Frontiers on the application of cellulase in aquaculture: future prospects and challenges.

This article reviews the scientific literature discussing the microbial interactions between water microbiota, live food microbiota, fish larvae immune system and gut microbiota, and biofilm microbial communities in rearing systems for marine fish larvae. Fish gut microbiota is the first line of defense against opportunistic pathogens, and marine fish larvae are vulnerable to high mortalities during the first weeks after hatching. The bacterial colonization of fish larvae is a dynamic process influenced by environmental and host-related factors. The bacteria transferred to larvae from the eggs can influence the composition of the gut microbiota in the early stages of fish. Fish larvae ingest free-living microorganisms present in the water, as marine fish larvae drink water for osmoregulation. In marine aquaculture systems, the conventional feeding-rearing protocol consists of zooplankton (rotifers, Artemia, and copepods). These live food organisms are filter-feeders. Once transferred to a new environment, they quickly adopt the microflora of the surrounding water. So, the water microbiota is similar to the microbiota of the live food at the time of ingestion of live food by the larvae. In aquaculture rearing systems, bacterial biofilms may harbor opportunistic pathogenic bacteria and serve as a reservoir for those microbes, which may colonize the water column. The methods applied for the study of fish larvae microbiota were reviewed.

Context-aware synthetic biology by controller design: Engineering the mammalian cell.

Evaluation of the presence and efficiency of potential probiotic bacteria in the gut of tilapia (Oreochromis niloticus) using the fluorescent in situ hybridization technique

Effects of biological flocculation technology (BFT) on water quality dynamics and immune response of grass carp (Ctenopharyngodon idella)

Synthetic biology provides powerful tools and novel strategies for designing and modifying microorganisms to function as cell factories for biomanufacturing, which is a promising approach for realizing chemical production in a green and sustainable manner. Recent advances in genetic component design and genome engineering have enabled significant progresses in the field of synthetic biology chassis that have been developed for enzymes or biochemical production based on synthetic biology strategies, with particular reference to model microorganisms, such as Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum, and Saccharomyces cerevisiae. In this review, strategies for engineering four different functional cellular modules which encompass the total process of biomanufacturing are discussed, including expanding the substrate spectrum for substrate uptake modules, refactoring biosynthetic pathways and dynamic regulation for product synthesis modules, balancing energy and redox modules, and cell membrane and cell wall engineering of product storage and secretion modules. Novel strategies of integrating and coordinating different cellular modules aided by synthetic co-culturing of multiple chassis, artificial intelligence-aided data mining for guiding strain development, and the process for designing automatic chassis development via biofoundry are expected to generate next generations of model microorganism chassis for more efficient biomanufacturing. KEY POINTS: • Engineering of functional cellular modules facilitate next generations of chassis construction. • Global optimization of biosynthesis can be improved by metabolic models. • Data-driven and automatic strain development can improve microorganism chassis construction.

In 1998, computer scientist Ehud Shapiro returned to the Weizmann Institute in Rehovot, Israel, as a group leader after a five‐year break as a software entrepreneur. At the peak of the Internet boom, it would have been easy to find an exciting topic to pursue in computer science. Instead, Shapiro became interested in the origin of life and began to train himself in molecular biology, which eventually sparked his idea to build computers from biological molecules. His team first constructed a molecular Turing machine based on DNA, restriction nuclease and ligase to perform simple computations (Benenson et al , 2001), soon followed by a more sophisticated system that performs stochastic computations using mRNA molecules as input (Benenson et al , 2004). What seems merely to be the intellectual interest of an Israeli computer scientist—using biological compounds and systems to create logical circuits—has in fact become the hottest area in the biological sciences: synthetic biology. Other engineers are also dropping their soldering guns for micropipettes to rewire genes and genomes with the aim of reprogramming living organisms. “Synthetic biology is the other side of the coin of systems biology,” commented Victor de Lorenzo, Vice Director of the National Centre of Biotechnology in Madrid, Spain. “What you want is to create or recreate systems that have some properties of life from engineering principles.” This includes a range of techniques from recombinant cloning, to synthesizing genomes de novo , to creating completely new entities such as Shapiro's artificial systems. However, more interesting than the technology itself is the ability to create artificial metabolic and regulatory pathways and to test their viability in living systems. It allows scientists to probe the complexity of an organism's innards and thus derive further insights into how cells work. As George Church, Professor of Genetics at Harvard Medical School …

16 - Synthetic biology strategies towards the development of new bioinspired technologies for medical applications

What exactly is synthetic biology?

