Amir Mohaghegh Motlagh

Bacteriophage therapy for membrane biofouling in membrane bioreactors and antibiotic‐resistant bacterial biofilms

To demonstrate elimination of bacterial biofilm on membranes to represent wastewater treatment as well as biofilm formed by antibiotic‐resistant bacterial (ARB) to signify medical application, an antibiotic‐resistant bacterium and its lytic bacteriophage were isolated from a full‐scale wastewater treatment plant. Based on gram staining and complete 16 S rDNA sequencing, the isolated bacterium showed a more than 99% homology with Delftia tsuruhatensis, a gram‐negative bacterium belonging to β‐proteobacteria. The Delftia lytic phages draft genome revealed the phage to be an N4‐like phage with 59.7% G + C content. No transfer RNAs were detected for the phage suggesting that the phage is highly adapted to its host Delftia tsuruhatensis ARB‐1 with regard to codon usage, and does not require additional tRNAs of its own. The gene annotation of the Delftia lytic phage found three different components of RNA polymerase (RNAP) in the genome, which is a typical characteristic of N4‐like phages. The lytic phage specific to D. tsuruhatensis ARB‐1 could successfully remove the biofilm formed by it on a glass slide. The water flux through the membrane of a prototype lab‐scale membrane bioreactor decreased from 47 L/h m2 to ∼15 L/h m2 over 4 days due to a biofilm formed by D. tsuruhatensis ARB‐1. However, the flux increased to 70% of the original after the lytic phage application. Overall, this research demonstrated phage therapys great potential to solve the problem of membrane biofouling, as well as the problems posed by pathogenic biofilms in external wounds and on medical instruments. Biotechnol. Bioeng. 2015;112: 1644–1654.

Biofilm control with natural and genetically-modified phages.

Bacteriophages, as the most dominant and diverse entities in the universe, have the potential to be one of the most promising therapeutic agents. The emergence of multidrug-resistant bacteria and the antibiotic crisis in the last few decades have resulted in a renewed interest in phage therapy. Furthermore, bacteriophages, with the capacity to rapidly infect and overcome bacterial resistance, have demonstrated a sustainable approach against bacterial pathogens-particularly in biofilm. Biofilm, as complex microbial communities located at interphases embedded in a matrix of bacterial extracellular polysaccharide substances (EPS), is involved in health issues such as infections associated with the use of biomaterials and chronic infections by multidrug resistant bacteria, as well as industrial issues such as biofilm formation on stainless steel surfaces in food industry and membrane biofouling in water and wastewater treatment processes. In this paper, the most recent studies on the potential of phage therapy using natural and genetically-modified lytic phages and their associated enzymes in fighting biofilm development in various fields including engineering, industry, and medical applications are reviewed. Phage-mediated prevention approaches as an indirect phage therapy strategy are also explored in this review. In addition, the limitations of these approaches and suggestions to overcome these constraints are discussed to enhance the efficiency of phage therapy process. Finally, future perspectives and directions for further research towards a better understanding of phage therapy to control biofilm are recommended.

Microbiological study of bacteriophage induction in the presence of chemical stress factors in enhanced biological phosphorus removal (EBPR)

Polyphosphate accumulating organisms (PAOs) are responsible for carrying the enhanced biological phosphorus removal (EBPR). Although the EBPR process is well studied, the failure of EBPR performance at both laboratory and full-scale plants has revealed a lack of knowledge about the ecological and microbiological aspects of EBPR processes. Bacteriophages are viruses that infect bacteria as their sole host. Bacteriophage infection of polyphosphate accumulating organisms (PAOs) has not been considered as a main contributor to biological phosphorus removal upsets. This study examined the effects of different stress factors on the dynamics of bacteriophages and the corresponding effects on the phosphorus removal performance in a lab-scale EBPR system. The results showed that copper (heavy metal), cyanide (toxic chemical), and ciprofloxacin (antibiotic), as three different anthropogenic stress factors, can induce phages integrated onto bacterial genomes (i.e. prophages) in an enriched EBPR sequencing batch reactor, resulting in a decrease in the polyphosphate kinase gene ppk1 clades copy number, phosphorus accumulation capacity, and phosphorus removal performance. This study opens opportunities for further research on the effects of bacteriophages in nutrient cycles both in controlled systems such as wastewater treatment plants and natural ecosystems.

Sustainability of Activated Sludge Processes

Recent studies revealed that two-thirds of US coastal systems are moderately to severely impaired because of excess nutrient loading, particularly nitrogen and phosphorus, and, therefore, the need for more efficient treatment procedures for wastewater is greater than ever. Activated sludge process has been used for a century for municipal and industrial wastewater treatment. This process can achieve high efficiency of biochemical oxygen demand, chemical oxygen demand, and nutrient removal. In order to improve the effluent wastewater quality and reduce the point-source nutrient loading on the water bodies, adequate information and knowledge must be acquired. Sustainable solutions to the wastewater treatment technologies can reduce the carbon footprint and the use of chemicals, and save energy and operational cost. The sustainability of activated sludge processes depends upon efficient nutrient and organic carbon removal and efficient sludge/biomass handling and processing. This chapter will introduce readers to the background information on the nutrients and their effects on the environment, different sustainable removal practices for nitrogen and phosphorus from municipal wastewater, and the microbiology of biological nitrogen and phosphorus removal, and finally, the chapter will conclude with a discussion on the need for process optimization and resource recovery.

Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood. This study begins to fill this knowledge gap by analyzing bacteriophage-host interactions in the Great Salt Lake, the largest prehistoric hypersaline lake in the Western Hemisphere. Our metagenomics analyses allowed us to comprehensively identify the bacterial and phage communities with Proteobacteria, Firmicutes, and Bacteroidetes as the most dominant bacterial species and Siphoviridae, Myoviridae, and Podoviridae as the most dominant viral families found in the metagenomic sequences. We also characterized interactions between the phage and prokaryotic communities of Great Salt Lake and determined how these interactions possibly influence the community diversity, structure, and biogeochemical cycles. In addition, presence of prophages and their interaction with the prokaryotic host was studied and showed the possibility of prophage induction and subsequent infection of prokaryotic community present in the Great Salt Lake environment under different environmental stress factors. We found that carbon cycle was the most susceptible nutrient cycling pathways to prophage induction in the presence of environmental stresses. This study gives an enhanced snapshot of phage and prokaryote abundance and diversity as well as their interactions in a hypersaline complex ecosystem, which can pave the way for further research studies.

Biological Phosphorus Removal

Eutrophication of water bodies has been considered to be a worldwide pollution problem for years. Eutrophication is a phenomenon caused by excess discharge of nutrients in an aqueous system, particularly by nitrogen and phosphorus, especially in lakes, estuaries, and slow-moving streams. One of the signs of eutrophication is dense algal blooms that cause high turbidity in aquatic systems, decreasing dissolved oxygen, and increasing hypoxia conditions in the deeper parts of water bodies because of plant decay in sediments. In addition, floating algal blooms, known as blue-green algae, formed in freshwaters is another symptom of nutrient excess, which is caused by nitrogen-fixing cyanobacteria. The increased supply of nutrients to surface waters results in an enhanced manufacture by primary producers, particularly phytoplankton and other aquatic plants. The main nutrients of concern are nitrogen and phosphorus, although their relative contribution to eutrophication is still under lots of debate. Although nitrogen and phosphorus are both necessary for the growth of algae, phosphorus input is more critical as many cyanobacteria are able to provide their nitrogen requirement from the available atmospheric nitrogen by way of nitrogen fixation ( Kortstee et al., 1994 ).