There is growing interest in the use of DNA barcoding and metabarcoding approaches to aid biological assessments and monitoring of waterbodies. While biodiversity measured by morphology and by DNA often has been found correlated, few studies have compared DNA data to established measures of impairment such as multimetric pollution tolerance indices used by many bioassessment programs. We incorporated environmental DNA (eDNA) metabarcoding of seston into a rigorous watershed-scale biological assessment of an urban stream to examine the extent to which eDNA richness and diversity patterns were correlated with multimetric indices and ecological impairment status designations. We also evaluated different filtering approaches and taxonomic classifications to identify best practices for environmental assessments. Seston eDNA revealed a wide diversity of eukaryotic taxa but was dominated by diatoms (36%). Differentiation among sites in alpha and beta diversity was greater when operational taxonomic units (OTUs) were classified taxonomically, but coarse resolution taxonomy (kingdom) was more informative than finer resolution taxonomy (family, genus). Correlations of DNA richness and diversity with multimetric indices for fish and macroinvertebrates were generally weak, possibly because Metazoa were not highly represented in our DNA dataset. Nonetheless, sites could be differentiated based on ecological impairment status, with more impaired sites having lower eDNA diversity as measured by the Shannon index, but higher taxonomic richness. Significant environmental drivers of community structure, as inferred from constrained ordination analyses, differed among kingdoms within the eDNA dataset, as well as from fish and macrobenthos, suggesting that eDNA provides novel environmental information. These results suggest that even a simple seston eDNA filtering protocol can provide biodiversity information of value to stream bioassessment programs. The approach bears further investigation as a potentially useful rapid assessment protocol to supplement more intensive field sampling efforts.
DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.
1. Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density or trait mediated.2. We studied a tri-trophic food chain comprised of (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum) and (iv) a parasite of the intermediate consumer (Holospora undulata). A fully factorial experimental manipulation of predator and parasite presence/absence was combined with analyses of population dynamics, modelling and analyses of host (Paramecium) morphology and behaviour.3. Predation and parasitism each reduced the abundance of the intermediate consumer (Paramecium), and parasitism indirectly reduced the abundance of the basal resource (Serratia). However, in combination, predation and parasitism had non-additive effects on the abundance of the intermediate consumer, as well as on that of the basal resource. In both cases, the negative effect of parasitism seemed to be effaced by predation.4. Infection of the intermediate consumer reduced predator abundance. Modelling and additional experimentation revealed that this was most likely due to parasite reduction of intermediate host abundance (a density-mediated effect), as opposed to changes in predator functional or numerical response.5. Parasitism altered morphological and behavioural traits, by reducing host cell length and increasing the swimming speed of cells with moderate parasite loads. Additional tests showed no significant difference in Didinium feeding rate on infected and uninfected hosts, suggesting that the combination of these modifications does not affect host vulnerability to predation. However, estimated rates of encounter with Serratia based on these modifications were higher for infected Paramecium than for uninfected Paramecium.6. A mixture of density-mediated and trait-mediated indirect effects of parasitism on non-host species creates rich and complex possibilities for effects of parasites in food webs that should be included in assessments of possible impacts of parasite eradication or introduction.
Summary1. Inducible trophic polymorphisms are greatly underappreciated forms of phenotypic plasticity that allow organisms to respond dynamically to the environmental variation by enabling them to change the trophic level upon which they feed. Although inducible trophic polymorphisms occur in a diverse array of organisms, their costs, benefits and their consequences for long-term population and community dynamics are poorly understood. 2. We studied the inducible trophic polymorphism of the freshwater hymenostome ciliate Tetrahymena vorax , whose isogenic populations can contain three distinct morphs: pyriform, bacterivorous microstomes; larger, carnivorous macrostomes; and elongate, 'tailed' microstomes. We tested whether (i) the tailed microstome constitutes an inducible defence against macrostomes and (ii) the transformation of microstomes into macrostomes is size-dependent. We also describe the dynamics of the three morphs in the presence and absence of an intraguild prey ( Colpidium ) across a gradient of growth medium concentrations to infer potential trade-offs in the success of different morphs at different productivity levels. 3. Macrostomes do not discriminate between pyriform microstomes and readily consumed heterospecific prey ( Colpidium ). Tailed microstomes display greatly reduced susceptibility to consumption by macrostomes as compared with undefended, pyriform microstomes. Morph dynamics are consistent with the hypothesis that tailed microstomes function as an inducible defence against cannibalism; tailed microstomes and macrostomes appear simultaneously, in both the presence and absence of Colpidium . At low productivity, T. vorax achieves higher rates of growth when feeding on Colpidium instead of on bacteria. At higher productivity, this pattern is reversed, with growth rates maximized in the absence of Colpidium . 4. The reduced consumption rate of tailed microstomes by cannibalistic macrostomes, together with the simultaneous induction of tailed microstomes and macrostomes, suggests that both morphs comprise a coordinated adaptive response to the presence of intraguild prey.
Apparent competition is of broad interest due to its effects on community structure and potential applications in agriculture, restoration, and medicine. It is well‐established that apparent competition can result from changes in predator abundance or behavior caused by interactions with alternate prey, but no previous empirical study has demonstrated that apparent competition can also result from prey‐induced changes in predator morphology. This trait‐mediated alternative mechanism of apparent competition would expand the range of conditions under which apparent competition might occur in nature and identify new ways to generate or modify apparent competition in applied contexts. Here, as a proof of concept, we show that trait‐mediated apparent competition can arise from inducible offenses and show how it operates using experiments involving three ciliates. When it feeds on Colpidium kleini, the intraguild predator Tetrahymena vorax increases in size to the extent that it can then consume Paramecium aurelia, an even larger prey. When feeding only on bacteria, however, Tetrahymena remains smaller and is unable to consume Paramecium. This trait‐mediated indirect effect leads to the predatory exclusion of Paramecium, while Tetrahymena and Colpidium coexist. Developmental expansions such as those underlying the interactions observed in our study are not limited to ciliates, such as Tetrahymena, but occur among many diverse taxa and may have a surprising degree of influence over the structure and dynamics of food webs.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.