Shrimp has been among the top value-added products targeted for production by the aquaculture industry. The increasing demand for shrimp has led to a massive increase in production in several countries across the world. Intensive and super-intensive production systems are facing great challenges handling newly emerging shrimp diseases. The use of antibiotics was one of the first approaches when dealing with such diseases, but the effects of misusing antibiotics and the appearance of antibiotic resistant bacteria are of public concern. As an alternative, probiotics have been applied in aquaculture systems to increase disease resistance, improve feed efficiency, maintain water quality and enhance the growth of aquatic organisms. In this study, the ability of three probiotic microbes to tolerate salinity levels commonly found in intensive shrimp production systems were evaluated. Lactobacillus casei, Saccharomyces cerevisiae and Rhodopseudomonas palustris were cultured in MRS broth, yeast and mold broth, and Van Neil’s broth, respectively, enriched with 1 and 2% NaCl. Microbial survival between treatments were compared as well as the metabolic activity in terms of acidity levels. Additionally, cell morphology was compared using scanning electron microscopy. L. casei and S. cerevisiae showed no significant differences (P>0.05) in media with 1% and 2% NaCl in terms of microbial survival and media acidity levels at 24 h. R. palustris showed a prolonged lag phase extending up to 12 h in 1% and 48 h in 2% NaCl media, and acidity of the media did not vary significantly. Cell morphology of all microbes did not change significantly across all treatments. From these results, it was concluded that L. casei, S. cerevisiae and R. palustris are suitable for application in aquaculture ponds with up to 2% salinity.

Abstract. Bamrungpanichtavorn T, Ungwiwatkul S, Boontanom P, Chantarasiri A. 2023. Diversity and cellulolytic activity of cellulase-producing bacteria isolated from the soils of two mangrove forests in Eastern Thailand. Biodiversitas 24: 3891-3902. The Southeast Asian countries hold the largest proportion of the world's mangrove area. Mangrove forests are a potential source for the isolation of economic microbial enzymes. Cellulases are a widely used microbial enzyme for cellulose degradation in various industries. Therefore, this study aimed to isolate, genetically identify, and enzymatically characterize cellulase-producing bacteria from the soils of two mangrove forests in Eastern Thailand. Twenty-six cellulase-producing bacteria were isolated and subsequently genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis of the 16S rRNA genes. Thirteen different RFLP patterns were obtained and genetically analyzed into six bacterial genera comprising Aeromonas, Bacillus, Chryseobacterium, Lysinibacillus, Pseudomonas, and Vibrio. The Bacillus species were the predominant cellulase-producing bacteria in the study sites. Moreover, the cellulase-producing Chryseobacterium and Lysinibacillus had hardly ever been reported. The Bacillus sp. strain RY08B was the most active cellulase-producing bacterium with 1.510±0.060 U/mL of CMCase activity. The optimum temperature and pH for the CMCase activity were determined to be 50°C at a pH of 7.0 with a thermal stability range of 25-50°C at a pH of 7.0. This bacterium could be applied in several environmentally friendly industries requiring mild conditions for their production processes.

