Samir Kumar Khanal

University of Hawaiʻi at Mānoa | UH Manoa · Department of Molecular Biosciences and Bioengineering

The rising demand for global food resources, combined with an overreliance on land-based agroecosystems, poses a significant challenge for the sustainable production of food products. Macroalgae cultivation is a promising approach to mitigate impending global food insecurities due to several key factors: independence from terrestrial farming, rapid...

The denitrifying sulfur (S) conversion-associated enhanced biological phosphorus removal (DS-EBPR) process for treating saline wastewater is characterized by its unique microbial ecology that integrates carbon (C), nitrogen (N), phosphorus (P), and S biotransformation. However, operational instability arises due to the numerous parameters and intri...

Bioponics is a nutrient-recovery technology that transforms nutrient-rich organic waste into plant biomass/ bioproducts. Integrating biochar with digestate from anaerobic wastewater treatment process can improve resource recovery while mitigating heavy metal contamination. The overarching goal of this study was to investigate the application of bio...

Anaerobic co-digestion (AcoD) is becoming increasingly popular in the biogas industry for its numerous advantages over mono-digestion, including balanced nutrient profiles, enhanced process stability, synergistic methane production, and reduced greenhouse gas emissions. However, varying results across AcoD studies highlight the need for an extensiv...

Anaerobic digestion (AD) is a proven technology widely adopted to treat diverse organic wastes and produce energy in the form of heat, electricity and/or transportation fuels. The application of AD systems still faces challenges due to process stability, digestate management, high costs, and regulatory concerns and requirements among others. In man...

Since the discovery of nanobubbles (NBs) in 1994, NBs have been attracting growing attention for their fascinating properties and have been studied for application in various environmental fields, including water and wastewater treatment. However, despite the intensive research efforts on NBs’ fundamental properties, especially in the past five yea...

Aquaponics is a climate-smart food production system that relies on nutrient recovery from aquaculture effluent. The availability of dissolved oxygen (DO) limits the performance of aquaponic systems. To address this issue, air micronanobubbles (MNBs) were tested as an alternative aeration method. Due to their small size (<50 μm) and long-term stabi...

Nanaerobes are a newly described class of microorganisms that use a unique cytochrome bd oxidase to achieve nanaerobic respiration at <2 μM dissolved oxygen (∼1% of atmospheric oxygen) but are not viable above this value due to the lack of other terminal oxidases. Although sharing an overlapping ecological niche with methanogenic archaea, the role...

This study investigated the effects of varying zero-valent iron (ZVI) (0 to 5,000 mg/L) on fermentative hydrogen (H2) production, metabolic pattern, and taxonomic profile by using kitchen waste as substrate. The study demonstrated that the supplementation of 500 mg ZVI/L resulted in the highest H2 yield (219.68 ± 11.19 mL H2/g-volatile solids (VS)a...

Microalgae are promising sources of valuable bioproducts such as biofuels, food, and nutraceuticals. However, harvesting microalgae is challenging due to their small size and low biomass concentrations. To address this challenge, bio-flocculation of starchless mutants of Chlamydomonas reinhardtii (sta6/sta7) was investigated with Mortierella alpina...

Food waste is rich in nutrients, such as nitrogen and phosphorus, and can be integrated with bioponics, a closed-loop agricultural system that combines hydroponics with biological nutrient recovery. Vermicompost leachate (VCL) supplementation has been shown to improve the co-composting of organic waste (i.e., compost quality) and the biodegradation...

In recent years, the digital transformation of bioprocesses, which focuses on interconnectivity, online monitoring, process automation, artificial intelligence (AI) and machine learning (ML), and real-time data acquisition, has gained considerable attention. AI can systematically analyze and forecast high-dimensional data obtained from the operatin...

In recent years, there has been growing interest in the varied applications of nanobubble technology. Given their unique physicochemical properties, such as minuscule size (< 1 µm), surface charge, and high internal pressure, nanobubbles (NB) could provide new opportunities in the fields of environmental engineering (including environmental remedia...

An increasing attention has been paid to the secure and sustainable management of agricultural wastes, especially lignocellulosic biomass. Nanobubble water (NBW) contains 106-108 bubbles/mL with diameter <1000 nm. Although previous studies have examined the enhancement effects of NBW on methane production from organic solid wastes, the NBW-based an...

