Biology subjects

Law, Y.

Publications and source records attributed to Law, Y..

7 recordsLinked to original sources

bioRxiv2021

Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling

Analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) have assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play a key role in mediating interactions between human and natural ecosystems. In this paper, we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogues from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing the co-assembly offers clear advantages over single-sample assembly. Around 1000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

genomics↗

bioRxiv2021

Global warming readiness: Feasibility of enhanced biological phosphorus removal from wastewater at 35oC

Recent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30{degrees}C to be stable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors with alternating anaerobic and aerobic phases for over 300 days at 30{degrees}C and 35{degrees}C, respectively, and followed the dynamics of the communities of phosphorus accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescent in-situ hybridization analyses. Stable and nearly complete P removal was achieved at 30{degrees}C; similarly, long term P removal was stable at 35{degrees}C with effluent PO43--P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundant Ca. Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. The slow-feeding strategy used effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures. Candidatus Competibacter was the main GAO, along with cluster III Defluviicoccus members. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. This specific lineage of GAOs warrants further study to establish how complete P removal can be maintained. Comparative cycle studies at two temperatures for each reactor revealed higher activity of Ca. Accumulibacter when the temperature was increased from 30{degrees}C to 35{degrees}C, suggesting that the stress was a result of the higher carbon (and/or P) metabolic rates of PAOs and GAOs, the resultant carbon deficiency, and additional community competition. An increase in the TOC to PO43--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited the proliferation of PAOs. In general, the slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at elevated temperature and represent basic conditions for full-scale applications.

microbiology↗

bioRxiv2020

Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read (MinION) obtained from an ensemble of activated sludge enrichment bioreactors, we 1) describe new methods for validating long read assembled genomes using their counterpart short read metagenome assembled genomes; 2) assess the influence of different correction procedures on genome quality and predicted gene quality and 3) contribute 21 new closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses: specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Accumulibacter and Dechloromonas, and Micropruina and Defluviicoccus, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Our findings further establish the feasibility of long read metagenome-assembled genome recovery, and demonstrate the utility of parallel sampling of moderately complex enrichments communities for recovery of genomes of key functional species relevant for the study of complex wastewater treatment bioprocesses.

bioinformatics↗

bioRxiv2020

Species level enrichment of AnAOB and associated growth morphology under the effect of key metabolites

Nineteen anaerobic ammonium oxidizing bacteria (AnAOB) species have been identified, yet the environmental factors that select for each species within a specialized ecological niche have not been described. We enriched AnAOB from a single inoculum under standard enrichment conditions (reactor R1) with stepwise increase in nitrite and ammonia concentration, nitric oxide (NO) supplementation (reactor R2), or with complex organic carbon using wastewater collected from mainstream wastewater treatment facility (reactor R3). AnAOB were enriched up to 80%, 90% and 50% relative abundance in R1, R2 and R3 respectively. Candidatus Brocadia caroliniensis predominated in all reactors, but a shift towards Ca. Brocadia sinica was consistently observed with increasing ammonium and nitrite concentrations beyond 270 mg NH4-N L-1 and 340 mg NO2-N L-1, respectively. In the presence of NO, growth of heterotrophs were inhibited, and Ca. Jettenia could coexist with Ca. B. caroliniensis before diminishing when nitrite increased to 160 mg NO2-N L-1. In contrast, supplementation of organic carbon led to the emergence of heterotrophic communities that coevolved with Ca. B. caroliniensis. Ca. B. caroliniensis and Ca. Jettenia preferentially form biofilms on reactor surfaces, whereas Ca. Brocadia sinica forms granules in suspension. Our results thus indicate that multiple AnAOB species co-exist and occupy sub-niches in anaerobic ammonium oxidation reactors, that the dominant population can be reversibly shifted by, for example, changing the nitrogen load (i.e. high nitrite concentration favors Ca. Brocadia caroliniensis), and that speciation has implications for wastewater process design, with the optimum cell immobilization strategy (i.e. carriers vs granules) dependent on which species dominates. IMPORTANCEThis study demonstrates how to reversibly and predictably shift dominant anammox population using operating parameters (e.g. high nitrite concentration favours Ca. Brocadia sinica), and that species selection has implications for wastewater process design, illustrated here in terms of dependence of optimum cell immobilization strategy (i.e. carriers vs granules) on which species dominates. The research informs the characterization of AnAOBs at species level as well process design and control strategies targeting Anammox species population dynamics in full scale waste water treatment systems.

