The quest for absolute abundance: The use of internal standards for DNA‐based community ecology

Harrison, Joshua G.; Calder, W. John; Shuman, Bryan N.; Buerkle, C. Alex

doi:10.1111/1755-0998.13247

Cited by 56 publications

(78 citation statements)

References 111 publications

(198 reference statements)

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“…To account for compositionality, we divided the proportion estimate for each taxon in a replicate by the proportion of reads assigned to the ISD for that replicate. By placing the relative abundances of all taxa on the scale of the ISD, we were able to better compare taxon abundances among treatment groups (for more details of the problem of compositionality and how an ISD can help see: [57,74]).…”

Section: Discussionmentioning

confidence: 99%

“…To characterize bacterial assemblages, the 16S (V4) locus was amplified using the 515-806 primer pair [55], while for fungal assemblages the ITS1 locus was amplified using the ITS1f-ITS2 primer pair [56]. A synthetic DNA internal standard (ISD) was added to template DNA prior to library creation [57]. Additionally, unique synthetic DNAs of our own design were added to each sample to allow cross-contamination to be detected (sensu Tourlousse et al [58]; we refer to these oligos as "coligos", which is short for cross-contamination checking oligos).…”

Section: Sequence and Culture-based Characterization Of The Foliar MImentioning

confidence: 99%

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A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression

Harrison

Beltran

Buerkle

et al. 2019

Preprint

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Endophytes are microbes that live, for at least a portion of their life history, within plant tissues. Endophyte assemblages are often composed of a few abundant taxa and many infrequently-observed, rare taxa. The ways in which most endophytes affect host phenotype are unknown; however, certain dominant endophytes can influence plants in ecologically meaningful ways-including by affecting growth and contributing to immune responses. In contrast, the effects of rare endophytes have been unexplored, and how rare and common endophytes might interact is also unknown. Here, we manipulate both the suite of rare foliar endophytes (including both fungi and bacteria) and Alternaria fulva-a dominant, verticallytransmitted fungus-within the fabaceous forb Astragalus lentiginosus. We report that rare, low-biomass endophytes affected host size and foliar %N, but only when the dominant fungal endophyte (A. fulva) was not present. A. fulva also reduced plant size and %N, but these deleterious effects on the host could be offset by a striking antagonism we observed between this heritable fungus and a foliar pathogen. These results are unusual in using experimental manipulation in a non-crop or non-grass system to demonstrate that interactions among taxa determine the net effect of endophytic assemblages on their hosts. We suggest that the myriad infrequently-observed endophytes within plant leaves may be more than a collection of uninfluential, commensal organisms, but instead have meaningful ecological roles.

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Section: Discussionmentioning

confidence: 99%

Section: Sequence and Culture-based Characterization Of The Foliar MImentioning

confidence: 99%

A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression

Harrison

Beltran

Buerkle

et al. 2019

Preprint

Self Cite

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“…Most recent studies advocate for the use of separate or spike-in mock communities in order to use the recovered relative abundance of the known mixed species to apply a correction factor to a sample’s relative abundances [ 163 ]. This approach appears to be particularly crucial in differential abundance analyses when taking into account the compositional bias of amplicon sequencing data [ 164 , 165 ].…”

Section: Amplicon Library Preparationmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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“…It is worth noting that OTU relative abundance is only correlated but does not reflect the relative abundance of the fish species under discussion. This is due to limitations with sequencing methods that yields platform specific data (reads), therefore making relative abundance analysis challenging (Harrison et al, 2020). Nevertheless, acknowledging these constraints imposed by compositional data is vital when analyzing sequencing data.…”

Section: Edna Data On Fish Abundancementioning

confidence: 99%

Multifunctionality of an Urbanized Coastal Marine Ecosystem

Asundi

Baker²

2020

Front. Mar. Sci.

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Coastal marine ecosystems provide numerous invaluable services and benefits to humankind. However, urbanization of coastal areas has homogenized and reduced the biodiversity of the surrounding marine environment and the sustainability of the multiple ecosystem services it provides. Studies have focused on single ecosystem functions despite human populations relying on several functions being delivered at once (known as multifunctionality). This study investigates five ecosystem functions (primary productivity, herbivory, predation, organic matter decomposition and carbon sequestration) and overall multifunctionality in four sites along a gradient of 16 environmental parameters. Ecosystem function varied significantly between sites that were farthest apart. In determining factors that drove ecosystem functioning, we found a positive relationship between coral cover and primary productivity but negative relationships between coral cover and levels of herbivory and predation intensity. Higher temperatures and greater concentrations of chlorophyll-a had a positive impact on predation and herbivory, respectively. Notably, we found a significant negative impact of total inorganic nitrogen and significant positive impact of total Kjeldahl nitrogen on carbon sequestration. Further, individual functions were compared with fish abundance (obtained from seawater eDNA), and benthic community composition (obtained from plate % coverage of autonomous reef monitoring structures). Increasing herbivorous fish abundance had a positive impact on Ulva mass loss. Overall, relative abundance of predatory, omnivorous and planktivorous fish exerted overriding influences on primary productivity and predation intensity, implying that fishing pressure and marine protected area status are important factors. Importantly, we found significant effects from environmental parameters indicating that reliably predicting the effects of future anthropogenic impacts will not be straightforward as multiple drivers are likely to have complex effects. Taken together, urbanized coastal ecosystems exhibit varying levels of multifunctionality depending on the extent of human impact, and the functional diversity of the benthic community present.

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The quest for absolute abundance: The use of internal standards for DNA‐based community ecology

Cited by 56 publications

References 111 publications

A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression

A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

Multifunctionality of an Urbanized Coastal Marine Ecosystem

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