Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes

Berry, Michelle A.; White, Jeffrey D.; Davis, Timothy W.; Jain, Sunit; Johengen, Thomas H.; Dick, Gregory J.; Sarnelle, Orlando; Denef, Vincent J.

doi:10.3389/fmicb.2017.00365

Cited by 60 publications

(66 citation statements)

References 41 publications

(60 reference statements)

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“…Appealing terminology such as "resolution of exact sequence variants" does not eliminate the limitations inherent to representing a complex biological organism by a short genetic barcode. For example, while necessarily better than the customary 3% ribosomal OTUs, there is still no guarantee of ecological coherence or even monophyly among genomes with the same ribosomal SV (Berry et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Exact sequence variants should replace operational taxonomic units in marker gene data analysis

Callahan

McMurdie²,

Holmes

2017

Preprint

604

740

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Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently that sequence variants (SVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer taxonomic resolution are immediately apparent, and arguments for SV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits deriving from the status of SVs as consistent labels with intrinsic biological meaning identified independently from a reference database . Here we discuss how those features grant SVs the combined advantages of closed-reference OTUs -including computational costs that scale linearly with study size, simple merging between independently processed datasets, and forward prediction -and of de novo OTUs -including accurate diversity measurement and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that SVs should replace OTUs as the standard unit of marker gene analysis and reporting.

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Section: Discussionmentioning

confidence: 99%

Exact sequence variants should replace operational taxonomic units in marker gene data analysis

Callahan

McMurdie²,

Holmes

2017

Preprint

604

740

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“…Previously, we found two distinct phylogenetic groups of Microcystis aeruginosa isolates from inland lakes of Michigan using a multilocus sequence typing analysis (Berry, White, et al, 2017). Here, we expand this analysis to include all publically available sequences of M. aeruginosa originating from multiple locations spanning six continents.…”

Section: Structural Genome Variation Within Microcystis Aeruginosamentioning

confidence: 99%

“…Extracted gene sequences were concatenated and aligned with MUSCLE using default parameters (Edgar, 2004). A phylogeny was constructed using RAxML v8.2.8 with a Synechococcus outgroup (Berry, White, et al, 2017;Stamatakis, 2006), and a Newick tree was visualized using Figtree v1.4.3 software (Rambaut, 2012).…”

Section: Sequencing Analysesmentioning

confidence: 99%

“…In contrast, we previously identified a monophyletic ecotype of M. aeruginosa occurring in oligotrophic inland lakes in Michigan (Berry, White, et al, 2017). Berry, White, et al (2017) constructed a phylogeny of M. aeruginosa isolates from inland lakes of Michigan using five housekeeping genes but did not investigate any further differences in the genomes or physiology of M. aeruginosa or host-associated microbiomes. Here, using this same data set, we investigated the underlying mechanisms that may increase fitness of different ecotypes across a phosphorus gradient.…”

Section: Introductionmentioning

confidence: 97%

“…Sequenced M. aeruginosa genomes from eutrophic habitats are highly variable, but this variation does not show clear biogeographic patterns (Meyer et al, 2017). In contrast, we previously identified a monophyletic ecotype of M. aeruginosa occurring in oligotrophic inland lakes in Michigan (Berry, White, et al, 2017). Berry, White, et al (2017) constructed a phylogeny of M. aeruginosa isolates from inland lakes of Michigan using five housekeeping genes but did not investigate any further differences in the genomes or physiology of M. aeruginosa or host-associated microbiomes.…”

Section: Introductionmentioning

confidence: 98%

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Genome evolution and host‐microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom‐forming Microcystis aeruginosa

et al. 2019

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Intraspecific niche divergence is an important driver of species range, population abundance and impacts on ecosystem functions. Genetic changes are the primary focus when studying intraspecific divergence; however, the role of ecological interactions, particularly host‐microbiome symbioses, is receiving increased attention. The relative importance of these evolutionary and ecological mechanisms has seen only limited evaluation. To address this question, we used Microcystis aeruginosa, the globally distributed cyanobacterium that dominates freshwater harmful algal blooms. These blooms have been increasing in occurrence and intensity worldwide, causing major economic and ecological damages. We evaluated 46 isolates of M. aeruginosa and their microbiomes, collected from 14 lakes in Michigan, USA, that vary over 20‐fold in phosphorus levels, the primary limiting nutrient in freshwater systems. Genomes of M. aeruginosa diverged along this phosphorus gradient in genomic architecture and protein functions. Fitness in low‐phosphorus lakes corresponded with additional shifts within M. aeruginosa including genome‐wide reductions in nitrogen use, an expansion of phosphorus assimilation genes and an alternative life history strategy of nonclonal colony formation. In addition to host shifts, despite culturing in common‐garden conditions, host‐microbiomes diverged along the gradient in taxonomy, but converged in function with evidence of metabolic interdependence between the host and its microbiome. Divergence corresponded with a physiological trade‐off between fitness in low‐phosphorus environments and growth rate in phosphorus‐rich conditions. Co‐occurrence of genotypes adapted to different nutrient environments in phosphorus‐rich lakes may have critical implications for understanding how M. aeruginosa blooms persist after initial nutrient depletion. Ultimately, we demonstrate that the intertwined effects of genome evolution, host life history strategy and ecological interactions between a host and its microbiome correspond with an intraspecific niche shift with important implications for whole ecosystem function.

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Deep sequencing across multiple host species tests pine‐endophyte specificity

Sarver

Apigo

Gernandt

et al. 2022

American J of Botany

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Premise: Foliar fungal endophytes vary in their distributions across landscapes or plant host taxa, indicative of specialized ecologies and host specific adaptations. Accounts of specialization, however, depend on the taxonomic breadth and geographic range of the host plants included in each study. A broad region-scale study or deep sampling of diverse potential host species still remains relatively rare but is becoming increasingly possible with high-throughput sequencing. Methods: Amplicon sequencing was used to rapidly identify the fungal endophytic community among six pine (Pinus, Pinaceae) species co-occurring across northeastern United States and to test for site and host specialization. We focused on the endophytic genus Lophodermium (Rhytismataceae), whose species members are thought to specialize on different pine species, to test if amplicon sequencing could rapidly verify previously implied or discover new patterns of host specificity. Results: While amplicon sequencing could analyze more samples at greater depths and recover greater numbers of unique Lophodermium taxa than when endophyte communities were surveyed with traditional culturing methods, patterns of specialization were not better supported. This may be because amplicon sequencing can indiscriminately capture non-host specific organisms found incidentally from plant tissues or because we have overestimated host-specificity in the past with biased culturing techniques. Conclusions: Amplicon sequencing can quickly identify patterns of host specificity by allowing large-scale surveys but has limitations in quantifying the level of intimacy of these relationships.

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Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes

Cited by 60 publications

References 41 publications

Exact sequence variants should replace operational taxonomic units in marker gene data analysis

Exact sequence variants should replace operational taxonomic units in marker gene data analysis

Genome evolution and host‐microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom‐forming Microcystis aeruginosa

Deep sequencing across multiple host species tests pine‐endophyte specificity

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