Municipal wastewater treatment which is associated with high energy consumption and excessive greenhouse gas (GHG) emissions, has been facing severe challenges toward carbon emissions. In this study, a high-rate activated sludge-two-stage vertical up-flow constructed wetland (HRAS-TVUCW) system was developed to reduce carbon emissions during munici...

Anaerobic co-digestion (AcoD) offers several merits such as better digestibility and process stability while enhancing methane yield due to synergistic effects. Operation of an efficient AcoD system, however, requires full comprehension of important operational parameters, such as co-substrate ratio, their composition, volatile fatty acids/alkalini...

Many traditional anaerobic digesters can benefit from a facelift that maximizes biogas production and enhancing process stability without major infrastructure modification. Moreover, a simple method to limit H2S in the biogas without expensive gas conditioning would all contribute to the sustainability and economic efficiency of the energy recovery...

A two-stroke engine run with flexible fuel of biogas or methanol is not established yet. It is the objective of this work to provide 2 stroke engine for an electric generator that can be run by using flexible fuels namely: methanol, biogas, and mixed methanol-biogas. A small single cylinder 2 stroke engine of an electric generator was set to be abl...

Biochar has been widely deemed as a soil conditioner to modify the physicochemical and biological properties of soil. In this research, the influence of different biochar application conditions on the effect of heavy metal Cu in soil was detected. In batch experiments, the combinations could definitely enhance the adsorption abilities, and under th...

Microbubbles (MBs) and nanobubbles (NBs) refer to bubbles of micrometer to nanometer sizes. Due to several unique attributes, including long-term stability, negative surface charge, and the ability to generate reactive oxygen species, MB and NB technology has garnered significant attention in water and wastewater treatment and ecological restoratio...

Pharmaceuticals are a diverse group of chemical compounds widely used for prevention and treatment of infectious diseases in both humans and animals. Pharmaceuticals, either in their original form or metabolites, find their way into the wastewater treatment plants (WWTPs) from different sources. Recently, anaerobic membrane bioreactors (AnMBR) has...

In bioponics, although chicken manure is an efficient substrate for vegetable production and nitrogen recovery, it is often contaminated with high Cu and Zn levels, which could potentially cause bioaccumulation in plants and pose health risks. The objectives of this study were to assess nitrogen recovery in lettuce- and pak choi-based bioponics wit...

Ammonia stress is a commonly encountered issue in anaerobic digestion (AD) process when treating proteinaceous substrates. The enhanced relationship between syntrophic bacteria and methanogens triggered by interspecies electron transfer (IET) stimulation is one of the potential mechanisms for an improved methane yield from the AD plant under ammoni...

Converting lignocellulose to bioenergy and biobased products requires targeted breakdown of complex plant polymers that protect structural sugars. To identify lignophenolic compounds that promote enzymatic hydrolysis, the lignophenolic composition of biomass across 12 species and varieties of the Poaceae (grass) family were measured using copper (I...

In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches f...

The mitigation of greenhouse gas (GHG) emission is one of the major focuses of The Glasgow Climate Pact, a global agreement that is believed to accelerate climate action. Following the energy sector, industrial and agro-wastes are the major contributors to global GHG emission. With the rapid growth in population, affluence, and urbanization, the GH...

Bioponics has the potential to recover nutrients from organic waste streams, such as chicken manure and digestate with high volatile fatty acid (VFA) contents through crop production. Acetic acid, a dominant VFA, was supplemented weekly (0, 500, 1000, and 1500 mg/L) in a chicken manure-based bioponic system, and its effect on the performance of bio...

Low economic gains from biogas drive research on shifting to volatile fatty acid (VFA) production during anaerobic sludge digestion. pH control and methanogenesis inhibition are widely used strategies for VFA production via anaerobic digestion of sludge. However, these strategies require perpetual dosing of chemicals, increasing cost and operation...

Hydrothermal carbonization (HTC) provides a promising alternative to valorize food waste digestate (FWD) and avoid disposal issues. Although hydrochar derived from FWD alone had a low calorific content (HHV of 13.9 MJ kg⁻¹), catalytic co-HTC of FWD with wet lignocellulosic biomass (e.g., wet yard waste; YW) and 0.5 M HCl exhibited overall superior...

