Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities

Abstract

Variation in microbial activity levels is increasingly being recognized as both an important dimension in community function and a complicating factor in sequencing-based survey methods. This study extends previous reports that rare taxa may contribute disproportionately to community activity in some natural environments, showing that this may also hold in artificially maintained model communities with well-described inputs, outputs, and biochemical functions. These results demonstrate that assessment of activity levels using the rRNA/rDNA ratio is robust across taxonomic unit formation methods and is independently corroborated by omics methods. The results also provide insight into the comparative advantages and disadvantages of different taxonomic unit formation methods in amplicon sequencing studies, showing that UNOISE3 provides comparable microbial diversity, structure, and activity information as the 97% sequence similarity method but potentially loses some phylogenetic diversity and creates more “phantom taxa” (which are present in the RNA pool but not the corresponding DNA pool).

Diversity and gene expression patterns of functional groups in sidestream and mainstream wastewater partial-nitritation anammox biofilms

“…The disproportionally high read abundances of rRNA at low rDNA abundances for most phyla 239 ( Figure S4) confirm previous similar observations, suggesting higher activity among rare taxa 240 (Campbell, et al 2011, Jia, et al 2019, Jones and Lennon 2010, Klein, et al 2016, Wilhelm, et al 241 2014. This phenomenon could perhaps be due to under-sampling (Steven, et al 2017), but higher 242 growth rate among rare taxa could arise due to intraspecific competition or predation of abundant taxa 243 (Jousset, et al 2017).…”

“…This phenomenon could perhaps be due to under-sampling (Steven, et al 2017), but higher 242 growth rate among rare taxa could arise due to intraspecific competition or predation of abundant taxa 243 (Jousset, et al 2017). In fact, by using metagenomic data, Jia, et al (2019) observed higher 244 replication rates for taxa at low relative abundances supporting that this is a real phenomenon. 245 246…”

Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

“…Knowing that the metabolic activities of certain microbes could be suppressed by antagonists and so may not be actively involved in a given condition (phenotype), capturing such bacteria due to their sheer presence may give a false positive association. This is supported by studies that have reported that taxonomic abundance does not correspond to transcriptional activities [ 25 , 26 , 27 ]. The library construction, assembly, and reference databases of metagenomics for annotation employ biases that are difficult to understand [ 21 ].…”

Similar but Not Identical Resuscitation Trajectories of the Soil Microbial Community Based on Either DNA or RNA after Flooding

“…We analyzed the sequence data according to a previously described procedure [34] using the QIIME pipeline v. 1.9.0 [35]. Briefly, after eliminating low quality reads and dereplicating, sequences were denoised and chimeras were removed with the UNOISE3 algorithm using USEARCH to form "zero-radius OTUs" (ZOTUs).…”