Electronic Theses and Dissertation

Penelitian disertasi ini dilatarbelakangi oleh peran penting makroinvertebrata bentik sebagai bioindikator kesehatan sungai serta oleh meningkatnya tekanan antropogenik di DAS Krueng Aceh (alih fungsi lahan, limbah domestik, erosi). Pada saat yang sama, kajian komprehensif yang mencakup seluruh bentang hulu–tengah–hilir, khususnya yang memasukkan aspek genetika, masih sangat terbatas. Tujuan utama penelitian adalah: (1) menganalisis keanekaragaman jenis dan pola distribusi makroinvertebrata bentik di DAS Krueng Aceh; (2) menilai kualitas air sungai menggunakan berbagai indeks biotik berbasis komunitas bentik; (3) mengkaji DNA barcoding (gen COI) beberapa spesies makroinvertebrata bentik untuk memperoleh identifikasi taksonomi yang lebih akurat serta informasi struktur kekerabatan; serta (4) menganalisis pola filogeografi makroinvertebrata bentik di DAS Krueng Aceh.
Penelitian dilaksanakan secara terintegrasi pada 10 stasiun yang mewakili segmen hulu, tengah, dan hilir DAS selama beberapa bulan pengamatan. Makroinvertebrata, air, dan sedimen dikoleksi sesuai prosedur standar, diidentifikasi secara morfologi, kemudian dianalisis kepadatan, frekuensi kehadiran, indeks keanekaragaman, keseragaman, dominansi, serta pola distribusi. Kualitas perairan dinilai melalui parameter fisika-kimia, indeks pencemaran (misalnya indeks Nemerow), dan beberapa indeks biotik (BMWP-CR, SingScore, SASS5-ASPT). Pada tahap genetika, sampel terpilih diekstraksi DNA-nya, diamplifikasi gen COI, disekuensing, kemudian dibandingkan dengan database GenBank/BOLD (BLAST), dianalisis jarak genetik, keragaman haplotipe, dan disusun pohon filogenetik model K2P–Neighbor Joining.
Hasil penelitian menunjukkan bahwa komunitas makroinvertebrata bentik yang ditemukan di DAS Krueng Aceh terutama Insekta berada dalam stadia larva, pupa/nimfa dan didominasi famili Hydropsychidae, terutama Hydropsyche angustipennis, serta dua spesies dengan frekuensi kehadiran tinggi, Afrobrianax ferdyi dan Tarebia granifera. Spesies yang terkait arus deras dan substrat keras (batuan, kerikil) banyak ditemukan di segmen hulu–tengah, sedangkan spesies yang menyukai substrat lunak berlumpur dan tepian bervegetasi dominan di bagian hilir. Indeks keanekaragaman mengindikasikan kondisi ekologis relatif lebih baik di bagian hulu–tengah (misalnya sungai di Desa Keureuweung/stasiun 4), sedangkan keanekaragaman rendah di sungai sekitar Desa Kampung Baru (stasiun 9) dan sungai di sekitar Desa Lampulo (stasiun 10) berkaitan dengan sedimentasi berlebih, tingginya TDS, serta tekanan aktivitas manusia di hilir. Analisis HCA mengelompokkan stasiun menjadi dua grup utama yang secara garis besar memisahkan hulu–tengah dari hilir, dengan Stasiun 10 sebagai lokasi yang paling berbeda karena sedimentasi dan TDS yang sangat tinggi sehingga hadirnya spesies toleran.
Analisis kualitas air menunjukkan bahwa DAS Krueng Aceh berada pada kondisi tercemar ringan hingga sedang, dengan tingkat pencemaran sedang terkonsentrasi di hilir yaitu sungai di sekitar Desa Lampulo (Stasiun 10). Peningkatan TDS, C-organik, N-total, salinitas, dan konduktivitas yang berkaitan dengan aktivitas pertanian, industri, limbah domestik, dan sedimentasi halus di hilir menjadi faktor utama penurunan kualitas habitat akuatik. Komunitas makroinvertebrata di lokasi ini didominasi spesies toleran sehingga menguatkan indikasi degradasi. Evaluasi indeks biotik menunjukkan bahwa BMWP-E (original), BMWP-CR, dan SASS5 cukup efektif untuk mengkategorikan tingkat pencemaran di konteks sungai tropis, terutama bila diintegrasikan dengan indeks pencemaran dan karakteristik sedimen.