Anaerobic digestion (AD) is widely adopted for remediating diverse organic wastes with simultaneous production of renewable energy and nutrient-rich digestate. AD process, however, suffers from instability, thereby adversely affecting biogas production. There have been significant efforts in developing strategies to control the AD process to mainta...

This study investigated organic removal performance, characteristics of the membrane dynamics, membrane fouling and the effects of biological sulfate reduction during high-salinity (1.0%) and high-sulfate (150 mgSO4²⁻-S/L) wastewater treatment using a laboratory-scale upflow anaerobic sludge bed reactor integrated with cross-flow dynamic membrane m...

Anaerobic mono- and co-digestion of coffee pulp (CP), cattle manure (CM), food waste (FW) and dewatered sewage sludge (DSS), were assessed using biochemical methane potential tests. The effects of two different inocula, anaerobically digested cattle manure (ADCM) and anaerobically digested waste activated sludge (ADWAS), and five different co-feeds...

Growing consumption of fossil reserves to meet the rising demand of energy has led to climate deterioration and simultaneous waste generation, urging modern society to find sustainable energy resource that can meet the growing energy demands and reduce greenhouse gas emissions and carbon footprints. In this aspect, hydrogen (H2) is one of the most...

Anaerobic digestion (AD) is a matured technology for waste (water) remediation/stabilization and bioenergy generation in the form of biogas. AD technology has several inherent benefits ranging from generating renewable energy, remediating waste (water), and reducing greenhouse gas emission to improving health/hygiene and the overall socio-economic...

Azo dye is the most versatile class of dyes used in the textile industry. Although the sulfidogenic process shows superiority in the removal of azo dye, the role of biogenic sulfide produced by sulfate-reducing bacteria (SRB) in the decolorization of azo dye is unclear. This study explored the mechanism of biogenic sulfide for removal of a model az...

Environmental contamination of heavy metals is now becoming increasingly a concern and a significant problem due to its harmful effects worldwide. The plant-meditated approach is encouraging to eliminate toxins avoiding side effects from polluted wastewater. For the development of appropriate plant species for the mechanisms of heavy metal absorpti...

The efficacy of C4 grasses as feedstocks for liquid fuel production and their climate mitigation potential remain unresolved in the tropics. To identify highly convertible C4 grasses, we measured final fuels and postprocess biomass produced in two laboratory-scale conversion pathways across 12 species and varieties within the Poaceae (grass) family...

Recently, anaerobic self-forming dynamic membrane bioreactors (AnSFDMBRs) have attracted increasing attention, and are considered as an alternative to conventional anaerobic membrane bioreactors (AnMBRs). The key advantages of AnSFDMBRs include high flux, low propensity towards fouling, and low capital and operational costs. Although there have bee...

Anaerobic digestion of organic wastes produces solid residues known as digestates, which have potential as a fertilizer and soil amendment. The majority of research on digestate focuses on their fertilizer value. However, there is a lack of information about additional effects they may have on plant growth, both positive and negative. Understanding...

Bioponics integrates the biological treatment of nutrient-rich waste streams with hydroponics. However, there are several challenges of bioponics, especially nutrient availability and qualities, which affect plant yield. In this study, chicken manure based-nutrient film technique bioponics was examined at manure loadings of 200, 300, and 400 g dry...

Nanobubble technology has significant potential to improve the anaerobic digestion (AD) process by ameliorating the rate-limiting steps of hydrolysis and methanogenesis, as well as providing process stability by reducing sulfide and volatile fatty acid (VFA) levels. Nanobubbles (NB) can enhance substrate accessibility, digestibility, and enzymatic...

Anaerobic digestion is a long-established technology for the valorization of diverse organic wastes with concomitant generation of valuable resources. However, mono-digestion (i.e., anaerobic digestion using one feedstock) suffers from challenges associated with feedstock characteristics. Co-digestion using multiple feedstocks provides the potentia...

This document it is established that 2 types of biogas anaerobic digester that usually found in developing country. First type is fixed dome type of anaerobic digester and secondly is floating drum biogas anaerobic digester. Both of this type have draw back that the anaerobic process is not completed with agitation process that yield low rate of bi...

