Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass

More, Ravi Prabhakar; Raju, Sajan C.; Kapley, Atya; Purohit, Hemant J.

doi:10.1016/j.biortech.2013.11.065

Cited by 33 publications

(10 citation statements)

References 32 publications

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“…A defined bioinformatics pipeline was used for mining the hemicellulose and lignin degrading gene pool and associated phylogens (More et al, 2014). Approximately 2.1 Gb raw data generated to capture dominating physiology of the AD for each sample was filtered using Trimmomatica with following optimized parameters; minimum read length-50, minimum quality -20 for generation of high quality reads.…”

Section: Isolation Of Metagenomic Dna Sequencing and Annotationmentioning

confidence: 99%

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community

Pandit

Gulhane

Khardenavis

et al. 2016

Bioresource Technology

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Section: Isolation Of Metagenomic Dna Sequencing and Annotationmentioning

confidence: 99%

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community

Pandit

Gulhane

Khardenavis

et al. 2016

Bioresource Technology

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“…We used the CRISPRTarget (Biswas et al, 2013) search tool to identify a list of 40 potential hits for L. pneumophila CRISPR-Cas, each with an appropriate PAM sequence (Table S2). Predicted L. pneumophila CRISPR-Cas targets with multiple hits include metagenome sequences from activated sludge (More et al, 2014) and marine sources (Venter et al, 2004), yet the incorporeal nature of these sequences currently prevents further investigation into their relevance to L. pneumophila biology. Remarkably, however, we predict that numerous CRISPR-Cas spacers from a set of geographically disparate, evolutionarily distinct strains share the same target: a 30 kb unstable genetic element previously identified in L. pneumophila str.…”

Section: B a Venn Diagrammentioning

confidence: 99%

Active and adaptive Legionella CRISPR‐Cas reveals a recurrent challenge to the pathogen

Rao

Guyard

Peláz

et al. 2016

Cellular Microbiology

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SummaryClustered regularly interspaced short palindromic repeats with CRISPR‐associated gene (CRISPR‐Cas) systems are widely recognized as critical genome defense systems that protect microbes from external threats such as bacteriophage infection. Several isolates of the intracellular pathogen Legionella pneumophila possess multiple CRISPR‐Cas systems (type I‐C, type I‐F and type II‐B), yet the targets of these systems remain unknown. With the recent observation that at least one of these systems (II‐B) plays a non‐canonical role in supporting intracellular replication, the possibility remained that these systems are vestigial genome defense systems co‐opted for other purposes. Our data indicate that this is not the case. Using an established plasmid transformation assay, we demonstrate that type I‐C, I‐F and II‐B CRISPR‐Cas provide protection against spacer targets. We observe efficient laboratory acquisition of new spacers under ‘priming’ conditions, in which initially incomplete target elimination leads to the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify the first known target of L. pneumophila CRISPR‐Cas: a 30 kb episome of unknown function whose interbacterial transfer is guarded against by CRISPR‐Cas. We provide evidence that the element can subvert CRISPR‐Cas by mutating its targeted sequences – but that primed spacer acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial fitness, this element drives a host specialization event – with improved fitness in Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These observations add to a growing body of evidence that host range restriction can serve as an existential threat to L. pneumophila in the wild.

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“…Although challenging because of the large volume of data and the reliance on incomplete databases available for annotation, shotgun metagenomics offers the possibility of revealing unknown genetic content of complex microbial communities in an unprecedented way. From one of the first reports that characterized the genetic diversity of a wastewater treatment plant using 454 sequencing technology (20) to the more recent studies that employed ultradeep Illumina sequencing (21,22), the shotgun metagenomics approach has allowed cataloging of many functional capabilities of activated sludge, including components of relevant catabolic pathways that are key in the wastewater treatment process (23,24). However, none of the previous studies was designed specifically to discriminate the different samples according to the observed molecular functional traits.…”

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Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

Ibarbalz

Orellana

Figuerola

et al. 2016

Appl Environ Microbiol

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This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols. IMPORTANCEThis work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.

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Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass

Cited by 33 publications

References 32 publications

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community

Active and adaptive Legionella CRISPR‐Cas reveals a recurrent challenge to the pathogen

Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

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