Molecular techniques and their limitations shape our view of the holobiont

Abstract

 All techniques have biases and limitations which may shape our view of holobionts  Tackling the complexity of holobionts will depend on continued technological advances especially in DNA sequencing and imaging. AbstractIt is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA gene amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.

Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia

“…This difference may arise from the additional niche space provided by the symbiosome, which was previously shown to harbor bacteria (Ainsworth et al, 2015), and through association with Symbiodiniaceae, which harbor their own microbial community (Deines et al, 2020;Maire et al, 2021). Visualization and enumeration of cnidarian-associated bacteria is still relatively rare (Neave et al, 2017;Cooke et al, 2019), in part because of the difficulties associated with fluorescent staining techniques in corals (Wada et al, 2016). As such, we relied on CFU counts, which avoid many of these difficulties but at the cost of media selectivity, as highlighted by the discrepancy between absence of CFUs in marine media and amplicon sequencing-based detection of some bacterial taxa.…”

“…Besides the broad importance of Symbiodiniaceae, which reside within the coral cells and cover almost the entire energy needs of the coral host through provision of photosynthates (Muscatine, 1990;Trench, 1993), bacteria presumably play important roles in metabolism, immunity, and environmental adaptation of the coral host (Ziegler et al, 2017;Ziegler et al, 2019;Robbins et al, 2019;Voolstra and Ziegler, 2020). However, functional studies that detail the specific contributions of specific microbial taxa are still rare, partially due to methodological limitations (Cooke et al, 2019;Robbins et al, 2019). One suggested avenue to elucidate host-bacteria interactions in cnidarians is the use of model organisms, in particular using gnotobiotic (i.e., bearing few remaining known bacteria) or axenic (i.e., bacteria-/germfree) host systems that allow controlled exposure or provision of cultured bacterial isolates (Jaspers et al, 2019).…”

Microbial Biotechnology: Innovations for Crop Protection and Improvement

“…Biotech crops have the potential to increase crop quality and yields, simplify labour for farmers, and improve safety for them, all of which may contribute to increased profitability in farming. It is possible that they will produce higher quality features, such as greater amounts of betacarotene in rice, superior oil compositions in canola, soybean, and maize, and crops that are able to thrive in saline soils or better survive drought conditions [19].Researchers have found the instruments of agricultural biotechnology to be very helpful in gaining a knowledge of the fundamental biology of living species [20]. These technologies have also made it possible for us to increase the safety of our food supply and generate superior animal and plant kinds.With the United States Department of Agriculture (USDA), the Environmental Protection Agency (EPA), and the Food and Drug Administration (FDA) working to ensure that crops produced through genetic engineering for commercial use are properly tested and studied to minimize significant risks to consumers and the environment, agricultural biotechnology has been the subject of extensive evaluation by breeders for centuries [47].…”

The coral microbiome: towards an understanding of the molecular mechanisms of coral–microbiota interactions

“…Recent advances in coral holobiont research have been possible due to the rise of ‘omics techniques, particularly genomics (Cooke et al 2019 , Jasper et al 2019 , Engelberts et al 2021 ). Among the most widely used methods to characterize the diversity of coral microbiomes and understand their role in light of climate change is amplicon sequencing studies (Fig.…”