Acta Limnologica Brasiliensia
https://app.periodikos.com.br/journal/alb/article/doi/10.1590/S2179-975X1626
Acta Limnologica Brasiliensia
Artigo Original

Freshwater sponges as natural eDNA samplers for biodiversity assessment in the Porong River, East Java, Indonesia

Esponjas de água doce como amostradores naturais de eDNA para avaliação da biodiversidade no Rio Porong, Java Oriental, Indonésia

Puspa Nirmala Kuncoro; Aunurohim; Ahmad Yanuar; Nova Maulidina Ashuri; Dwi Sendi Priyono; Edwin Setiawan

http://dx.doi.org/10.1590/S2179-975X1626 Acta Limnol. Bras. (Online), vol.38, e23, 2026
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Abstract

Aim: The Porong River, a heavily impacted tropical waterway in East Java, Indonesia, is poorly documented regarding biodiversity. This study evaluated the freshwater sponges Eunapius carteri and Oncosclera asiatica as passive in situ eDNA samplers by comparing sponge-derived eDNA signals with conventional water eDNA sampled at the same site and time.

Methods: Ten sponge specimens (five per species) and five water-filter samples were collected from the midstream region of the Porong River. Sponge tissue was preserved in Longmire’s buffer, and water was vacuum filtered through 0.45 µm membrane filters. DNA was extracted using the Tiangen Genomic DNA Kit (sponge) and the Zymo Research DNA Extraction Kit (water) and quantified using NanoDrop. The mitochondrial COI gene was amplified with universal Leray primers using a touchdown PCR protocol, and amplicons were sequenced on an Illumina MiSeq platform (2×300 bp paired end). Reads were quality-filtered, trimmed, merged, and assembled de novo in Geneious Prime 2025, and taxonomically assigned using BLAST against the MIDORI2 database. Alpha diversity (Shannon-Wiener index, richness) and beta diversity (Jaccard index) were used to compare the community composition among sample types.

Results: Sequencing yielded approximately 398,000 raw reads per sample for each sample. Insecta and algal taxa dominated all the samples. Water showed the highest richness (87 classes) and Shannon index (H′ = 3.53 ± 0.06), followed by O. asiatica (60.5; H′ = 3.23 ± 0.17), and E. carteri (42.5; H′ = 2.71 ± 0.06). The Jaccard similarity ranged from 15% to 50%, being highest between water and E. carteri (39.25%) and lowest between water and O. asiatica (23.42%). Twenty-eight taxa were shared among all matrices; water, O. asiatica, and E. carteri had 51, 47, and 5 unique taxa, respectively.

Conclusions: Freshwater sponges captured biologically meaningful, spatially localized biodiversity signals that complemented, but were less comprehensive than, water eDNA, supporting their use as passive natural eDNA samplers for monitoring dynamic tropical riverine systems.

Keywords

 biodiversity; eDNA; freshwater filter feeder; metabarcoding; East Java River

Resumo

Objetivo: O rio Porong, um curso d’água tropical fortemente impactado no leste de Java, Indonésia, é pouco documentado quanto à sua biodiversidade. Este estudo avaliou as esponjas de água doce Eunapius carteri e Oncosclera asiatica como amostradoras passivas de eDNA in situ, comparando os sinais de eDNA das esponjas com os obtidos pela amostragem convencional de eDNA da água, coletada no mesmo local e momento.

Métodos: Dez espécimes de esponjas (cinco por espécie) e cinco amostras de filtro de água foram coletados no trecho médio do rio Porong. O tecido das esponjas foi preservado em tampão de Longmire, e a água foi filtrada a vácuo em membranas de 0,45 µm. O DNA foi extraído com o Tiangen Genomic DNA Kit (esponjas) e o Zymo Research DNA Extraction Kit (água), e quantificado em NanoDrop. O gene mitocondrial COI foi amplificado com os primers universais de Leray sob protocolo de PCR touchdown, e os amplicons foram sequenciados em plataforma Illumina MiSeq (2×300 pb, pareado). As leituras foram filtradas por qualidade, aparadas, unidas e montadas de novo no Geneious Prime 2025, e atribuídas taxonomicamente por BLAST contra o banco de dados MIDORI2. A diversidade alfa (índice de Shannon-Wiener e riqueza) e a diversidade beta (índice de Jaccard) foram comparadas entre os tipos de amostra.

Resultados: O sequenciamento gerou aproximadamente 398.000 leituras brutas por amostra. Táxons de Insecta e de algas predominaram em todos os tipos de amostra. A água apresentou a maior riqueza (87 classes) e índice de Shannon (H′ = 3,53 ± 0,06), seguida por O. asiatica (60,5; H′ = 3,23 ± 0,17) e E. carteri (42,5; H′ = 2,71 ± 0,06). A similaridade de Jaccard variou de 15% a 50%, sendo maior entre água e E. carteri (39,25%) e menor entre água e O. asiatica (23,42%). Vinte e oito táxons foram compartilhados entre todas as matrizes; água, O. asiatica e E. carteri apresentaram, respectivamente, 51, 47 e 5 táxons exclusivos.

Conclusões: As esponjas de água doce capturaram sinais de biodiversidade biologicamente relevantes e espacialmente localizados, complementares, porém menos abrangentes, aos obtidos pelo eDNA da água, o que sustenta seu uso como amostradoras naturais passivas de eDNA no biomonitoramento de sistemas fluviais tropicais dinâmicos.

Palavras-chave

biodiversidade; eDNA; esponja filtradora de água doce; metabarcoding; Rio no Leste de Java

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