Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome

Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.

Microbial Removal from Secondary Treated Wastewater Using a Hybrid System of Ultrafiltration and Reverse Osmosis

The efficiency of advanced membranes towards removal of general and specific microbes from wastewater was investigated. The treatment included a subsequent system of activated sludge, ultrafiltration （hollow fibre membranes with 100 kDa cut-off, and spiral wound membranes with 20 kDa cut-off）, and RO （reverse osmosis）. The removal evaluation of screened microbes present in treated wastewater showed that hollow fibre membrane rejected only 1 log （90% rejection） of the TPC （total microbial count）, TC （total coliforms）, and FC （faecal coliforms）. A higher effectiveness was observed with spiral wound, removing 2-3 logs （99%-99.9%） of TPC and complete rejection of TC and FC. The RO system was successful in total rejection of all received bacteria. The removal evaluation of inoculated specific types of bacteria showed that the hollow membranes removed 2 logs （99%） of inoculated E. coli （10^7-10^8 cfu/mL inoculum）, 2-3 logs （99%-99.9%） of Enterococus spp. （10^7-10^10 cfu/mL inoculum）, 1-2 logs （90%-99%） of Salmonella （10^8-10^10 cfu/mL inoculum） and 1-2 logs （90%-99%） of Shigella （10^5-10^6 cfu/mL inoculum）. The spiral wound was significantly efficient in rejecting further 3 logs of E. coil, 5 logs of Enterococus spp., 4 logs of Salmonella, and a complete rejection of all received bacteria was accomplished by RO membrane. The results indicate that Gram positive bacteria were removed much more efficiently compared to the Gram negative ones, the rationale behind such behaviour is based on cell walls elasticity.

Influence of Sanitization Process on Maintaining Sweet Potato Quality for Export

The whole cold-chain for exporting sweet potato(native variety“Abees”),to foreign market included immediate curing operation directly after harvest helped in healing skin texture,however,in order to reduce postharvest soft rot(Rhizopus stolonifer)incidence following trimming,and washing,ultraviolet light(UV-C)treatment was used as a main sanitizer for eliminating the soft rot.Exposure of the roots to UV-C(254 nm)was applied in a UV-C room on freshly harvested and cured sweet potato while rolling up on a movable line at 20 cm distance for 1,2,and 3 hr.As combining UV-C treatment with chlorine(200 ppm)on roots,marked and significant reduction of the total microbial load and Rhizopus potential was achieved on root surfaces respectively compared with chlorine alone.It also reduced soft rot percentage to almost 0%infection.After 3 months of cold-storage,quality assessment of sweet potato showed that root characteristics were markedly maintained.The ability of UV-C light to induce phenylalanine ammonia lyase(PAL)enzyme activity in root tissue and maintain the activities of peroxidase and polyphenol oxidase,however with slight increase,was detected.UV-C caused an increase of phenol content in sweet potato tissue that made an activation of defense reaction against the rot causal pathogen.As the exposure time to UV-C light increased,a higher content of phenols occurred.Moreover,UV-C application caused decrease in sugar content of root tissue that is flavored by soft rot-causal pathogen.

Pulsed light processing of foods for microbial safety

The demand for processed foods and the awareness about food quality and safety are increasing rapidly.The consumers’demand for minimally processed foods and growing competition in the market have made the processors to adopt newer non-thermal technologies that preserve nutrients and sensory properties of the products.Conventionally,heat processing of foods is carried out to convert raw material into value-added product,reduce or eliminate microbial load to improve safety,and extend shelf life.Some of the limitations of thermal processing techniques can be overcome by employing non-thermal processes.High hydrostatic pressure,pulsed electric field,ultrasound,cold plasma,dense phase carbon dioxide,ozone,and pulsed light(PL)processing are gaining popularity in food processing.PL technology is a non-thermal technology,where sterilization and decontamination are achieved by impinging high-intensity light pulses of short durations on surfaces of foods and high-transmission liquids.Although a few reports on the PL technology are available,in-depth studies on this are needed to adopt at a commercial level.The present review provides an overview of light-based processing of foods and covers important aspects such as different PL systems used for processing of foods,mode of action of PL on microbes,the effect of PL on liquid foods,surface decontamination of foods and parameters that affect PL efficacy,combination processing with PL.With the growing demand in non-thermal processing for the technological advancement in the area of generation of light,light-based processing will be a promising technology for microbial load reduction.

Decoding the microbiome for sustainable agriculture

Root-associated microbiota profoundly affect crop health and productivity.Plants can selectively recruit beneficial microbes from the soil and actively balance microbe-triggered plant-growth promotion and stress tolerance enhancement.The cost associated with this is the root-mediated support of a certain number of specific microbes under nutrient limitation.Thus,it is important to consider the dynamic changes in microbial quantity when it comes to nutrient condition-induced root microbiome reassembly.Quantitative microbiome profiling(QMP)has recently emerged as a means to estimate the specific microbial load variation of a root microbiome(instead of the traditional approach quantifying relative microbial abundances)and data from the QMP approach can be more closely correlated with plant development and/or function.However,due to a lack of detailed-QMP data,how soil nutrient conditions affect quantitative changes in microbial assembly of the root-associated microbiome remains poorly understood.A recent study quantified the dynamics of the soybean root microbiome,under unbalanced fertilization,using QMP and provided data on the use of specific synthetic communities(SynComs)for sustaining crop productivity.In this editorial,we explore potential opportunities for utilizing QMP to decode the microbiome for sustainable agriculture.

Invasion of parasitic isopods in marine fishes

Objective:To carry out a detailed three-year observation study on isopod parasites infestation in fish.Methods:Fish samples were collected from different localities in various landing centers along the Tamil Nadu coastal area.The prevalence and mean intensity were calculated.The proximate composition of infestation and uninfestation were studied in different marine fishes.A comparative analysis of bacteria and fungi in the infected and uninfected regions of fishes were analysed.Results:Tweenty six species including 12 genera of isopods(Cymothoidae)distributed in 39 species of marine fishes along the Tamil Nadu coast.The isopod parasites were attached in three different microhabitats in host fishes viz.,buccal,branchial and body surfaces.They exhibited host and site specific occurrence.Maximum prevalence 17.11%was recorded in March 2010 and minimum 0.27%in Febuary 2010.The intensity ranged from 1 to 1.7 parasites per fish during the different months from Decmber 2008 to November 2011.There was a decrease in the protein,carbohydrate and lipid content in the infested fishes compared to uninfected fishes.A comparative analysis of bacteria and fungi in the infected and uninfected region of fishes were analysed.It revealed that infected portions had dense bacterial load as observed in the lesions of infected fishes than uninfected fishes.Conclusion:Factors which are able to induce parasitic manifestation are stock quality,stocking density,environmental conditions,biological and physiological characteristics of parasite,zoo technical measures,food quantity,feeding strategies,etc.