Hubungan antara Symbiodiniaceae dan Karakteristik Terumbu Karang Berdasarkan DNA Lingkungan di Perairan Pulau Lombok
Date
2022Author
Pratomo, Arief
Bengen, Dietriech Geofrey
Zamani, Neviaty Putri
Madduppa, Hawis
Metadata
Show full item recordAbstract
Symbiodiniaceae merupakan biota asosiasi karang penting dan berkontribusi dalam kesehatan ekosistem terumbu karang. Sebagai endosimbion karang, Symbiodiniaceae menyediakan energi, menyerap sisa metabolit, dan membantu pertumbuhan karang. Hingga saat ini, dikenali 11 genera resmi dalam famili Symbiodiniaceae dan masih terdapat lima klade mewakili genera yang belum terdeskripsi secara formal. Karena itu, memahami keragaman Symbiodiniaceae dalam ekosistem karang menjadi penting dan diduga, Symbiodinaiaceae dapat menjadi indikator kondisi terumbu karang. Namun, informasi Keragaman Symbiodiniaceae di Indonesia masih sedikit. Lagipula, identifikasi Symbiodiniaceae tidak mudah, terlebih bila memerlukan pengambilan dan pengisolasian dari banyak lokasi dan inang. DNA lingkungan (eDNA) adalah materi genetika yang terlepas ke lingkungan, dapat digunakan untuk menilai potensi keragaman Symbiodiniaceae secara non destruktif, cepat, relatif luas, efisien, dan efektif.
Melalui pendekatan survei eDNA, penelitian mengkaji keragaman hayati dan karakteristik komunitas Symbiodiniaceae, menelaah hubungan antara keragaman Symbiodiniaceae dan karakteristik terumbu karang dan menganalisa nilai indikator dan preferensi komunitas Symbiodiniaceae pada pengelompokan karateristik terumbu karang lokasi tertentu di Perairan Lombok.
Pengambilan sampel eDNA dan pengamatan kondisi bentik karang dilakukan di zona inti, di luar zona inti, dan luar kawasan konservasi Perairan Lombok Barat, Utara, dan Timur. Materi eDNA dalam sampel air laut dan sedimen yang tersaring di kertas saring pada fraksi ukuran pori-pori 12 µm (fraksi >12 µm) dan 0,4 µm (fraksi 0,4-12 µm), diekstraksi dan diamplifikasi DNA-nya dengan primer gen V9-SSU 18S rRNA, kemudian disekuensing melalui platform MiSeq-Ilumina. Analisis bioinformatika melalui platform Qiime2 dilakukan untuk memperoleh amplicon sequence variants (ASV), identifikasi Symbiodiniaceae setelah mengindentifikasi eukaryota laut terlebih dahulu, dan analisis filogenetika. Pengamatan kondisi bentik karang dilakukan dengan metode point intercept transect (PIT) untuk menentukan kondisi tutupan kategori bentik, tingkat rugositas karang, tingkat tutupan bentuk karang hidup, indeks kematian karang (IKK), genera karang, dan keterwakilan genera karang. Dilakukan analisis statistik untuk analisis perbandingan sebaran dan komposisi kelimpahan, keragaman alfa dan beta, kluster, indikator dan preferensi komunitas Symbiodiniaceae terhadap kondisi terumbu karang di Perairan Lombok.
Penelitian memperoleh 2.737.734 sekuens yang terdiri atas 20.478 ASV sebagai wakil individu. Identifikasi eukaryota laut mengungkap lima kingdom dengan komposisi Chromista (35%), Animalia (32%), Fungi (3%), Plantae (2%), dan Protozoa (2%), dengan 43,34 % total ASV tidak terindentifikasi sama sekali. Keragaman alfa (Shannon H’) eukaryota berkisar {minimum-maksimum (median)} antara 4,90-9,59 (7,63). Faktor alam terkait media habitat lebih mempengaruhi keragaman alfa eukaryota daripada faktor geografi skala lokal dan zonasi konservasi perairan. Aspek teknis terkait media sumber dan pembagian fraksi sampel menentukan perolehan eDNA eukaryota. Keragaman beta (Bray-Curtis) komunitas eukaryota berkisar {minimum-maksimum (median)} antara 0,72-0,99 (0,92). Terdapat perbedaan signifikans antar lokasi, media dan fraksi namun faktor manajemen terkait penetapan zonasi konservasi tidak mempengaruhi variasi heterogenitas komunitas eukaryota.