ecology↗

bioRxiv2019

Isolation of a putative S-layer protein from anammox biofilm extracellular matrix using ionic liquid extraction

Anaerobic ammonium oxidation (anammox) performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 {+/-} 0.9 and 41.4 {+/-} 1.4% (w/w) more solubilization of Candidatus Brocadia sinica-enriched anammox granules than DNase and amylase respectively. Nuclear magnetic resonance profiling of the granules confirmed that proteins were dominant. We applied ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N- dimethylacetamide (EMIM-Ac/DMAc) mixture to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous S/T-rich proteins BROSI_A1236 and UZ01_01563, which were major components of the extracted proteins and sequentially highly similar to putative anammox surface-layer (S-layer) protein KUSTD1514. EMIM-Ac/DMAc extraction enriched for these putative S-layer proteins against all other major proteins, along with six monosaccharides (i.e. arabinose, xylose, rhamnose, fucose, galactose and mannose). The sugars, however, contributed <0.5% (w/w) of total granular biomass, and were likely co-enriched as glycoprotein appendages. This study demonstrates that S-layer proteins are major constituents of anammox biofilms and can be isolated from the matrix using an ionic liquid-based solvent.

bioengineering↗

bioRxiv2018

Apparent oxygen half saturation constant for nitrifiers: genus specific, inherent physiological property, or artefact of colony morphology?

We report that a single Nitrospira sublineage I OTU performs nitrite oxidation in several full-scale domestic wastewater treatment plants (WWTPs) in the tropics (29-31 {degrees}C). Contrary to the prevailing theory for the relationship between nitrite oxidizing bacteria (NOB) and ammonia oxidizing bacteria (AOB), members of the Nitrospira sublineage I OTU had an apparent half saturation coefficient, Ks(app) lower than that of the full-scale domestic activated sludge cohabitant AOB (0.09 {+/-} 0.02 g O2 m-3 versus 0.3 {+/-} 0.03 g O2 m-3). Paradoxically, NOB may thus thrive under conditions of low oxygen supply. Low dissolved oxygen (DO) conditions could enrich for and high aeration inhibit the NOB in a long-term lab-scale reactor. The relative abundance of Nitrospira gradually decreased with increasing DO until it was washed out. Nitritation was sustained even after the DO was lowered subsequently. Based on 3D-fluorescence in situ hybridization (FISH) image analysis, the morphologies of AOB and NOB microcolonies responded to DO levels in accordance with their apparent oxygen half saturation constant Ks(app). When exposed to the same oxygenation level, NOB formed densely packed spherical clusters with a low surface area-to-volume ratio compared to the Nitrosomonas-like AOB clusters, which maintained a porous and non-spherical morphology. Microcolony morphology is thus a way for AOB and NOB to regulate oxygen exposure and sustain the mutualistic interaction. However, short-term high DO exposure can select for AOB and against NOB in full-scale domestic WWTPs and such population dynamics depend on which specific AOB and NOB species predominate under given environmental conditions.

systems biology↗

bioRxiv2017

Draft Genome Sequence Of A Candidatus Brocadia Bacterium Enriched From Tropical-Climate Activated Sludge

We present the draft genome of an anaerobic ammonium-oxidizing (anammox) bacterium, cluster III Candidatus Brocadia, which was enriched in an anammox reactor. A 3.2 Mb genome sequence comprising 168 contigs was assembled, in which 2,765 gene-coding regions, 47 tRNAs, and 5S, 16S and 23S ribosomal RNAs were annotated. No evidence for the presence of a nitric oxide-forming nitrite reductase was found.

microbiology↗