Synthetic Biology and the U.S. Biotechnology Regulatory System: Challenges and Options Sarah R. Carter, Ph.D., J. Craig Venter Institute; Michael Rodemeyer, J.D., University of Virginia; Michele S. Garfinkel, Ph.D., EMBO; Robert M. Friedman, Ph.D., J. Craig Venter Institute In recent years, a range of genetic engineering techniques referred to as “synthetic biology” has significantly expanded the tool kit available to scientists and engineers, providing them with far greater capabilities to engineer organisms than previous techniques allowed. The field of synthetic biology includes the relatively new ability to synthesize long pieces of DNA from chemicals, as well as improved methods for genetic manipulation and design of genetic pathways to achieve more precise control of biological systems. These advances will help usher in a new generation of genetically engineered microbes, plants, and animals. The JCVI Policy Center team, along with researchers at the University of Virginia and EMBO, examined how well the current U.S. regulatory system for genetically engineered products will handle the near-term introduction of organisms engineered using synthetic biology. In particular, the focus was on those organisms intended to be used or grown directly in the environment, outside of a contained facility. The study concludes that the U.S. regulatory agencies have adequate legal authority to address most, but not all, potential environmental, health and safety concerns posed by these organisms. Such near-term products are likely to represent incremental changes rather than a marked departure from previous genetically engineered organisms. However, the study also identified two key challenges for the regulatory system, which are detailed in the report. First, USDA’s authority over genetically engineered plants depends on the use of an older engineering technique that is no longer necessary for many applications. The shift to synthetic biology and other newer genetic engineering techniques will leave many engineered plants without any pre-market regulatory review. Second, the number and diversity of engineered microbes for commercial use will increase in the near future, challenging EPA’s resources, expertise, and perhaps authority to regulate them. For each of these challenges, the report sets out a series of options, including an analysis of the advantages and disadvantages of each option from a variety of perspectives, for policy makers to consider. Policy responses will depend on the trade-offs chosen among competing considerations. This report, funded by the Department of Energy with additional funds from the Alfred P. Sloan Foundation, is the result of a two-year process that included interviews, commissioned background papers, discussions, and two workshops that sought input from a wide range of experts, including U.S. federal agency regulators, legal and science policy experts, representatives from the biotechnology indus¬try, and non-governmental organiza¬tions. This cross-section of views informed this report, but the conclusions are solely those of the authors. An Executive Summary, full Report, and background papers are available at: http://www.jcvi.org/cms/research/projects/synthetic-biology-and-the-us-biotechnology-regulatory-system/overview/

Synthetic biology aims at the rational design and construction of devices, systems and organisms with desired functionality based on modular well-characterized biological building blocks. Based on first proof-of-concept studies in bacteria a decade ago, synthetic biology strategies have rapidly entered mammalian cell technology providing novel therapeutic solutions. Here we review how biological building blocks can be rewired to interactive regulatory genetic networks in mammalian cells and how these networks can be transformed into open- and closed-loop control configurations for autonomously managing disease phenotypes. In the second part of this tutorial review we describe how the regulatory biological sensors and switches can be transferred from mammalian cell synthetic biology to materials sciences in order to develop interactive biohybrid materials with similar (therapeutic) functionality as their synthetic biological archetypes. We develop a perspective of how the convergence of synthetic biology with materials sciences might contribute to the development of truly interactive and adaptive materials for autonomous operation in a complex environment.

Review: 83 refs.

With the increasing sustainability challenges, synthetic biology is offering new possibilities for addressing the emerging problems through the cultivation and fermentation of mushrooms. In this perspective, we aim to provide an overview on the research and applications mushroom synthetic biology, emphasizing the need for increased attention and inclusion of this rapidly advancing field in future mushroom technology over China and other countries. By leveraging synthetic biology, mushrooms are expected to play a more versatile role in various area, including traditional fields like circular economy, human wellness and pharmaceutics, as well as emerging fields like vegan meat, mushroom-based materials and pollution abatement. We are confident that these efforts using synthetic biology strategies have the potential to strengthen our capacity to effectively address sustainable challenges, leading to the development of a more sustainable social economy and ecology.

Host gut-derived Bacillus probiotics supplementation improves growth performance, serum and liver immunity, gut health, and resistive capacity against Vibrio harveyi infection in hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus)