomass. The
physiology of candidate MPB species were evaluated against some environmental
parameters, revealing their high abilities in adapting to temperature increase andwide salinity range, and also their unique mechanisms to respond high light
exposure. MPB also played an important role in the primary production in the watercolumns because of their high occurrence among other planktonic species. The
occurrence of dense MPB may contribute as an important primary producer for theswamps as well as the adjacent coastal waters. In the future, these secret function of
secret garden in the mangrove forest should be clarified to elucidate high biologicalproduction of mangrove forest.