Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS

The right tool for the job: Chemical biology and microbiome science

Microbiomes exist in ecological niches ranging from the ocean and soil to inside of larger organisms like plants and animals. Within these niches, microbes play key roles in biochemical processes that impact larger phenomena, such as biogeochemical cycling or health. By understanding of how these processes occur at the molecular level, it may be possible to develop new interventions to address global problems. The complexity of these systems poses challenges to more traditional techniques. Chemical biology can help overcome these challenges by providing tools that are broadly applicable and can obtain molecular-level information about complex systems. This primer is intended to serve as a brief introduction to chemical biology and microbiome science, to highlight some of the ways that these two disciplines complement each other, and to encourage dialog and collaboration between these fields.

Microbial single-cell applications under anoxic conditions

The field of microbiology traditionally focuses on studying microorganisms at the population level. Nevertheless, the application of single-cell level methods, including microfluidics and imaging techniques, has revealed heterogeneity within populations, making these methods essential to understand cellular activities and interactions at a higher resolution. Moreover, single-cell sorting has opened new avenues for isolating cells of interest from microbial populations or complex microbial communities. These isolated cells can be further interrogated in downstream single-cell "omics" analyses, providing physiological and functional information. However, applying these methods to study anaerobic microorganisms under in situ conditions remains challenging due to their sensitivity to oxygen. Here, we review the existing methodologies for the analysis of viable anaerobic microorganisms at the single-cell level, including live-imaging, cell sorting, and microfluidics (lab-on-chip) applications, and we address the challenges involved in their anoxic operation. Additionally, we discuss the development of non-destructive imaging techniques tailored for anaerobes, such as oxygen-independent fluorescent probes and alternative approaches.

High-Throughput Single-Cell Metabolic Labeling, Sorting, and Sequencing of Active Antibiotic-Resistant Bacteria in the Environment

Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified. The percentage and concentration of active ARB ranged from 0.28% to 45.3% and from 1.1 × 104 to 2.09 × 107 cells/mL, respectively. Notably, the final effluents retained up to 4.79 × 104 cells/mL of active ARB. Targeted FACS and genomic sequencing revealed a distinct taxonomic composition of active ARB compared with that of the overall population. The coexistence of antibiotic resistome and mobilome in active ARB was also identified, including three high-quality metagenomic assembly genomes assigned to pathogenic bacteria, highlighting the substantial health risks due to their activity, phenotypic resistance, mobility, and pathogenicity. This study advances our understanding of previously overlooked active ARB in the environment by linking their resistance phenotype to their genotype. This high-throughput method will enable efficient quantitative surveillance of active AMR, providing valuable insights into risk control and management.

Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation

The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.

Combined Phototrophic Simultaneous Nitrification-Endogenous Denitrification with Phosphorus Removal (P-SNDPR) System Treating Low Carbon to Nitrogen Ratio Wastewater for Potential Carbon Neutrality

Conventional biological nutrient removal processes rely on external aeration and produce significant carbon dioxide (CO2) emissions. This study constructed a phototrophic simultaneous nitrification-denitrification phosphorus removal (P-SNDPR) system to treat low carbon to nitrogen (C/N) ratios wastewater and investigated the impact of sludge retention time (SRT) on nutrient removal performance, nitrogen conversion pathway, and microbial structure. Results showed that the P-SNDPR system at SRT of 15 days had the highest nutrient removal capacity, achieving over 85% and 98% removal of nitrogen and phosphorus, respectively, meanwhile maintaining minimal CO2 emissions. Nitrogen removal was mainly through assimilation at SRTs of 5 and 10 days, and nitrification-denitrification at SRTs of 15 and 20 days. Stable partial nitrification was facilitated by photoinhibition and low DO levels. Flow cytometry sorting technique results revealed SRT drove community structural changes in translational activity (BONCAT+) microbes, where BONCAT+ microbes were mainly simultaneous nitrogen and phosphorus removal bacteria (Candidatus Accumulibacter), denitrifying bacteria (Candidatus Competibacter and Plasticicumulans), ammonia-oxidizing bacteria (Nitrosomonas), and microalgae (Chlorella and Dictyosphaerium). The P-SNDPR system represents a novel, carbon-neutral process for efficient nutrient removal from low C/N ratio wastewater without aeration and external carbon source additions.

Applications and opportunities of click chemistry in plant science

The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.

The successful application of light to the system of simultaneous nitrification/endogenous denitrification and phosphorus removal: Promotion of partial nitrification and glycogen accumulation metabolism

Partial nitrification (PN) and high glycogen accumulating metabolism (GAM) activity are the basis for efficient nitrogen (N) and phosphorus (P) removal in simultaneous nitrification endogenous denitrification and phosphorus removal (SNDPR) systems. However, achieving these processes in practical operations is challenging. This study proposes that light irradiation is a novel strategy to enhance the nutrient removal performance of the SNDPR system with low carbon to nitrogen ratios (C/N of 3.3-4.1) domestic wastewater. Light energy densities (Es) of 55-135 J/g VSS were found to promote the activity of ammonia-oxidizing bacteria (AOB) and GAM, while inhibiting the activity of nitrite-oxidizing bacteria (NOB) and polyphosphate accumulating metabolism (PAM). Long-term exposure to different light patterns at Es of 55-135 J/g VSS revealed that continuous light rapidly achieved PN by inhibiting NOB activity and promoted the growth of glycogen accumulating organisms (GAOs), allowing the removal of above 82 % N and below 80 % P. Intermittent light maintained stable PN by inhibiting the activity and growth of NOB and promoted the growth of polyphosphate accumulating organisms (PAOs) with high GAM activity (Accmulibacer IIC-ii and IIC-iii), allowing the removal of above 82 % N and 95 % P. Flow cytometry and enzyme activity assays showed that light promoted GAM-related enzyme activity and the metabolic activity of partial Accmulibacer II over other endogenous denitrifying bacteria, while inhibiting NOB translation activity. These findings provide a new approach for enhancing nutrient removal, especially for achieving PN and promoting GAM activity, in SNDPR systems treating low C/N ratio domestic wastewater using light irradiation.

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.

Opportunities in optical and electrical single-cell technologies to study microbial ecosystems

New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

Using click chemistry to study microbial ecology and evolution

Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.

Plastic-microbe interaction in the marine environment: Research methods and opportunities

Approximately 9 million metric tons of plastics enters the ocean annually, and once in the marine environment, plastic surfaces can be quickly colonised by marine microorganisms, forming a biofilm. Studies on plastic debris-biofilm associations, known as plastisphere, have increased exponentially within the last few years. In this review, we first briefly summarise methods and techniques used in exploring plastic-microbe interactions. Then we highlight research gaps and provide future research opportunities for marine plastisphere studies, especially, on plastic characterisation and standardised biodegradation tests, the fate of "environmentally friendly" plastics, and plastisphere of coastal habitats. Located in the tropics, Southeast Asian (SEA) countries are significant contributors to marine plastic debris. However, plastisphere studies in this region are lacking and therefore, we discuss how the unique environmental conditions in the SEA seas may affect plastic-microbe interaction and why there is an imperative need to conduct plastisphere studies in SEA marine environments. Finally, we also highlight the lack of understanding of the pathogenicity and ecotoxicological effects of plastisphere on marine ecosystems.