The different dominance microbial groups between seawater and coral
The results of paired Wilcoxon test showed that seawater samples' diversity was not significantly different (p>0.05) with the two coral samples carried out in pairs. Another study also showed similar results that the bacterial community associated with corals Acropora millepora, Galaxea fascicularis and Porites lutea was not significantly different from the bacterial community in the surrounding waters despite the high community diversity . This is presumably because there are many minor OTUs, only found in one sample with a small number of readings.
The results of the taxonomic assignment to the SILVA reference showed, from all samples, the predominant microbial class in samples from the phylum Proteobacteria was Alphaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. All three are considered to be the major bacterial classes of the dominant coral microbial resident community group across coral species, geographic areas and at various depths . In contrast to the aquatic microbial community, the Cyanobacteria phylum was found to be more abundant in seawater samples than the two groups of coral samples. This phylum has the highest diversity in shallow water where they can form stretches in the intertidal and infralittoral zones . As aquatic bacteria, the abundance of cyanobacteria found on corals can cause black band disease (BBD) due to the formation of a layer covering the coral skeleton . Furthermore, phylum Thaumarchaeota and Euryarchaeota which are Archaea were also found abundantly in seawater samples but not in coral samples. The diversity of seawater microbes is higher than the microbes that live in corals tissue, as indicated by the Shannon index of 6.82 and the number of OTUs owned by 7,746. The aquatic environment is more volatile due to the influence of tides and changes in physical and chemical properties that encourage microbial diversity.
The predominance of the phylum Acidobacteria is represented by the classes Acidobacteriia and Holophagae, which are well annotated at the class level, but most of the sequences from this phylum are annotated in unidentified or unclassified Acidobacteria. At least 2% reads of seawater samples have not been annotated at a level below kingdom, while on coral samples has not about 43% to do so. The large percentages aforementioned are owned by 1 OTU (OTU 7639), which is only annotated on Kingdom Bacteria which indicates that the base sequence of this bacterium is unique or has not been cultured. Taxonomic identification in microbial metabarcoding studies generally facilitated by using reference databases such as Silva  or Greengenes . However, these references include sequences from biomedical-based studies and are often difficult to use to identify sequences derived from marine biota . Database enrichment, especially related to coral microbes, needs to be improved considering that this research topic is still in great demand. On the other hand, considering that the primers used targeting the V4 region of the 16S rRNA gene, where this region is the lowest mutation rate or most conservative, the sequences obtained will have poor resolution in identification at lower taxa levels (below of class). On the other hand, regions V2 and V8 are the areas that mutate the fastest so that they are able to distinguish genera in one family or even species in one genus . Metabarcoding analysis using the V2 or V8 regions of the 16S rRNA gene will provide an overview of community diversity in lower taxa that is useful for further studies.
The microbial diversity of the seawater samples compared to the coral samples depicted in the PCoA ordinate plot shows the two samples representing seawater apart from the coral samples. In contrast, coral microbial diversity did not differ between SM and SF because it was scattered in clusters between coral samples. These results were corroborated by the PERMANOVA test which was carried out between types of samples with a value of p<0.05. The diversity of microbial species seems to be relatively the same within one species and is more influenced by other factors such as differences in season, location, type and environmental stress , regarding different species, time and location and related to different environmental pressures .
Microbial communities at the genus level, namely Cupriavidus, Acinetobacter, Mesorhizobium and Caulobacter were found to be abundant in coral samples but few in aquatic samples (Figure 5). This indicates that this microbial group is generally associated with coral A. pulchra. The abundant genus in seawater samples is associated with roles related to natural biochemical processes such as Acidibacter as a sulfur oxidizing agent and Fe(III) iron , Gaiella from the only strain studied that plays a role in the assimilation of carbohydrates, organic acids , and amino acids , and Streptomyces produce various bioactive compounds and enzymes so that they are potential sources of antibiotics .
