Cassava genome from a wild ancestor to cultivated varieties

Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology

Perchlorate reduction using salt-tolerant cultures

The wide use of ion-exchange processes to remove perchlorate from drinking water creates an urgency for the regeneration or treatment of perchlorate-laden ion-exchange resins and/or regenerant brines. The use of biological processes with a salt-tolerant culture NP30 has been demonstrated as a promising cost-effective approach. In this study, the kinetics and ecology of NP30 were studied. A pure culture was isolated from the mixed culture, identified and characterized. Perchlorate–laden ion-exchange resins were effectively regenerated by the mixed culture in laboratory batch reactors. A numerical model was developed to describe the regeneration process and for design predictions. A unique “resin phase” regeneration, in which the culture degraded perchlorate on the resin instead of only what desorbed into the bulk medium, was proposed in the model. The model generated an acceptable correlation to experimental data and the degradation from the “resin phase” accounted for the majority of the perchlorate removal. The microbial composition of NP30 and the changes during a pilot plant experiment treating perchlorate- and nitrate-laden ion-exchange brine were analyzed using DGGE (denaturing gradient gel electrophoresis) and FISH (fluorescence in situ hybridization). Halomonas was the dominant (>18%) nitrate-reducing organism and Azoarcus/Denitromonas was the dominant (>22%) perchlorate-reducing organism. A shift towards nitrate-reducing organisms with time in the reactors was observed and attributed to the non-obvious perchlorate reduction seen in operation data. A pure salt-tolerant, perchlorate-reducing strain P4B1 (Marinobacter multirespiro sp. nov. proposed name) was successfully isolated from the mixed culture. P4B1 could grow in the presence of 1.8%-10.2% NaCl. A molar Mg²⁺/Na⁺ ratio of ~0.11 optimized the perchlorate degradation and cell growth when perchlorate was the sole electron acceptor. It could use perchlorate, nitrate and oxygen as electron acceptors. P4B1 preferred perchlorate to nitrate as the electron acceptor. A perchlorate reductase, which is only induced by perchlorate, is active in both perchlorate and nitrate reduction. When nitrate was used as the sole electron acceptor, the strain eventually lost the ability to reduce nitrate. The maximum specific substrate utilization rate (Vm) and the half saturation coefficient (Ks) for P4B1 were determined to be 0.050 ±0.007 mg ClO₄⁻/mg VSS-hr and 22±12 mg ClO₄⁻/L respectively.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat

In tandem effects of activated carbon and quorum quenching on fouling control and simultaneous removal of pharmaceutical compounds in membrane bioreactors

This study aimed to integrate the quorum quenching (QQ) strategy with powdered activated carbon (PAC) adsorption for fouling control and simultaneous removal of trace amounts of selected pharmaceutically active compounds (PhACs) in laboratory membrane bioreactors (MBRs). With the addition of QQ strains immobilized in PAC-alginate beads, a 4.6-folds delay in fouling was achieved. The QQ strains not only altered the sludge properties, but also influenced the microbial communities in the MBRs, thus leading to distinct quorum sensing signal molecule (acyl-homoserine lactones, AHLs) profiles. Despite the difference in AHL profiles, the total AHL concentrations were greatly reduced in bulk sludge, and completely quenched in biocake with QQ supplementation. PAC addition enabled high removals of all PhACs, and also resulted in a prominent increase in sludge floc size, which further enhanced sludge filterability. These QQ-entrapped PAC-alginate beads provide a novel MBR setting with less biofouling and high removal efficiency of PhACs.Accepted versio

Insights into quorum quenching mechanisms to control membrane biofouling under changing organic loading rates

A quorum quenching (QQ) consortium comprised of both acyl homoserine lactones (AHLs)- and autoinducer-2 (AI-2)-degrading bacteria, either immobilized in polymer-coated alginate beads or in liquid suspension, was examined for fouling control in lab-scale MBRs under both steady and changing organic loading rates (OLRs). Under steady conditions the QQ consortium retarded biofouling by a factor of 3. However, a continuous increase in OLR vastly reduced the effectiveness of QQ bacteria; the biofouling was retarded only by factors of 1.4–1.8. A significant increase in extracellular polymeric substance (EPS), especially loosely-bound EPS in mixed liquor together with an increase in polysaccharide content up to 4 times in EPS resulted from the increase in OLR, was attributed to the impaired QQ efficacy. In control MBRs, cake layer resistance was the major factor (>60%) contributing to the increased trans-membrane pressure, as compared with pore blockage resistance and intrinsic membrane resistance. In contrast, the pore blockage resistance became dominant in QQ MBRs (>40%).Accepted versio

Autoinducer-2-mediated quorum sensing partially regulates the toxic shock response of anaerobic digestion

This study discovered a strong correlation between the autoinducer-2 (AI-2)-mediated quorum sensing (QS) with the performance of a submerged anaerobic membrane bioreactor during its recovery from a pentachlorophenol (PCP) shock: a decrease in AI-2 levels coincided with a reduction in volatile fatty acid concentrations, and corresponded significantly to a decrease in the relative abundance of Firmicutes, and to an increase in the relative abundance of Bacteroidetes and Synergistetes. Further batch experiments with the addition of an AI-2-regulating Escherichia coli mutant culture showed that a reduction in AI-2 levels resulted in the highest biogas production rate during a PCP shock. In contrast, an increase in AI-2 levels via addition of the E. coli wild type strain or an AI-2 precursor showed no obvious effects on biogas production. These results suggest that the AI-2 level in anaerobic sludge was governed primarily by Firmicutes, and the AI-2-mediated QS partially regulates the toxic shock response of anaerobic sludge via tuning the activities of Firmicutes and Synergistetes. A decrease in the AI-2 level might reduce acetogenesis and favor hydrogenotrophic methanogenesis, thus resulting in less VFA accumulation and higher methane production during the PCP shock. This study is the first of this type that exploits the role of quorum sensing in the toxic shock response of anaerobic sludge; it demonstrates a novel approach to shortening the recovery period of anaerobic processes via manipulating the AI-2-mediated QS.National Research Foundation (NRF)The project was supported and administrated by the Environment & Water Industry Programme Office (EWI) for and on behalf of the National Research Foundation Board (NRF), Singapore (EWI-IRIS-0807). The project was also supported by the Shantou University Scientific Research Foundation for Talents (No.: NTF16015) and the National Natural Science Foundation of China (No.: 51750110514)

