Antimicrobials are essential for combating infectious diseases. However, an increase in resistance to them is a major cause of concern. The empirical use of drugs in managing COVID-19 and the associated secondary infections have further exacerbated the problem of antimicrobial resistance. Hence, the situation mandates exploring and developing efficient alternatives for the treatment of bacterial and fungal infections in patients suffering from COVID-19 or other viral infections. In this review, we have described the alternatives to conventional antimicrobials that have shown promising results and are at various stages of development. An acceleration of efforts to investigate their potential as therapeutics can provide more treatment options for clinical management of drug-resistant secondary bacterial and fungal infections in the current pandemic and similar potential outbreaks in the future. The alternatives include bacteriophages and their lytic enzymes, anti-fungal enzymes, antimicrobial peptides, nanoparticles and small molecule inhibitors among others. What is required at this stage is to critically examine the challenges in developing the listed compounds and biomolecules as therapeutics and to establish guidelines for their safe and effective application within a suitable time frame. In this review, we have attempted to highlight the importance of rational use of antimicrobials in patients suffering from COVID-19 and boost the deployment of alternative therapeutics.

Summary: The antagonistic bacterium Pseudomonas protegens secretes the cyclic lipopeptide (CLiP) orfamide A, which triggers a Ca²⁺ signal causing rapid deflagellation of the microalga Chlamydomonas reinhardtii. We performed chemical synthesis of orfamide A derivatives and used an aequorin reporter line to measure their Ca²⁺ responses. Immobilization of algae was studied using a modulator and mutants of transient receptor potential (TRP)‐type channels. By investigating targeted synthetic orfamide A derivatives, we found that N‐terminal amino acids of the linear part and the terminal fatty acid region are important for the specificity of the Ca²⁺‐signal causing deflagellation. Molecular editing indicates that at least two distinct Ca²⁺‐signaling pathways are triggered. One is involved in deflagellation (Thr³ change, fatty acid tail shortened by 4C), whereas the other still causes an increase in cytosolic Ca²⁺ in the algal cells, but does not cause substantial deflagellation (Leu¹ change, fatty acid hydroxylation, fatty acid changes by 2C). Using mutants, we define four TRP‐type channels that are involved in orfamide A signaling; only one (ADF1) responds additionally to low pH. These results suggest that the linear part of the CLiP plays one major role in Ca²⁺ signaling, and that orfamide A uses a network of algal TRP‐type channels for deflagellation.

Bacteriophages, the ubiquitous bacterial viruses, are the most abundant biological entities on Earth. However, information regarding the impact of environmental factors on the genetic makeup of phages is scarce. Based on the analysis of genomes of 45 phage isolates from different ecosystems we demonstrate a significant ( p < 0.0001) positive correlation of the number of structural genes and their placement in above-average guanine-cytosine (GC) content of the genome. This feature appears to be more evident in isolates from deep-sea and sea-ice environments compared to desert and Baltic Sea slick, indicating a potential ecosystem-based factor (although insignificant due to low sample size). Additionally, the percentage of structural genes in above-average GC regions was found to be significantly ( p = 0.0038) negatively correlated with the genome size of the phages and significantly ( p = 0.0266) positively correlated with the overall GC for phage genomes > 50 kb, but not for genomes < 50 kb ( p = 0.556). We therefore propose a relationship of structural genes and GC content, a property that may influence the adaptation and evolution of phages in various environmental niches.

Studying airborne viral diversity in pristine, remote environments like the sub-Antarctic island South Georgia provides crucial insights into viral ecology and their role in sustaining unique ecosystems. Viruses influence microbial dynamics and nutrient cycles, which are vital for ecological balance and long-term ecosystem sustainability. We explored the community composition of airborne viral operational taxonomic units (vOTUs) of two sites in South Georgia, using various sampling devices and viral metagenomics. The Coriolis µ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were from sea-level samples, indicating that location impacts viral diversity. Protein-based clustering of 39 vOTUs revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the island's airborne viral community. Genes related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed in the major oceans, emphasizing the potential resilience in changing climates. Host predictions indicated associations with bacterial genera like Rickettsia, Myroides, and Bacteroidota. Some vOTUs matched viruses from extremophiles, indicating adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems, underscoring the need for continued monitoring in the face of environmental change.