The aquatic microbial community is more diverse, while the coral microbial community is dynamic due to different environmental factors and different habitats where the colony lives . However, interactions between coral resident microbes and waters near corals can occur by influencing the selection of associated microbes on corals. At least 3,783 OTUs (Fig. 2) were found in coral and aquatic samples, indicating that microbial members of corals could be recruited in the environment. This group of microbes may be bacteria that facilitate the exchange of coral metabolites into the surrounding microbial food web so that biogeochemical cycles between corals and surrounding waters can occur .
Environmental factors affecting coral microbial abundance
The temperature records demonstrate a diurnal tidal type, which is defined by the presence of one high tide and one low tide in a half-day (12-hour) period. In the intertidal plains, a diurnal temperature change of roughly 2–4°C during a sunny day is considered usual . As indicated in the study, environmental parameters in shallow water areas encounter fluctuations in temperature, oxygen concentration, pH, salinity, and nutrient content during the tidal period . During the day, photosynthesis can raise the concentrations of oxygen and pH while decreasing the concentrations of nutrients. On the other hand, due to increased biota respiration in the waters at night, oxygen concentration and pH decreased. Of particular, the physical and chemical characteristics of the waters have such an impact on the presence of associated biota in the area.
The highest temperature recorded was 33.64°C during daytime heating, and the average heating in a week was 31.37°C. Even though the temperature at the study site was outside the optimum temperature for coral growth (27°C), the corals were still able to survive and adapt well. A study stated that an increase in sea surface temperature with a difference of 2°C from the average monthly temperature could significantly reduce corals' calcification process and linear elongation . Another study showed an increase in temperature of 4°C with exposure to light can cause death and loss of color on the 22nd day of treatment . With the increasing sea surface temperature, corals adapt to survive in conditions outside of their optimum temperature. Subsequent studies suggested that adaptation may occur in corals located in intertidal areas and exposed during tidal periods with temporary and sporadic changes in microbial communities .
When the water temperature warms up, coral will respire more actively and increase their metabolic rate such their production of waste (containing nitrogenous waste) also increases. The genera that were abundant in the SF were a group of bacteria that supported the enhancement of this function, for example Endozoicomonas plays a role in the carbohydrate cycle and provides protein for its host , , Stenotrophomonas plays a role in the sulfur cycle  along with Herbaspirillum both are nitrogen-fixing bacteria  and Ralstonia has denitrifying ability . In addition, the effect of light on corals is associated with primary production that occurs during the day, promoting metabolism that affects pH and oxygen concentration in the water. Some coral microbes utilize light to regulate the production of metabolites that function specifically to combat opportunistic pathogens .
The genera Methyloversatilis, Methylobacillus, Flavobacterium, Sphingopyxis, Novosphingobium, and Brevundimonas were the most abundant in the SM. Methyloversatilis and Methylobacillus are a group of methylotrophic bacteria that have the ability to utilize single-carbon compounds (such as methane and methanol) as carbon and energy sources . The abundance of methylotrophic bacteria in SM may be influenced by the availability of C1 compounds in the water column and the ability of these bacteria to denitrify . Flavobacterium includes opportunistic bacteria and often causes disease in fish. Although this bacterium is found everywhere, including in soil and aquatic habitats, it is sensitive to high temperatures and grows well in the temperature range of 30−35°C . Novosphingobium and Sphingopyxis of the same family (Sphingomonadaceae) have been associated with their adaptability to nutrient deficient (oligotrophic) conditions and their role in the degradation of polyaromatic compounds . From these characteristics, the abundance of the two genera can be an indication of polluted environmental conditions .
Microbial diversity in the two coral conditions in the study did not differ significantly, but differences in microbial types could be detected from the unique OTUs in both coral samples, where there were 645 OTUs in Surface samples and 417 OTUs in Submerged samples. Corals acquire their symbionts in two ways, namely horizontally, which means that new symbionts are taken from the environment by each generation of hosts, and vertically by passing through the female lineage . The difference in species in the two samples could occur because the corals obtained their symbionts vertically and horizontally. Meanwhile, differences in the abundance of coral microbial communities can be influenced by environmental conditions (such as temperature, light and the presence of nutrients) and host preferences for survival in certain conditions. Therefore, the addition of an analysis of other environmental factors in future research will provide a more comprehensive understanding of the research results.