The current study is the first to directly compare the differences in eukaryotic community diversity by metabarcoding eRNA and eDNA from an estuarine benthic ecosystem. This is also the first study to compare the diversity of environmental RNA and DNA using two of the most common loci examined in metabarcoding applications: COI and 18S. Only a handful of studies have used eRNA to assess diversity through metabarcoding and have demonstrated some differences in detected diversity between eRNA and eDNA in metabarcoding19,29,38. Environmental DNA has many useful applications, but one of the downfalls of DNA is that it can be detected long after an organism has inhabited an area, such as from dead organisms and even significant distances away from the source1. While the persistence of eDNA may be useful in detecting the presence of endangered, rare, or invasive species in marine systems, the persistence of eDNA, such as legacy DNA, may skew the accurate representation of community structure immediately after a disturbance event or during the exact moment of sampling21. Environmental RNA proves to be a useful tool because it is far less persistent in marine environments2,27. In the current study, RNA provides a snapshot of living organisms present in the mesocosms at the time of sampling, compared to DNA which detects past and present organisms in the sample.
Benthic ecosystems often have high biodiversity because they are dynamic environments with various substrates favorable for hosting communities39. To date, there is no one loci and associated primer pair that will effectively detect all eukaryotic organisms, and in particular metazoans, so it is beneficial to use multiple loci when looking for a variety of taxa6. Previous marine eDNA studies have demonstrated the preferred method of using two loci to achieve comprehensive metabarcoding for taxonomically diverse environments5,30,40. The current study further demonstrates the need to use at least two different loci for targeted PCR and sequencing to truly capture the wide diversity in rich systems, such as the top oxygenated layer of the marine benthos. Our results demonstrate the types of organisms detected using the 18S loci vary widely from the organisms detected by COI. The 18S loci also detected a higher number of organisms than using the COI loci. The 18S allowed greater detection of metazoans whereas COI was useful in the detection of Oomycota (i.e., a eukaryotic microorganism that resembles fungi) protozoa. Protozoa are often food sources for meiofauna41; therefore, using COI for protozoan detection and 18S for metazoan detection showcases multiple trophic levels present in the mesocosms of the current study. Utilizing multiple loci not only broadens taxonomic diversity detection but can also highlight multiple trophic levels for understanding food webs originating in benthic environments15.
A study evaluating arctic benthic diversity similarly found that COI detected fewer taxa than 18S using eDNA metabarcoding, and there was only ~ 40% taxa overlap between markers at the class level42. In the current study, the COI marker using both nucleic acid templates yielded a higher percentage of unassigned taxa after filtering for presence in the majority of mesocosms compared to 18S. A possible explanation for the low metazoan detection by COI may be that the unassigned taxa are metazoans rather than more SAR organisms. Additionally, singly detected metazoans were filtered out of the analysis if they were not detected in at least 4 mesocosms. For example, one type of amphipod was detected in only 3 mesocosm by RNA using the COI marker, but was not detected in any mesocosms using DNA. Therefore, the amphipod observation was excluded from the COI results in Fig. 3 and Table S3 because it was not found in at least 4 mesocosms.
Overall, RNA provides a broader assessment of benthic community structure than DNA, particularly when using two loci/ markers for sequencing. In the current study, we used nuclear 18S ribosomal RNA and DNA and mitochondrial COI RNA and DNA sequences as markers for metabarcoding. The number of copies of ribosomal RNA per cell is higher than the copies of ribosomal DNA, and the ratio of RNA: DNA is higher in single-cell organisms, such as protists43. The higher number of unique ASVs detected using eRNA is likely attributed to the higher number of RNA copies of each marker in small, single-cell organisms successfully amplified during PCR, therefore making rare organisms easier to detect. The DNA of highly abundant or higher biomass organisms may “drown out” (i.e., mask) the sequences from lower abundance and biomass organisms during PCR amplification, thus resulting in lower detected α-diversity. The increased detection of ciliates and protozoa using eRNA are consistent with other recent eRNA metabarcoding results that found higher ciliate and protozoan diversity compared to eDNA using the same Uni18S primers19. Positive correlations between organism biomass and sequence copy numbers have been demonstrated for DNA metabarcoding conducted on invertebrate species44. In the current study, RNA allowed for the detected of both larger meiofauna and smaller microfauna, which is optimal for assessing true biodiversity with molecular assays. Chaetonotida, a type of gastrotrich, was the only taxa detected in 4 of the mesocosms using DNA that was not found with RNA. It is possible the chaetonotida may have died during the experiment due to sensitivities to new environmental conditions, and therefore were not detected with RNA. The temperature of the flowing seawater in the mesocosms was approximately 18 °C, and many marine chaetonotida prefer 23–28 °C and high organic matter substrate45.