Nitrogen, a critically important nutrient that boosts yields in agriculture and food production, is currently overused to meet the rising demand for food. Surplus nitrogen ends up in the environment in excess of the capacity of natural nitrogen cycle, thereby leading to serious environmental pollutions, such as eutrophication of water bodies and em...

Intermittent (every other day) microaerobic [picomolar oxygen by oxidation-reduction potential (ORP) set at +25 mV above anaerobic baseline] digestion of lignocellulosic biomass showed higher digestibility and better stability at a high organic loading rate (OLR) of 5 g volatile solids (VS)/L/d than that under strict anaerobic conditions. However,...

While rumen microorganisms are known to facilitate the hydrolysis of lignocellulosic substrates in anaerobic digestion (AD), it is unclear how rumen content can be used to maintain rumen microorganisms in continuous-flow AD systems. We used rumen content as either an inoculum or a cosubstrate in two separate AD experiments, and performed microbial...

Ciprofloxacin (CIP), one of the most widely used fluoroquinolone antibiotics, is frequently detected in the effluents of wastewater treatment plants and aquatic environments. In this study, a CIP-degrading bacterial strain was isolated from the sulfate reducing bacteria (SRB)-enriched sludge, identified as Paraclostridium sp. (i.e., strain S2). The...

Ibuprofen (IBU) is one of the frequently detected non-steroidal anti-inflammatory drugs (NSAIDs) in wastewater treatment plants (WWTPs) and aquatic environment. However, little is known about the effect of IBU and its biotransformation products (TPs) on different biological sludge systems and aquatic environment. The effects and toxicity of IBU and...

Population growth and unprecedented economic growth and urbanization, especially in low- and middle-income countries, coupled with extreme weather patterns, the high-environmental footprint of agricultural practices, and disposal-oriented waste management practices, require significant changes in the ways we produce food, feed and fuel, and manage...

Current Developments in Biotechnology and Bioengineering: Sustainable Bioresources for the Emerging Bioeconomy outlines recent advances in bioenergy, biorefinery and the bioeconomy, an essential element for a 21st century bio-based society. The book provides information on biomass and various conversion technologies with different parameters that a...

Sulfur-driven autotrophic denitrification (SdAD) represents an effective alternative to heterotrophic denitrification process for the treatment of organic carbon deficient or organic carbon free water and wastewater streams. The electron supply by oxidation of sulfur substrates (i.e., total dissolved sulfide (TDS) and chemical elemental sulfur (S⁰c...

This study investigated the phosphorus adsorption behaviors of pristine and MgO modified biochars produced from woody biomass precursors (having different anatomical characteristics and similar specific gravities) and their MgCl2 impregnated counterparts. The biomass precursors were Longleaf pine wood shavings, Red Oak and Hard Maple sawdusts. The...

In recent years, aquaponics has generated significant attention for recovery of resources (vegetables/fruits) from aquaculture effluent. Aquaponics produces organic vegetables by recycling nutrients in aquaculture effluent under a symbiotic environment among fish, plants, and bacteria. Linking the understanding of nutrient recycling processes to th...

The potential for microbial protein production in the mixture of yellow wine lees and rice soaking wastewater was examined. Strong symbiotic effect was observed in fermentation with yeast-fungus mixed culture of Candida utilis and Geochichum candidum at a ratio of 1:1 (v/v). The maximum specific biomass yield of 4.91 ± 0.48 g final biomass/g initia...

Experimental conditions of liquid hot water (LHW) pretreatment were tested for two dedicated energy crops, Napiergrass (Pennisetum purpureum) and Energycane (Saccharum officinarum × Saccharum robustum). Both crops showed differential resistance to temperature during pretreatment and differences in response to biomass and enzyme loadings during subs...

This study examined the use of biochar to alleviate sulfide toxicity to methane producing archaea (MPA) and sulfate-reducing bacteria (SRB) during anaerobic treatment of sulfate-rich wastewater with concomitant sulfur recovery. At the sulfate concentration of 6000 mg SO42-/L, the dissolved sulfide (DS) of 131 mg S/L resulted in total volatile fatty...

Ibuprofen (IBU), a common non-steroidal anti-inflammatory drug (NSAID), is widely used by humans for controlling fever and pain, and is frequently detected in the influent of wastewater treatment plants and different aquatic environments. In this study, the biotransformation of IBU in activated sludge (AS), anaerobic methanogenic sludge (AnMS) and...