Controlling a toxic shock of pentachlorophenol (PCP) to anaerobic digestion using activated carbon addition

Several powdered and granular activated carbons (PACs and GACs) were tested for adsorption of pentachlorophenol (PCP) in bench-scale anaerobic digestion reactors to control the toxicity of PCP to acetoclastic methanogenesis. Results showed that the adsorption capacities of PAC were reduced by 21–54%, depending on the PAC addition time, in the presence of the methanogenic sludge compared to the controls without sludge. As a preventive measure, PAC at a low dose of 20% (mass ratio to the VSS) added 24 h prior to, or simultaneously with, the addition of PCP could completely eliminate the toxic effects of PCP. At the same dose, PAC also enabled methanogenesis to recover immediately after the sludge had been exposed to PCP for 24 h. GAC was not effective in enabling the recovery of methanogenesis due to its slow adsorption kinetics; however, at a dose of 80% it could partially ameliorate the toxic shock of PCP.NRF (Natl Research Foundation, S’pore)Accepted versio

Size-dependent microbial diversity of sub-visible particles in a submerged anaerobic membrane bioreactor (SAnMBR) : implications for membrane fouling

Sub-visible particles, an often-overlooked fine particle (0.45–10 μm) with a size between sludge solids and soluble microbial products (SMP), have recently been identified as a critical foulant in anaerobic membrane bioreactors (AnMBRs), and our recent new insights into the size-fractionation and composition of sub-visible particles in AnMBRs have enabled fouling to be understood in more depth. Here, we investigated the microbial diversity of the sub-visible particles in three size fractions (i.e., 5–10, 1–5, and 0.45–1 μm) from bulk and cake solutions in a lab-scale AnMBR, and their fouling potential was further explored based on their filtration behavior and biofilm formation. Results show that with decreasing particle size, a significant shift in microbial communities was observed for the sub-visible particles in both bulk and cake solutions; (a) with notable decreases in filamentous microbes in the order SJA-15, GCA004, and Anaerolineales of phylum Chloroflexi, and, (b) with substantial increases in sulfate-reducing bacteria (i.e., the family Syntrophobacteraceae, genus DCE29 of family Thermodesulfovibrionaceae, Desulfovibrio, and Geobacter). More importantly, the filamentous microbes associated with micro-particles (5–10 μm) led to higher cake fouling resistances while free living cells in the form of colloidal particles (0.45–1 μm) induced severer pore blocking. Moreover, the micro-particles had an enhanced capacity to favor biofilm formation (OD595 = 1.0–2.5, categorized as highly positive), thus potentially aggravating biofouling. This work advances our knowledge on the effect of particle size on communities and underlying fouling behavior of microbes associated with fine particles in AnMBRs.Environment & Water Industry Development Council (EWI)This work was funded by the Environmental & Water Industry Programme Office (PUB IDD 21100/36/6) in Singapore. It was also supported by the National Natural Science Foundation of China (No. 51608546) and the Fundamental Research Funds for the Central Universities (No. 17lgpy94). We are grateful to Dr. Guangyi Su for support with community analysis

Draft genome sequence of Marinobacter sp. strain P4B1, an electrogenic perchlorate-reducing strain isolated from a long-term mixed enrichment culture of marine bacteria

The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a long-term perchlorate-degrading enrichment culture seeded with marine sediment. The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes).Published versio

Characterization and Significance of Sub-Visible Particles and Colloids in a Submerged Anaerobic Membrane Bioreactor (SAnMBR)

The distribution, composition and morphological structure of subvisible particles and colloids (0.01–10 μm) in the supernatant of a lab-scale submerged anaerobic membrane bioreactor (SAnMBR), and their role in membrane fouling, was investigated. Photometric analysis showed that the supernatant and membrane foulants were dominated by particles and colloids (0.45–10 μm), which accounted for over 90% of the total organics (proteins and polysaccharides). Excitation–emission matrix (EEM) fluorescence spectra and monosaccharide analysis showed that these particles and colloids were rich in fluorescent proteins, rhamnose, ribose and arabinose, all of which could be related to cellular and extracellular substances. Fluorescence and scanning electron microscopy confirmed the presence of bacterial cells in/on the subvisible particles and colloids. The microparticles (5–10 μm) were primarily composed of Streptobacilli and/or filamentous bacteria in the form of microcolonies, while the submicrometer particles and colloids (1–5 μm and 100 kDa-1 μm) had more free/single cocci and bacilli. The ratio of live/dead cells varied in different size-fractions, and the particles (1–10 μm) contained more live cells compared with the colloids (100 kDa-1 μm). Our findings suggest that bacterial cells in/on the particles and colloids could have an important effect on fouling in SAnMBRs as they represent pioneering species attaching to membranes to form fouling layers/biofilm. Such insights reveal that previous foulant-characterization studies in MBRs tended to overestimate organic fouling, while the biofouling induced by these bacteria in/on the particles and colloids was overlooked