Pendekatan DNA barcoding berhasil mengidentifikasi 18 spesies Insekta dari enam ordo dan enam spesies Gastropoda dari dua famili (Thiaridae dan Neritidae), dengan tingkat kemiripan sekuens COI terhadap referensi GenBank/BOLD umumnya >99%. Sebanyak 14 spesies Insekta tercatat sebagai catatan baru bagi perairan Indonesia dalam barcoding, sehingga memperluas basis data fauna nasional dan memperkuat Aceh Benthic Barcode Database. Secara filogenetik, klaster Insekta dan Gastropoda yang terbentuk konsisten dengan identifikasi morfologi dan mendukung keandalan COI sebagai penanda untuk biomonitoring berbasis DNA di DAS Krueng Aceh.
Dalam analisis filogeografi, makroinvertebrata bentik di DAS Krueng Aceh, khususnya Isoperla signata dan Vittina coromandeliana, memiliki struktur genetik yang unik dan sangat berbeda dari populasi di wilayah lain. Populasi di Krueng Aceh menunjukkan keragaman genetik lokal yang rendah, tetapi jarak genetik dan nilai Fst yang tinggi mengindikasikan bahwa mereka merupakan unit evolusioner tersendiri yang penting untuk dilindungi.
Secara keseluruhan, disertasi ini menyimpulkan bahwa (1) keanekaragaman dan struktur komunitas makroinvertebrata bentik di DAS Krueng Aceh sangat dipengaruhi gradien hulu–hilir, kondisi fisik-kimia, dan tekanan antropogenik; (2) kualitas air sungai berada pada kategori tercemar ringan–sedang dengan indikasi degradasi yang nyata di segmen hilir; dan (3) integrasi identifikasi morfologi dan DNA barcoding menghasilkan basis data taksonomi dan genetik yang kuat untuk pemanfaatan makroinvertebrata bentik sebagai bioindicator; serta (4) penelitian ini menunjukkan bahwa Isoperla signata dan Vittina coromandeliana di DAS Krueng Aceh membentuk unit evolusioner genetik yang unik dan penting untuk dilindungi.
Berdasarkan temuan tersebut, penelitian ini merekomendasikan: (1) penerapan rutin biomonitoring berbasis makroinvertebrata bentik dan DNA barcoding (serta pengembangan eDNA/metabarcoding) dalam sistem pemantauan kualitas air DAS Krueng Aceh; (2) penguatan kebijakan pengelolaan DAS yang menekan sumber pencemar dan sedimentasi, terutama di hilir, melalui pengendalian erosi, pengelolaan limbah domestik dan pertanian, serta penataan penggunaan lahan; dan (3) perluasan cakupan riset genetika makroinvertebrata bentik (lebih banyak taksa, titik, dan penanda genetik) agar hubungan antara variasi genetik, kualitas habitat, dan tekanan antropogenik dapat dipahami lebih baik sebagai dasar pengambilan keputusan konservasi dan pengelolaan sungai yang berkelanjutan.

Kata kunci: Biomonitoring, DNA barcoding (COI), DAS Krueng Aceh, Makroinvertebrata bentik, Kualitas air sungai

This doctoral dissertation is motivated by the key role of benthic macroinvertebrates as bioindicators of river health and by the intensifying anthropogenic pressures on the Krueng Aceh watershed (land-use change, domestic wastewater, erosion). At the same time, comprehensive studies spanning the full headwaters–midstream–downstream continuum and explicitly incorporating genetic aspects remain very limited. The main objectives of this research were to: (1) analyse the species diversity and distribution patterns of benthic macroinvertebrates in the Krueng Aceh watershed; (2) assess river water quality using a range of biotic indices based on benthic communities; (3) apply DNA barcoding (COI gene) to selected benthic macroinvertebrate species to obtain more accurate taxonomic identification and information on phylogenetic relationships; and (4) investigate the phylogeographic patterns of benthic macroinvertebrates in the Krueng Aceh watershed. The study was conducted in an integrated manner at 10 stations representing upstream, midstream, and downstream segments over several months of observation. Macroinvertebrates, water, and sediment were collected following standard procedures. Macroinvertebrates were identified morphologically, and their density, frequency of occurrence, diversity, evenness, dominance, and distribution patterns were analysed. Water quality was evaluated using physico-chemical parameters, pollution indices (e.g. Nemerow index), and several biotic indices (BMWP-CR, SingScore, SASS5-ASPT). For the genetic component, selected samples were subjected to DNA extraction, COI amplification and sequencing, followed by BLAST comparison with GenBank/BOLD reference databases, genetic distance and haplotype diversity analysis, and reconstruction of phylogenetic trees using the K2P–Neighbor Joining model. The results of the study indicate that the benthic macroinvertebrate community found in the Krueng Aceh watershed, especially Insecta, are in the larval and pupal/nymphal stages and dominated by the family Hydropsychidae, particularly Hydropsyche