Previous studies have compared the accuracy of conventional morphological identification to molecular metabarcoding methods for assessing biodiversity. In estuarine-specific studies, metabarcoding methods are able to detect the majority of taxa identified with traditional methods and often detected higher species richness, or higher numbers of unique organisms, that was not found conventionally10,46,47. The limiting factor for higher resolution of taxonomic identification is the availability of species-specific sequences in barcoding databases48. However, barcoding databases are becoming more robust as an increasing number of researchers contribute high quality sequencing data to databases7. Therefore, eRNA metabarcoding techniques perform similarly to conventional morphological methods, and may even uncover higher biodiversity in systems like estuaries where meiofauna have been historically understudied and identified.
Although eRNA α-diversity is higher compared to eDNA, there is some overlap between ASVs detected with eRNA and eDNA. The higher percentage of overlap between eDNA and eRNA ASVs is predominantly seen in the ASVs detected in all 7 of the mesocosms. The increased overlap in ASVs detected in all 7 mesocosms compared to the relatively lower overlap of ASVs found in only 1 of the 7 mesocosms is due to the filtering of random organisms found in only 1 mesocosm. Detection of a unique organism in a single mesocosm is likely not representative of the sample community and filters potential artifacts that may be introduced during cDNA synthesis from eRNA. However, all uniquely identified ASVs are used in the β-diversity analysis, so the higher number of unique ASVs detected from eRNA are likely driving the significant differences observed between eRNA and eDNA β-diversity. It is possible that using eRNA could increase the statistical power of a study design compared to eDNA because eRNA detects a higher number of ASVs. It is unlikely that a higher number of RNA ASVs could be due to splice variants contributing to unique sequences because the amplified regions of both markers do not contain introns. Therefore, no splicing of transcripts would be expected. Thus, the detected DNA ASVs are from living organisms in the mesocosms and the higher diversity of ASVs detected from RNA demonstrate that RNA is a more suitable option for assessing diversity of living organisms.
It is evident that the mesocosms in the current study were rich with meio- and microfauna due to the number of unique organisms and broad diversity of different taxa. It is likely that collecting samples for nucleic acid extraction directly from the field site may result in higher diversity because there is no mechanical disturbance during the laboratory acclimation period and the presence of other organisms in the system, such as fish, macroinvertebrates, or birds. eDNA molecular abundance in samples has been shown to correlate to actual organismal abundance in laboratory environments, but the same correlation is not as apparent in field samples, which is likely due to a variety of collection and processing methods49. eRNA may be the better nucleic acid template for field collection once flash frozen, especially for the detection of protozoans. Future studies will compare the diversity of eukaryotic communities detected using eDNA and eRNA collected directly from the field rather than from sediment core mesocosms. Repeated sampling from a field site may help reduce transient eRNA detection when establishing accurate baseline community composition in field-based biomonitoring studies.
