Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “<i>Candidatus</i>Accumulibacter”

Petriglieri, Francesca; Singleton, Caitlin M.; Kondrotaite, Zivile; Dueholm, Morten Simonsen; McDaniel, Elizabeth A.; McMahon, Katherine D.; Nielsen, Per Halkjær

doi:10.1128/msystems.00016-22

Cited by 43 publications

(71 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, we followed a second-best strategy only requiring that the probes can target the corresponding strains considering the two strains are dominant populations (information on FISH probes can be found in Table S6). Simultaneously hybridized with EUB338-mix (targeting nearly all bacteria) and PAO-mix (targeting all Accumulibacter) cells respectively targeted Bin208 and Bin142 specific probes, which are both coccoid, similar to other reported Accumulibacter strains (17). The size of the former was slightly larger than that of the latter (Figures 4B&C).…”

Section: Retrieving Full-length 16s Rrna and Fish Detection Of Bin142...supporting

confidence: 75%

Expanding the diversity ofAccumulibacterwith a novel type and deciphering the transcriptional and morphological features among co-occurring strains

Wang¹,

Song²,

Zhang

et al. 2022

Preprint

View full text Add to dashboard Cite

Accumulibacteris the major polyphosphate-accumulating organism (PAO) in global wastewater treatment systems. Its phylogenetic and functional diversity has been continuously updated in recent years. In addition to its widely recognized two sublineages, Types I and II, here we discovered a novel type enriched in laboratory bioreactors. Core gene- and machine learning-based gene feature profiling supported that Type IIIAccumulibacterwas a potential PAO with the unique function of using dimethyl sulfoxide as electron acceptor. On the basis of the correlation between the similarity of ppk1 and genome, the number of ppk1-representedAccumulibacterspecies was estimated to be over one hundred, suggesting that the currently recognized species are only the tip of the iceberg. Meanwhile, multipleAccumulibacterstrains co-occurring in a bioreactor were investigated for their inter-strain transcriptional and morphological features. Metatranscriptomics of seven co-occurring strains indicated that the expression level and interphasic dynamics of PAO phenotype-related genes had minimal correlation with their phylogeny. In particular, expression of denitrifying and poly-P metabolism genes had higher inter-strain and interphasic divergence compared with glycogen and polyhydroxyalkanoates metabolic genes. A strategy of cloning rRNA genes from different strains based on similar genomic synteny was successfully applied to differentiate their morphology via fluorescence in situ hybridization. Our study further expanded the phylogenetic and functional diversity ofAccumulibacter. We also proposed that deciphering the function and capability of certainAccumulibactershould be environment- and population-specific.

show abstract

Section: Retrieving Full-length 16s Rrna and Fish Detection Of Bin142...supporting

confidence: 75%

Expanding the diversity ofAccumulibacterwith a novel type and deciphering the transcriptional and morphological features among co-occurring strains

Wang¹,

Song²,

Zhang

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…These Accumulibacter genomes are no more than 85% similar by genome-wide ANI, and are therefore well below the sequence-based 95% ANI threshold for differentiating different species at the genomic level (20, 44). Additionally, clades IA and IIA of Accumulibacter were recently reevaluated and reclassified as separate species (70), but we retain the ppk1 -based nomenclature throughout to aid in comparison to prior work. We assembled 167 bacterial species-representative MAGs of the bacterial flanking community (non-Accumulibacter) mostly spanning Actinobacteria, Bacteroidetes , and Proteobacteria phyla (Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…Accumulibacter has traditionally been designated into two types and several clades based on ppk1 locus sequence identity (49, 54, 69), as the 16S rRNA gene is nearly identical among the known breadth of Accumulibacter clades (11, 44, 49). Although the nomenclature of Accumulibacter was recently redefined into several different species (70), we maintain the ppk1 -based nomenclature throughout for ease of comparison to prior studies. The bioreactor was mainly comprised of clades IA, IC, and IIA (Supplementary Figure 1), representative strains of which were all previously characterized by various multi-omics analyses (11, 40, 44, 46, 47).…”

Section: Resultsmentioning

confidence: 99%

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

McDaniel

Moya-Flores

Méndez

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Microbial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variants. Ecological forces act on a shifting template of population-level diversity that is shaped by evolutionary processes. However, understanding the ecological and evolutionary forces contributing to microbial community interactions and overall ecosystem function is difficult to interrogate for complex, naturally occurring microbial communities. Here, we use two time series of lab-scale engineered enrichment microbial communities simulating phosphorus removal to explore signatures of microbial diversity at multiple phylogenetic scales. We characterized microbial community dynamics and diversity over the course of reactor start-up and long-term dynamics including periods of eubiosis and dysbiosis as informed by the intended ecosystem function of phosphorus removal. We then compared these signatures to lineages from full-scale WWTPs performing phosphorus removal. We found that enriched lineages in lab-scale bioreactors harbor less intra-population diversity than lineages from the full-scale WWTP overall. Our work establishes a foundation for using engineered enrichment microbial communities as a semi-complex model system for addressing the fundamental ecological and evolutionary processes necessary for developing stable microbiome based biotechnologies.

show abstract

“…It should, therefore, not be considered a replacement for proper phylogenetic classification, which ideally requires phylogenomic analyses (Hug et al, 2016 ; Parks et al, 2018 , 2020 ; Zhu et al, 2019 ). However, the placeholder taxonomy allows us to identify new ecological relevant lineages that should be targeted for the recovery of high-quality metagenome-assembled genomes (MAGs), phylogenomics, and further investigations (Nierychlo et al, 2021 ; Petriglieri et al, 2022 ; Singleton et al, 2022 ). A good example is the de novo genus AsCoM_g_8878 within the family Roseiflexaceae for which many ASVs displayed strong host enrichment.…”

Section: Discussionmentioning

confidence: 99%

Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling

et al. 2022

View full text Add to dashboard Cite

Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5–V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5–V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.

show abstract

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

Cited by 43 publications

References 72 publications

Expanding the diversity ofAccumulibacterwith a novel type and deciphering the transcriptional and morphological features among co-occurring strains

Expanding the diversity ofAccumulibacterwith a novel type and deciphering the transcriptional and morphological features among co-occurring strains

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling

Contact Info

Product

Resources

About