The layered costs and benefits of translational redundancy.

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species' evolutionary history with feasts and famines.

Translation is the process by which cellular machines called ribosomes use the information encoded in genes to make proteins . Every organism requires two types of RNA molecules to make new proteins: ribosomal RNAs (rRNAs, which form part of the ribosome) and transfer RNAs (tRNAs, which transport the amino acid molecules that form proteins to the ribosomes). These RNA molecules are coded in the genome, but different organisms have different 'copy numbers': some genomes contain just a few copies of each of these genes, while others have thousands. This apparent redundancy ­ the presence of several copies of the same gene ­ is puzzling because it is costly to make and maintain DNA and RNA. This leads to an important question: how does redundancy in these important genes (coding for tRNAs and rRNAs) evolve? The answer is key to understanding how one of the most fundamental cellular processes, the making of proteins from DNA, has evolved. A possible reason for organisms to have many copies of the genes required to make proteins is to allow rapid translation, which allows cells to divide faster, and populations of cells to grow more quickly. However, this would likely mean that, when nutrients are scarce, carrying and translating many copies of the same gene would become a burden on the cell. Raval et al. set out to test this idea by measuring the costs and benefits of seemingly redundant translation components. To do this, Raval et al. deleted some of the redundant gene copies in the bacterium Escherichia coli and asked if that changed bacterial growth. The experiments showed that when nutrients were plentiful, cells with more copies of the genes (high redundancy) were better able to use the nutrients and divide rapidly. However, when nutrients were limited, bacteria with extra gene copies divided more slowly, showing that the extra genes are indeed a big burden on the cell. Raval et al. propose that nutrients available in the environment ultimately determine whether redundancy of the translation machinery is a blessing or a curse. This suggests that the redundancy and underlying growth strategies of different organisms are forged by their experiences of feast and famine during their evolutionary past. Importantly, by testing the joint effect of many different molecules involved in translation, Raval et al. uncovered several strategies that may maximize bacterial growth and protein production. Their results could thus be useful for optimizing the synthesis of important products that use growing cells as factories ­ from beer to insulin ­ where the rate of growth is critical.

Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches.

The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level.

Questioning the source of identified non-foodborne pathogens from food-contact wooden surfaces used in Hong Kong's urban wet markets.

In this study, a phylogenic analysis was performed on pathogens previously identified in Hong Kong wet markets' cutting boards. Phylogenetic comparisons were made between phylotypes obtained in this study and environmental and clinical phylotypes for establishing the possible origin of selected bacterial species isolated from wet market cutting board ecosystems. The results reveal a strong relationship between wet market bacterial assemblages and environmental and clinically relevant phylotypes. However, our poor knowledge of potential cross-contamination sources within these wet markets is further exacerbated by failing to determine the exact or presumed origin of its identified pathogens. In this study, several clinically relevant bacterial pathogens such as Klebsiella pneumoniae, Streptococcus suis and Streptococcus porcinus were linked to cutting boards associated with pork; Campylobacter fetus, Staphylococcus aureus, Escherichia coli, and A. caviae in those associated with poultry; and Streptococcus varanii, A. caviae, Vibrio fluvialis, and Vibrio parahaemolyticus in those associated with seafood. Identifying non-foodborne clinically relevant pathogens in wet market cutting boards in this study confirms the need for safety approaches for wet market meat, including cold storage. The presented study justifies the need for future systematic epidemiological studies to determine identified microbial pathogens. Such studies should bring about significant improvements in the management of hygienic practices in Hong Kong's wet markets and work towards a One Health goal by recognizing the importance of wet markets as areas interconnecting food processing with animal and clinical environments.

Exploring the optimization of aerobic food waste digestion efficiency through the engineering of functional biofilm Bio-carriers.

The possibility of breaking down cellulose-rich food waste through biofilm engineering was investigated. Six previously isolated strains from naturally degrading fruits and vegetables, screened for biofilm-forming ability and cellulolytic activity, were selected to enrich a biocarrier seeding microbial consortium. The food waste model used in this study was cabbage which was aerobically digested under repeated water rinsing and regular effluent drainage. The engineered biocarrier biofilm's functionality was evaluated by tracing microbial succession following metagenomic sequencing, quantitative PCR, scanning electron microscopy, and cellulolytic activity before and after the digestion processes. The engineered microbial consortium demonstrated superior biofilm-forming ability on biocarriers than the original microbial consortium and generally displayed a higher cellulolytic activity. The presented study provides one of the few studies of food waste aerobic digestion using engineered biofilms. Insights presented in this study could help further optimize aerobic food waste digestion.

Effects of sodium citrate on the structure and microbial community composition of an early-stage multispecies biofilm model.