This study developed an intermittent oxidation-reduction potential (ORP)-controlled micro-aeration system for high solids anaerobic digestion (AD) of lignocellulosic biomass without volatile fatty acids (VFA) accumulation at high organic loading rate (OLR). Traditional AD of Napier grass, a model lignocellulosic biomass, at an OLR of 5 g volatile s...

The pyrolysis kinetics of sewage sludge was studied to determine the constituent of sludge and explore the feasibility of pyrolytic post-treatment. Both flocculent sludge and granular sludge were pyrolysed in a thermogravimetric analyser under inert atmospheric conditions. The pyrolysis of granular sludge and flocculent sludge were described by thr...

Adsorption plays an important role on ciprofloxacin (CIP) removal in biological wastewater treatment systems. In this study, mechanisms and thermodynamics of CIP adsorption by sulfate-reducing bacteria (SRB) sludge were examined via a series of batch studies. CIP adsorption by SRB sludge was a pH-dependent process and was strongly correlated with C...

Anaerobic digestion (AD) of lignocellulosic biomass has received significant attention for bioenergy production in recent years. However, hydrolysis is a rate-limiting in AD of such feedstock. In this study, effects of hydrothermal pretreatment of Napier grass, a model lignocellulosic biomass, on methane yield were examined through series of batch...

Antibiotics, the most frequently prescribed drugs of modern medicine, are extensively used for both human and veterinary applications. Antibiotics from different wastewater sources (e.g., municipal, hospitals, animal production and pharmaceutical industries), ultimately are discharged into wastewater treatment plants. Sorption and biodegradation ar...

This study investigated sulfamethoxazole (SMX) removal and fate in sulfate-reducing up-flow sludge bed (SRUSB) reactors inoculated with sulfate-reducing bacteria (SRB) granules and flocs. The resilience of SRB granules and flocs against varying pHs and hydraulic retention times (HRTs) was also examined. SRB granules and flocs efficiently removed SM...

In this study, we examined eight typical and widely detected pharmaceuticals (PhAs) removal in an anaerobic sulfate-reducing bacteria (SRB) sludge system (five antibiotics: sulfadiazine (SD), sulfamethoxazole (SMX), trimethoprim (TMP), ciprofloxacin (CIP) and enoxacin (ENO), and three nonsteroidal anti-inflammatory drugs (NSAIDs): ibuprofen (IBU),...

Anaerobic digestion (AD) has gained significant attention in recent years. In addition to producing renewable energy and bio-based chemicals from diverse organic feedstock, AD process also remediates organic waste streams along with curtailing greenhouse gas (GHG) emission. Operational conditions and anaerobic reactor configurations are continuousl...

Aquaponics recycles nitrogen from nitrogen-rich aquaculture effluent into organic crops (fish and vegetables/fruits) in hydroponic grow beds. Fundamental understanding of nitrogen transformations in aquaponics is critically important to improve nitrogen use efficiency (NUE) within aquaponics systems and to reduce release of environmentally harmful...

Aquaponics is a technology for food production (fish and vegetables/fruits) with concomitant remediation of nitrogen-rich aquaculture effluent. There is, however, a critical need to improve the nitrogen use efficiency (NUE) in aquaponics. Here, we employed quantitative polymerase chain reactions and next-generation sequencing to evaluate the bacter...

Antibiotics are widely used for the prevention and treatment of infectious diseases in both humans and animals, as well as growth promoters in livestock production (e.g., cattle, swine and poultry) and aquaculture. Human consumption of antibiotics increased by 39% between 2000 and 2015 and is expected to further increase by 15% by 2030 based on cur...

Exposure of a small amount of oxygen/air (microaeration) has been reported to benefit the anaerobic digestion (AD) process in enhancing hydrolysis, improving methane yield, stabilizing the process and scavenging hydrogen sulfide among others. The underlying mechanism of enhancing AD process via microaeration is the augmentation of activity and dive...

In this study, hydrogenotrophic methanogenesis with respect to methanogenic activity and microbial structures under extreme-thermophilic conditions were examined, and compared with the conventional thermophilic condition. The hydrogenotrophic methanogens were successfully acclimated to the temperatures of 55, 65 and 70 °C. Although acclimation was...