Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge

Barr, Jeremy J.; Slater, Frances R.; Fukushima, Toshikazu; Bond, Philip L.

doi:10.1111/j.1574-6941.2010.00967.x

Cited by 62 publications

(52 citation statements)

References 71 publications

(100 reference statements)

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“…Samples were hybridized with PAOMix (Crocetti et al, 2000) and EUBMix (Amann et al, 1990;Daims et al, 1999) probes for Accumulibacter and total bacterial abundance respectively. Bacterial populations binding fluorescent DNA probes were visualized as previously described (Barr, Slater, et al, 2010).…”

Section: Fluorescence In Situ Hybridization (Fish) Quantificationmentioning

confidence: 99%

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

Barr

Dutilh

Skennerton

et al. 2015

Environmental Microbiology

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Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal (EBPR). Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods we investigated the proteomic differences between these two biofilm communities, identifying a total of 2,022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance (EPS) and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.

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Section: Fluorescence In Situ Hybridization (Fish) Quantificationmentioning

confidence: 99%

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

Barr

Dutilh

Skennerton

et al. 2015

Environmental Microbiology

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“…However, the host-specificity of the phage could not be suggested based on sequence similarity to prophages in sequenced genomes. Phages have recently been found to affect population dynamics of Accumulibacter in laboratory-scale enrichments (Kunin et al, 2008b;Barr et al, 2010), and the presence of phages in the metagenome of the full-scale plant suggests that deeply-sequenced metagenomic studies show promise for identifying the active phages in full-scale WWTPs.…”

Section: Similarity Of Metagenome Species To Known Genomesmentioning

confidence: 99%

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

et al. 2011

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Enhanced biological phosphorus removal (EBPR) is widely used for removal of phosphorus from wastewater. In this study, a metagenome (18.2 Gb) was generated using Illumina sequencing from a full-scale EBPR plant to study the community structure and genetic potential. Quantitative fluorescence in situ hybridization (qFISH) was applied as an independent method to evaluate the community structure. The results were in qualitative agreement, but a DNA extraction bias against gram positive bacteria using standard extraction protocols was identified, which would not have been identified without the use of qFISH. The genetic potential for community function showed enrichment of genes involved in phosphate metabolism and biofilm formation, reflecting the selective pressure of the EBPR process. Most contigs in the assembled metagenome had low similarity to genes from currently sequenced genomes, underlining the need for more reference genomes of key EBPR species. Only the genome of 'Candidatus Accumulibacter', a genus of phosphorus-removing organisms, was closely enough related to the species present in the metagenome to allow for detailed investigations. Accumulibacter accounted for only 4.8% of all bacteria by qFISH, but the depth of sequencing enabled detailed insight into their microdiversity in the full-scale plant. Only 15% of the reads matching Accumulibacter had a high similarity (495%) to the sequenced Accumulibacter clade IIA strain UW-1 genome, indicating the presence of some microdiversity. The differences in gene complement between the Accumulibacter clades were limited to genes for extracellular polymeric substances and phage-related genes, suggesting a selective pressure from phages on the Accumulibacter diversity.

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“…This model is a simplified version of the shift seen in many communities where one predominant OTU is replaced with another. For example, in enhanced biological phosphorus removal communities, the primary strains of phosphate-accumulating Candidatus 'Accumulibacter phosphatis' can decrease dramatically, with a concomitant increase in the frequency of other organisms such as Candidatus 'Competibacter', possibly due to viral predation (Barr et al, 2010;Slater et al, 2010). To simulate this scenario, we initially perturb only the two most abundant OTUs in the seed sample in order to create the starting distributions for each cluster.…”

Section: Simulated Cluster Datamentioning

confidence: 99%

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities

Parks

Beiko

2012

The ISME Journal

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High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic b-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic b-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic b diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic b diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic b-diversity measures evaluated in this manuscript is available at

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Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge

Cited by 62 publications

References 71 publications

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities

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