Flow of terrestrial carbon though aquatic ecosystems (allochthony) is an important but underestimated component of the global carbon cycle. A lack of clear consensus about the importance of allochthonous (terrestrial) organic carbon is sometimes attributed to uncertainties associated with conventional ‘bulk’ isotope data, the most widely used ecological tracer. Amino acid‐specific isotope analysis is an emerging research method promising to address existing limitations of bulk C and N isotope analyses. We tested the efficacy of amino acid δ13C data as a generalizable measure of allochthony by analysing an aggregated dataset (n = 168) of primary and secondary data of carbon sources from disparate geographical locations across the globe. We found the δ13C fingerprints amino acids to be consistently distinct between allochthonous (terrestrial) and autochthonous (aquatic) carbon sources. We also found that our approach is most effective when we use only essential amino acid tracers (i.e. isoleucine, leucine, phenylalanine, threonine and valine). Predictive trends in δ13C fingerprints appear to be largely compatible across studies and/or laboratories. As a case study, we used this approach to quantify the contribution of terrestrial carbon to an endemic cavefish, Cryptotora thamicola, and found that its biomass was comprised largely of autochthonous carbon (~75%).

Compound‐specific isotope analysis of amino acids (CSIA‐AA) is a promising nascent technique that alleviates many shortcomings of conventional bulk‐tissue stable isotope analysis (“bulk SIA”) in ecological studies involving the tracing/reconstruction of carbon and nitrogen pathways. While CSIA‐AA has been increasingly applied to preserved tissue samples (e.g., material in natural history collections), the effects of sample preservation on amino acid δ13C and δ15N profiles are poorly understood. It is therefore unclear if mathematical correction factors are necessary for interpreting isotopic profiles of preserved samples. In this study, we investigated effects of ethanol preservation and formalin fixation on amino acid δ13C and δ15N profiles. We also assess how these effects translate to two ecological applications of CSIA‐AA: quantification of organic carbon sources, and estimation of trophic positions. Results from an 8‐week controlled experiment on freshwater fish tissue show negligible preservation effects on most amino acid δ15N profiles, and results are similar for δ13C profiles of essential amino acids. Findings from mixing models using essential amino acid δ13C profiles similarly show that preserved samples can yield robust estimates of carbon source contributions. We also empirically demonstrate, for the first time, the use of amino acid δ13C profiles to enhance δ15N‐based estimates of trophic position in food webs with multiple producers, and show that these estimates are not compromised by preservation effects. Overall, our findings support the view that amino acid δ13C and δ15N profiles from ethanol‐ and formalin‐treated CSIA‐AA samples can be directly used for addressing ecological questions.

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Land‐use change is a leading driver of biodiversity loss, especially in tropical fresh waters where the conversion of natural forest to monoculture plantations impacts freshwater fish assemblages. The environmental pathways underpinning shifts in fish assemblages, however, are poorly understood, but could potentially be inferred from trait–environment relationships. We addressed this knowledge gap using eco‐morphological traits to explain fish occurrences in oil palm‐impacted streams of the Endau drainage in Peninsular Malaysia. We also investigated how traits relate to differences in environmental conditions associated with land‐use change. We then integrate findings from the above to test how potential pathways of land‐use driven environmental changes can impact species occurrences through effects on life history, feeding habits, and mobility. Mixed‐effects models show that fishes with superior (upward‐facing) mouths and low body mass were more likely to occur in oil palm streams than forest streams, and these traits were associated with grass‐dominated riparian zones and reduced woody debris in oil palm streams, respectively. Structural equation models show that mouth positions statistically mediated the effect of riparian vegetation on fish species occurrences in oil palm streams. Specifically, fishes with superior mouths were more likely to feed on terrestrial invertebrates. Our analysis of easily measurable traits revealed pathways of land‐use impact that are potentially more widely applicable than conventional taxa‐based approaches. Fishes with superior mouths tended to occur in oil palm streams as they were able to more effectively exploit inputs of terrestrial invertebrates that are potentially associated with grass‐dominated riparian vegetation. Moreover, shifts in traits may suggest land‐use driven changes in stream ecosystem functioning (e.g. in terms of the role of terrestrial subsidies), thereby informing targeted management actions in land‐use impacted habitats (e.g. retention/restoration of riparian trees).

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In Southeast Asia, biodiversity-rich forests are being extensively logged and converted to oil palm monocultures. Although the impacts of these changes on biodiversity are largely well documented, we know little about how these large-scale impacts affect freshwater trophic ecology. We used stable isotope analyses (SIA) to determine the impacts of land-use changes on the relative contribution of allochthonous and autochthonous basal resources in 19 stream food webs. We also applied compound-specific SIA and bulk-SIA to determine the trophic position of fish apex predators and meso-predators (invertivores and omnivores). There was no difference in the contribution of autochthonous resources in either consumer group (70-82%) among streams with different land-use type. There was no change in trophic position for meso-predators, but trophic position decreased significantly for apex predators in oil palm plantation streams compared to forest streams. This change in maximum food chain length was due to turnover in identity of the apex predator among land-use types. Disruption of aquatic trophic ecology, through reduction in food chain length and shift in basal resources, may cause significant changes in biodiversity as well as ecosystem functions and services. Understanding this change can help develop more focused priorities for mediating the negative impacts of human activities on freshwater ecosystems.

Studies have shown that food chain length is governed by interactions between species richness, ecosystem size and resource availability. While redundant trophic links may buffer impacts of species loss on food chain length, higher extinction risks associated with predators may result in bottom‐heavy food webs with shorter food chains. The lack of consensus in earlier empirical studies relating species richness and food chain length reflects the need to account robustly for the factors described above. In response to this, we conducted an empirical study to elucidate impacts of land‐use change on food chain length in tropical forest streams of Southeast Asia. Despite species losses associated with forest loss at our study areas, results from amino acid isotope analyses showed that food chain length was not linked to land use, ecosystem size or resource availability. Correspondingly, species losses did not have a significant effect on occurrence likelihoods of all trophic guilds except herbivores. Impacts of species losses were likely buffered by initial high levels of trophic redundancy, which declined with canopy cover. Declines in trophic redundancy were most drastic amongst invertivorous fishes. Declines in redundancy across trophic guilds were also more pronounced in wider and more resource‐rich streams. While our study found limited evidence for immediate land‐use impacts on stream food chains, the potential loss of trophic redundancy in the longer term implies increasing vulnerability of streams to future perturbations, as long as land conversion continues unabated.

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