RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

Kong, Hejun; Yang, Eun Jin; Jiao, Nianzhi; Lee, Young-Ju; Jung, Jinyoung; Cho, Kyoung‐Ho; Moon, Jong-Kuk; Kim, Jee-Hoon; Xu, Dapeng

doi:10.1016/j.scitotenv.2023.162608

Cited by 10 publications

(4 citation statements)

References 78 publications

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“…In community ecology, eRNA is a complementary monitoring tool to eDNA due to its sensitivity to detection (Kong et al, 2023; Littlefair et al, 2022; Miyata et al, 2021). Despite the potential of eRNA, there are still many uncertainties surrounding its application and reliability (Stevens & Parsley, 2022).…”

Section: Resultsmentioning

confidence: 99%

Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Bunholi,

Foster,

Casey

2023

Environmental DNA

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Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range of organisms and aquatic systems. Environmental DNA (eDNA) and environmental RNA (eRNA), collectively referred to as environmental nucleic acids (eNAs), have revolutionized biodiversity monitoring due to their noninvasive nature and high‐resolution capabilities when compared to traditional survey methods. While eNA applications have grown exponentially over the past decade, methodological inconsistencies hinder reproducibility and comparability. To assess the current state of eNA methodologies in aquatic ecology, we conducted a systematic review of 300 peer‐reviewed eNA studies that assess ecological communities across diverse aquatic systems. Of these papers, 291 examine eDNA, four examine eRNA, and five consider both eDNA and eRNA. The small number of eRNA studies compared to eDNA highlights the eRNA field is in its infancy. Of the eNA studies looked at, we found a clear geographic bias, with approximately 50% of all eNA studies occurring in six high‐income countries, while less than 10% of eNA studies occur across South America and Africa. Further, we report a lack of methodological standardization across eNA studies, showing high variability in water filtration volume, filter material, filter pore size, eNA extraction method, marker choice, and bioinformatic pipelines. We further highlight that incomplete reference sequence databases for both eRNA and eDNA limit taxonomic assignment and biodiversity inferences. Finally, we identify a systematic issue across eNA studies in community ecology: missing methodological details, which compromise reproducibility, especially in newly emerging eRNA applications. To facilitate the standardization of eNA monitoring across aquatic systems and permit the further integration of eNA applications in biodiversity monitoring, we recommend the improvement of reference databases alongside guidelines that encourage methodological transparency.

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Section: Resultsmentioning

confidence: 99%

Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Bunholi,

Foster,

Casey

2023

Environmental DNA

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“…5 ), aligning with prior research [ 24 , 26 ]. While eRNA is generally recognized for its greater spatial discriminative capabilities [ 27 ] and stronger correlation with environmental parameters [ 23 ], there are exceptions, such as instances where eRNA identified less spatial differences in metazoan populations due to reduced species richness [ 60 ]. Furthermore, our findings underscored a significant increase in the ratio of spatial community variations between eDNA and eRNA as organismal size increased ( Supplementary Material Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Existing studies have produced mixed results, showing variation in the comparison of species detectability and community compositions using eDNA and eRNA [ [18] , [19] , [20] ]. These studies generally reported either a strong connection between eDNA- and eRNA-derived communities [ 19 , 21 , 22 ] or notable differences [ 18 , 23 , 24 ]. Typically, eDNA tended to exhibit higher alpha diversity but was also associated with higher false positive rates [ 20 , 25 ], with some exceptions (e.g., higher macroinvertebrate alpha diversity in eRNA in Ref.…”

Section: Introductionmentioning

confidence: 99%

Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates

Zhang,

Qiu,

Liu

et al. 2024

Environmental Science and Ecotechnology

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“…Studies using both rRNA and rDNA have found general agreement and differences between the two methods [72][73][74][75] ; some of the observed differences may have been overlooked if only rDNA had been studied 70 . Moreover, rRNA sequencing has been suggested to be superior to rDNA approaches 76 , for instance, in its sensitivity to environmental conditions 77,78 . This is an important factor to note in the context of a changing AO.…”

Section: Challenges In Microbial Community Studiesmentioning

confidence: 99%

Vulnerability of Arctic Ocean microbial eukaryotes to sea ice loss

Jackson,

Grevesse,

Kilias

et al. 2024

Preprint

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The Arctic Ocean (AO) is changing at an unprecedented rate, with ongoing sea ice loss, warming and freshening impacting the extent and duration of primary productivity over summer months. Surface microbial eukaryotes are vulnerable to such changes, but basic knowledge of the spatial variability of surface communities is not well understood. Here, we sampled microbial eukaryotes in surface waters of the Beaufort Sea from four contrasting environments: the Canada Basin (open ocean), the Mackenzie Trough (river-influenced), the Nuvuk region (coastal) and the under-ice system of the Canada Basin. Microbial community structure and composition varied significantly among the systems, with the most phylogenetically diverse communities being found in the more coastal systems. Further analysis of environmental factors showed potential vulnerability to change in the most specialised community, which was found in the samples taken in water immediately beneath the sea ice, and where the community was distinguished by rare species. In the context of ongoing sea ice loss, specialised ice-associated microbial assemblages may transition towards more generalist assemblages, with implications for the eventual loss of biodiversity and associated ecosystem function in the Arctic Ocean.

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RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

Cited by 10 publications

References 78 publications

Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates

Vulnerability of Arctic Ocean microbial eukaryotes to sea ice loss

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