In recent years, most biofilm studies have focused on fundamental investigations using multispecies biofilm models developed preferentially in simulated naturally occurring low-nutrient medium than in artificial nutrient-rich medium. Because biofilm development under low-nutrient growth media is slow, natural media are often supplemented with an additional carbon source to increase the rate of biofilm formation. However, there are knowledge gaps in interpreting the effects of such supplementation on the resulting biofilm in terms of structure and microbial community composition. We investigated the effects of supplementation of a simulated freshwater medium with sodium citrate on the resulting structure, bacterial community composition, and microbial network interactions of an early-stage multispecies biofilm model. Qualitative and quantitative analyses of acquired confocal laser scanning microscopy data confirmed that sodium citrate supplementation distinctly increased biofilm biomass. Sequencing data revealed that the microbial community structure of biofilms grown in sodium citrate-supplemented conditions was characterized with increased relative abundance and dominance of Proteobacteria compared with that of biofilms grown in sodium citrate-free conditions. Our findings suggest that the supplementation of a low-nutrient medium with a carbon source in experiments involving multispecies biofilms may lead to structural and compositional biases of the microbial community, causing changes in biofilm phenotype.

Impacts of Wet Market Modernization Levels and Hygiene Practices on the Microbiome and Microbial Safety of Wooden Cutting Boards in Hong Kong.

Accessing food through wet markets is a common global daily occurrence, where fresh meat can be purchased to support an urbanizing world population. Similar to the wet markets in many other metropolitan cities in Asia, Hong Kong wet markets vary and are characterized by differing hygiene routines and access to essential modern technologies. The lack of risk assessments of food contact surfaces in these markets has led to substantial gaps in food safety knowledge and information that could help improve and maintain public health. Microbial profiling analyses were conducted on cutting boards that had been used to process pork, poultry, and seafood at 11 different wet markets. The markets differed in hygiene protocols and access to modern facilities. Irrespective of whether wet markets have access of modern infrastructure, the hygiene practices were largely found to be inefficient based on the prevalence of bacterial species typically associated with foodborne pathogens such as Campylobacter fetus, Clostridium perfringens, Staphylococcus aureus, and Vibrio parahaemolyticus; indicator organisms such as Escherichia coli; as well as nonfoodborne pathogenic bacterial species potentially associated with nosocomial infections, such as Klebsiella pneumoniae and Enterobacter cloacae. Other Vibrio species, V. parahaemolyticus and V. vulnificus, typically associated with contaminated raw or undercooked seafood with the potential to cause illness in humans, were also found on wooden cutting boards. This study indicated that the hygienic practices used in Hong Kong wet markets are not sufficient for preventing the establishment of spoilage or pathogenic organisms. This study serves as a basis to review current hygiene practices in wet markets and provides a framework to reassess existing safety protocols.

Could benthic biofilm analyses be used as a reliable proxy for freshwater environmental health?

The quality of freshwater undoubtedly reflects the health of our surrounding environment, society, and economy, as these are supported by various freshwater ecosystems. Monitoring efforts have therefore been considered a vital means of ensuring the ecological health of freshwater environments. Nevertheless, most aquatic environmental monitoring strategies largely focus on bulk water sampling for analysis of physicochemical and key biological indicators, which for the most part do not consider pollution events that occur at any time between sampling events. Because benthic biofilms are ubiquitous in aquatic environments, pollution released during sporadic events may be absorbed by these biofilms, which can act as repositories of pollutants. The aim of this study was to assess whether benthic biofilm monitoring could provide an efficient way of properly characterizing the extent of pollution in aquatic environments. Here, bulk water and benthic biofilms were sampled from three Hong Kong streams having various pollution profiles, and subsequently compared via high-resolution microscopy, metagenomic analysis, and analytical chemistry. The results indicated that biofilms were, indeed, reservoirs of environmental pollutants, having different profiles compared with that of the corresponding bulk water samples. Moreover, the results also suggested that biofilms sampled in polluted areas were characterized by a higher species richness. While the analytical testing of benthic biofilms still needs further development, the integration of chemical-pollutant profiles and biofilm sequencing data in future studies may provide unique perspectives for understanding and identifying pollution-related biofilm biomarkers.

A Field Study Into Hong Kong's Wet Markets: Raised Questions Into the Hygienic Maintenance of Meat Contact Surfaces and the Dissemination of Microorganisms Associated With Nosocomial Infections.

Millions every day purchase their raw meat in wet markets around the globe, especially in Hong Kong city, where modern and a traditional way of living is made possible. While food hygiene standards in Hong Kong have more recently focused on the safety of meat sold in these wet markets, the hygienic surface level of wooden cutting boards used for processing meats is seldom observed. This original study performed microbial community profiling, as well as isolating and identifying various strains multiple wooden cutting boards from nine wet markets located on Hong Kong Island. Our study also investigated the efficiency of scraping the surface of cutting boards as a traditional cleaning technique in Hong Kong. Results indicate that these hygienic practices are inefficient for guarantying proper surface hygiene as some most tested cutting boards were found to harbor microbial species typically associated with hospital nosocomial infections, such as Klebsiella pneumoniae. Further analysis also led to discovering the presence of antibiotic-resistant genes (ARGs) among isolated strains. Our results showcase the significance and effects of cross-contamination in Hong Kong wet markets, especially with regards to the potential spreading of clinically-relevant strains and ARGs on food processing surfaces. This study should, therefore, serve as a basis to review current hygienic practices in Hong Kong's wet market on a larger scale, thereby improving food safety and ultimately, public health.