Clouds have been regarded as atmospheric oasis for microbes including psychrophilic bacteria (Delort et al., 2017; Péguilhan et al., 2023). However, adaptations of bacteria to the cloud environment and interactions with viruses are not fully understood. In this study, cloudwater was sampled with six compact Caltech active strand cloud water collectors (Demoz et al., 1996) on the Mount Verde, a mountain of 744 m height on the São Vicente island in the tropical Atlantic Ocean (van Pinxteren et al., 2020) and stored frozen. From iron-flocculated and filtered cloudwater samples, DNA was short-read sequenced for metagenomics, and 24 bacteria were additionally isolated from these samples on Luria-Bertani (LB) and Reasoner's 2A (R2A) agar. After purification, the bacterial DNA was subjected to whole-genome sequencing, revealing a diverse array of microbial taxa. The isolate genomes were identified as belonging to Gram-positive species, including Agrococcus sp., Alkalihalobacillus_A gibsonii_A, Arthrobacter sp., Bacillus spizizenii, Cytobacillus oceanisediminis, Curtobacterium spp., Deinococcus sp., Micrococcus luteus, and Rossellomorea spp., as well as Gram-negative species such as Paracoccus marcusii, and Sphingomonas sp. This microbial diversity highlights the presence of spore-forming, halotolerant, and marine-associated bacteria in cloudwater. The genomes had an average GC content of 58.3% (range 41% – 73%) and encoded for cold-shock genes probably supporting survival during sample freezing and in supercooled cloudwater. The presence of 24 prophages and a diverse arsenal of antiviral defense systems, including adaptive CRISPR immunity targeting viral operational taxonomic units (vOTUs), indicates ongoing bacterial-viral interactions in cloudwater. On average, bacterial strains encoded for five defense systems, with restriction-modification systems being the most common. Interestingly, the isolated strain Sphingomonas sp. MPC37 encoded for the highest number of defense systems (12), indicating its potential ecological significance in this unique environment. Metagenomic sequencing identified 458 vOTUs, with major bacterial hosts predicted as Sphingomonas spp. (75 vOTUs), Deinococcus spp. (15), Novosphingobium spp. (14), and Methylobacterium spp. (13). Analysis of air mass trajectories for the cloudwater suggests a marine origin for certain samples, which were associated with the highest counts of both unique and total vOTUs. We also find genetic variability within a population of closely related viruses (microdiversity). Viral variants arise sequentially during different cloud events and are shared among temporally proximate events. Our results reveal clouds as dynamic microbial and viral ecosystems with complex survival strategies and interactions.ReferencesDelort, A. M., Vaïtilingom, M., Joly, M., … & Deguillaume, L. (2017). Clouds: a transient and stressing habitat for microorganisms. Microbial ecology of extreme environments, 215-245. https://doi.org/10.1007/978-3-319-51686-8_10Demoz, B. B., Collett, J. L., & Daube, B. C. (1996). On the Caltech Active Strand Cloudwater Collectors. Atmospheric Research, 41(1), 47-62. https://doi.org/10.1016/0169-8095(95)00044-5Péguilhan, R., Rossi, F., Joly, M., … & Amato, P. (2023). Clouds, oases for airborne microbes – Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situations. bioRxiv, 2023.2012.2014.571671. https://doi.org/10.1101/2023.12.14.571671van Pinxteren, M., Fomba, K. W., Triesch, N., . . . & Herrmann, H. (2020). Marine organic matter in the remote environment of the Cape Verde islands – an introduction and overview to the MarParCloud campaign. Atmos. Chem. Phys., 20(11), 6921-6951. https://doi.org/10.5194/acp-20-6921-2020