The putative functions of lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment

Genome characterization of a multi-drug resistant Escherichia coli strain, L1PEag1, isolated from commercial cape gooseberry fruits (Physalis peruviana L.)

Introduction

Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question.

Methods

This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes.

Results

The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood).

Conclusion

Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.

Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts

Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.

A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems

Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.

Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters

Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under lysogen-induced and non-induced treatments. The lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Alteromonadaceae, and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.