Penelitian berhasil mendeteksi dan mengidentifikasi 16 wakil individu Symbiodiniaceae yang terdiri atas enam genera (subklade): Symbiodinium (A.sym21), Breviolum (B.sym18), Cladocopium (C.sym1, C.sym5, C.sym7, C.sym8, C.sym10, C.sym15, C.sym16, and C.sym17), Durusdinium (D1.sym2, D1.sym6, D1.sym19, and D1.sym22), Klade G Foraminifera (G2.sym4), dan Halluxium (H.Sym12). Komposisi dominan pada Cladocopium (71%), disusul Durusdinium (18,2%), dan Klade G Foraminifera (8,4%). Komunitas Symbiodiniaceae mencirikan keragaman alfa rendah dan keragaman beta tinggi, namun tidak memperlihatkan perbedaan secara nyata antar lokasi, zona, media, maupun fraksi. Sejauh diketahui, studi eDNA Symbiodiniaceae belum pernah dilakukan di kawasan Asia Tenggara. Halluxium dan Klade G Foraminifera merupakan genera Symbiodiniaceae yang pertama kali dilaporkan di wilayah Indonesia bahkan kawasan Asia Tenggara.
Kondisi tutupan bentik, karang hidup, indeks kematian karang (IKK), rugositas, dan keterwakilan genera karang, secara relatif lebih baik di Lombok Timur dan zona inti. Kondisi bentik membentuk tiga kluster secara nyata dengan karakteristik relung terumbu karang yang berbeda berdasarkan pada 66,47% total variasi sebaran komunitas Symbiodiniaceae. Subklade Durusdinium D1.sym2 memberi nilai indikator dan preferensi kuat terhadap karakteristik relung terumbu karang dengan karakteristik utama rugositas dan tutupan bentik berbatuan (rock), dan subklade Cladocopium C.sym1 memberi nilai indikator dan preferensi kuat terhadap relung terumbu karang dengan karakteristik yang diindikasikan oleh D1.sym2, ditambah dengan karakteristik utama lifeform karang bercabang dan karang Acropora bercabang, serta genera Seriatopora, Porites, Acropora, Stylophora, dan Montipora. Berdasarkan pada peran Cladocopium dan Durusdinium dalam mekanisme adaptasi karang, diduga, nilai indikator para subklade tersebut mungkin berhubungan dengan riwayat respon karang yang pulih dan tahan bleaching di ekosistem terumbu karang Perairan Lombok. Symbiodiniaceae is a crucial coral association biota and contributes to the health of coral reef ecosystems. As coral endosymbionts, Symbiodiniaceae provide energy, absorb residual metabolites, and support coral growth. To date, 11 named genera have been classified as members of the Symbiodiniaceae family, and there are still five clades representing the undescribed genera. Therefore, understanding the diversity of Symbiodiniaceae in coral ecosystems is essential, and it is supposed that Symbiodiniaceae can be an indicator of coral reef conditions. However, the information on Symbiodiniaceae diversity in Indonesia is still limited. Moreover, identifying Symbiodiniaceae requires collection and isolation from multiple locations and hosts. Environmental DNA (eDNA) is genetic material released into the environment, which can be employed to assess the potential for diversity of Symbiodiniaceae in a non-destructive, rapid, widespread, and cost-effective manner.