Recently, meiofaunal organisms and communities are being explored as bioindicators, which are organisms whose presence are indicators for environmental stress and pollution17. For example, lower meiofaunal diversity and abundance is associated with higher pollution in harbors, and the presence of some genera of nematodes are correlated with higher concentrations of polycyclic aromatic hydrocarbons because they are more tolerant to pollution50. A previous study that used field-collected mesocosms from the same location as our current study found similar phyla detected with a metabarcoding approach; the majority of the sequences detected in benthic communities were from nematodes, arthropods, and the microfaunal SAR clade10. Similarly, the majority of the ASVs detected from the current study also corresponded with nematodes, arthropods, and the SAR clade, as well as other commonly detected meiobenthic organisms, such as polychaetes and Homalorhagida (i.e., mud dragons). A recent study exposed a benthic foraminiferal community to chromium, and found that eRNA metabarcoding was more robust for detecting changes in diversity at lower chromium concentrations compared to eDNA51. The eRNA metabarcoding method used in the current study detected meiofaunal taxa typical of marine or estuarine environments. Therefore, eRNA metabarcoding may be useful for efficiently identifying bioindicator species or taxa impacted by exposures to different contaminants and environmental stressors to aid with management of aquatic systems. Another advantage of eRNA is that RNA provides functional information about how organisms response to stress through altered transcription of activated pathways. eRNA will likely be a more powerful tool than eDNA because it allows for the detection of both bioindicator species and, in the future with increase development of genetic databases, environmental detection of biomarkers of stress through increased transcription of response genes.
Many academic researchers are adopting molecular methods using High Throughput Sequencing as the future of biomonitoring surveys; however, few regulatory and environmental management organizations/ agencies have adopted metabarcoding into their routine biomonitoring practices for regulatory purposes. In marine benthic communities, metabarcoding provides a comprehensive assessment of diversity and is useful for detecting a broader array of organisms in biomonitoring surveys especially when using two markers47. eDNA is also useful for monitoring discrete communities (i.e., benthic versus pelagic)52, so it is possible that using eRNA could provide vital information about living organisms in specific environments compared to eDNA. Metabarcoding sequencing and bioinformatic approaches for benthic environments vary among studies, thus requiring some standardization between methods to further advance the use of metabarcoding in conservation and regulatory applications30,53.
Like eDNA, some advancements must be made with eRNA to be used as a quantitative tool in molecular ecology. Validation of eDNA metabarcoding for assessing relative abundance of species is rapidly progressing by correlating laboratory studies of DNA shedding with field experiments1,54. Similar validation techniques can be used to develop eRNA metabarcoding as a quantitative or semi-quantitative method. There is growing interest in optimizing eRNA extraction protocols from different types of environmental media to standardize the use of eRNA in downstream molecular applications55. Thus, standardizing eRNA protocols will help with integration into environmental management toolkits for regulatory purposes.
RNA poses unique barcoding challenges compared to DNA because the number of RNA transcripts from a gene are not always present in the same proportion compared to the gene copy number per genome (i.e., one DNA copy per cell), especially for differentially expressed genes. However, one possible way to work around this issue is to utilize constitutively expressed marker loci where transcription is generally stable and unaffected by environmental stressors, such as those used as reference genes for quantitative real-time PCR49. Fortunately, many loci chosen for metabarcoding purposes fit this criterium; the transcription of 18S and COI remain steady within the cell regardless of environmental stress.
Collecting sediment cores from the environment and bringing them into controlled laboratory settings for community analysis through eRNA metabarcoding is a powerful tool that opens opportunities for this method to be used in a broad range of fields. For instance, field-collected mesocosms could be used in controlled settings to investigate the effects of individual or mixtures of toxicants on entire community and population-level outcomes. Marine sediments are often the ultimate sink for environmental contaminants, such as organic pollutants , heavy metals56, and plastic particles57, yet few studies investigate actual community-level changes in contaminant exposures. Marine benthic environments have high biodiversity, but the breadth of diversity in micro- and meiofaunal organisms is often understudied because traditional morphological methods are immensely time consuming. Sediment core mesocosms could also be used to understand the effects of global climate change stressors, such as fluctuating temperatures, surface water salinity and pH, on communities as well as conventional and emerging contaminants in combination with climate change stressors. Additionally, this method could also be used to understand how communities respond to a significant disturbance event or smaller series of stressors, which are often difficult to measure in environmental settings32,58. In these applications, eRNA is favorable for constructing community composition at a specific moment of the experiment to better regulate anthropogenic causes of environmental stress.
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