angustipennis, together with two species with high frequency of occurrence, Afrobrianax ferdyi and Tarebia granifera. Species associated with fast flow and coarse substrates (boulders, cobbles, gravel) were mainly found in the upstream–midstream segments, whereas species preferring soft, muddy substrates and vegetated margins were dominant in the downstream reaches. Diversity indices indicated relatively better ecological conditions in the upstream–midstream section (e.g. the river at Keureuweung Village, Station 4), whereas low diversity in the river near Kampung Baru Village (Station 9) and near Lampulo Village (Station 10) was associated with excessive sedimentation, elevated TDS, and intense human pressures in the lower reaches. Hierarchical cluster analysis (HCA) grouped the sampling stations into two main clusters, broadly separating the upstream–midstream sites from the downstream sites. Station 10 emerged as the most distinct location, likely due to extremely high sedimentation and total dissolved solids (TDS), which favored the occurrence of tolerant taxa. Water quality analysis indicated that the Krueng Aceh watershed is in a lightly to moderately polluted condition, with moderate pollution concentrated at the downstream station near Lampulo Village (Station 10). Increases in TDS, organic carbon, total nitrogen, salinity, and conductivity, related to agricultural activities, industrial inputs, domestic wastewater, and fine sedimentation in the lower reaches, were identified as the main drivers of aquatic habitat degradation. At these locations, benthic macroinvertebrate communities were dominated by tolerant species, reinforcing the evidence of ecological degradation. Evaluation of biotic indices demonstrated that the original BMWP-E, BMWP-CR, and SASS5 are reasonably effective for categorising pollution levels in a tropical river context, especially when interpreted alongside pollution indices and sediment characteristics. The DNA barcoding approach successfully identified 18 insect species from six orders and six gastropod species from two families (Thiaridae and Neritidae), with COI sequence similarity to GenBank/BOLD references generally exceeding 99%. Fourteen insect species represent new barcoding records for Indonesian freshwaters, thereby expanding the national faunal database and strengthening the Aceh Benthic Barcode Database. Phylogenetically, the insect and gastropod clusters were congruent with morphological identifications, supporting the reliability of COI as a genetic marker for DNA-based biomonitoring in the Krueng Aceh watershed. Phylogeographic analyses showed that benthic macroinvertebrates in the Krueng Aceh watershed, particularly Isoperla signata and Vittina coromandeliana, possess unique genetic structures that differ markedly from populations in other regions. Populations in Krueng Aceh exhibited low local genetic diversity but high genetic distances and Fst values, indicating that they constitute distinct evolutionary units that merit targeted conservation. Taken together, this dissertation concludes that: (1) the diversity and community structure of benthic macroinvertebrates in the Krueng Aceh watershed are strongly shaped by the upstream–downstream gradient, physico-chemical conditions, and anthropogenic pressures; (2) river water quality falls within the lightly to moderately polluted category, with clear evidence of degradation in the downstream segment; (3) the integration of morphological identification and DNA barcoding yields a robust taxonomic and genetic database for the use of benthic macroinvertebrates as bioindicators; and (4) Isoperla signata and Vittina coromandeliana in the Krueng Aceh watershed form unique evolutionary genetic units that warrant specific protection. Based on these findings, the study recommends: (1) routine implementation of biomonitoring based on benthic macroinvertebrates and DNA barcoding (and further development of eDNA/metabarcoding) within the water quality monitoring system of the Krueng Aceh watershed; (2) strengthening watershed management policies to reduce pollutant inputs and sedimentation, particularly in the downstream area, through erosion control, improved management of domestic and agricultural waste, and better land-use planning; and (3) expanding the scope of genetic research on benthic macroinvertebrates (including more taxa, sites, and genetic markers) to better elucidate the relationships among genetic variation, habitat quality, and anthropogenic pressure as a basis for evidence-informed conservation and sustainable river management. Keywords: Biomonitoring, DNA barcoding (COI), Krueng Aceh watershed, Benthic macroinvertebrates, River water quality