Through eDNA, the research examines the biodiversity and characteristics of the Symbiodiniaceae community and the potential of Symbiodiniaceae as an indicator of the condition of coral reefs in Lombok waters.
eDNA sampling and observation of coral benthic were conducted within the core zone, the non-core zone, and the outside conservation areas of west, north, and east Lombok. The eDNA material in seawater and sediment samples filtered on filter paper at a pore size fraction of 12 μm (fraction >12 μm) and 0,4 μm (fraction 0,4-12 μm) were extracted and amplified with the primer set of V9-SSU 18S rRNA gene was then sequenced via the MiSeq-Illumina platform. Bioinformatics analyses through the Qiime2 platform were carried out to obtain amplicon sequence variants (ASV), identify marine eukaryotes and Symbiodiniaceae, and conduct phylogenetic analysis. Observation of the conditions of coral benthic was carried out using the point intercept transect (PIT) method to determine the benthic category cover, coral rugosity level, live coral cover level, coral mortality index (IKK), coral genera, and coral genera representation. Statistical analyses were carried out for distribution and abundance comparison, diversity of alpha and beta, clusters, indicators, and preferences of the Symbiodiniaceae community on the condition of coral reefs in Lombok waters.
The study obtained 2.737.765 sequences consisting of 20.478 ASV as individual representatives. Identification of marine eukaryotes showed five kingdoms with the composition of Chromista (35%), Animalia (32%), Fungi (3%), Plantae (2%), and Protozoa (2%), with 43,34 % of the total ASV were not unidentified at all. The alpha diversity (Shannon H') of eukaryotes ranges from {minimum-maximum (median)} between 4,90-9,59 (7,63). Natural factors related to habitat media affect eukaryote alpha diversity more than local scale geography and aquatic conservation zoning. Technical aspects related to the source media and the separation of sample fractions determine the acquisition of eukaryote eDNA. Beta diversity (Bray-Curtis) of the eukaryote community ranged from {minimum-maximum (median)} between 0,72-0,99 (0,92). There were significant differences between locations, media, and fractions, but management factors related to the determination of conservation zoning did not affect the heterogeneity of the eukaryote community.
The study succeeded in detecting and identifying 16 individual representatives of Symbiodiniaceae which consisted of six genera (subclades): Symbiodinium (A.sym21), Breviolum (B.sym18), Cladocopium (C.sym1, C.sym5, C.sym7, C.sym8, C.sym10, C.sym15, C.sym16, and C.sym17), Durusdinium (D1.sym2, D1.sym6, D1.sym19, and D1.sym22), Foraminifera Clade G (G2.sym4), and Halluxium (H.Sym12). The dominant composition was Cladocopium (71%), followed by Durusdinium (18,2%), and Foraminifera Clade G (8,4%). The Symbiodiniaceae community characterized low alpha diversity and high beta diversity but did not show significant differences between locations, zones, media, or fractions. As far as is known, Symbiodiniaceae eDNA has not been studied yet in Southeast Asia. Halluxium is the first record in Indonesia, even in Southeast Asia.
Conditions of benthic cover, live coral, coral mortality index (MI), rugosity, and coral genera representation were relatively better in East Lombok and the core zone. The benthic conditions formed into three distinct clusters with different coral reef niche conditions based on 66,47% of the total variation in the distribution of the Symbiodiniaceae community. Durusdinium subclade D1.sym2 as an indicator of coral reef niche condition with the main characteristics of rugosity and benthic rock cover, and Cladocopium C.sym1 subclade as an indicator of coral reef niche with conditions indicated by D1.sym2, plus coral reef niche condition with the main characteristics of coral lifeform, branched corals, and branched corals Acropora, and the genera Seriatopora, Porites, Acropora, Stylophora, and Montipora. Based on the role of Cladocopium and Durusdinium in the mechanism of coral adaptation, it is presumed that the indicator values of these subclades may be related to the history of coral responses that have recovered and are resistant to bleaching in the coral reef ecosystems of Lombok waters.
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