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1. Phage-Encoded Sigma Factors Alter Bacterial Dormancy

   https://doi.org/10.1128/msphere.00297-22  

   Schwartz, D. A.; Lehmkuhl, B. K.; Lennon, J. T. (August 2022, mSphere)

   Imperiale, Michael J. (Ed.)

   ABSTRACT By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to tolerate suboptimal conditions that would otherwise reduce their fitness. Dormancy may also benefit bacteria by serving as a refuge from parasitic infections. Here, we focus on dormancy in the Bacillota , where endospore development is transcriptionally regulated by the expression of sigma factors. A disruption of this process could influence the survivorship or reproduction of phages that infect spore-forming hosts with implications for coevolutionary dynamics. We characterized the distribution of sigma factors in over 4,000 genomes of diverse phages capable of infecting hosts that span the bacterial domain. From this, we identified homologs of sporulation-specific sigma factors in phages that infect spore-forming hosts. Unlike sigma factors required for phage reproduction, we provide evidence that sporulation-like sigma factors are nonessential for lytic infection. However, when expressed in the spore-forming Bacillus subtilis , some of these phage-derived sigma factors can activate the bacterial sporulation gene network and lead to a reduction in spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate a complex and ancient trait in one of the most abundant cell types on Earth. IMPORTANCE As obligate parasites, phages exert strong top-down pressure on host populations with eco-evolutionary implications for community dynamics and ecosystem functioning. The process of phage infection, however, is constrained by bottom-up processes that influence the energetic and nutritional status of susceptible hosts. Many phages have acquired auxiliary genes from bacteria, which can be used to exploit host metabolism with consequences for phage fitness. In this study, we demonstrate that phages infecting spore-forming bacteria carry homologs of sigma factors, which their hosts use to orchestrate gene expression during spore development. By tapping into regulatory gene networks, phages may manipulate the physiology and survival strategies of nongrowing bacteria in ways that influence host-parasite coevolution. 

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2. Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems

   https://doi.org/10.1146/annurev-virology-091919-075914  

   Koskella, Britt; Hernandez, Catherine A.; Wheatley, Rachel M. (September 2022, Annual Review of Virology)

   Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. 

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3. Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

   https://doi.org/10.3390/v15020581  

   Dart, Emily; Fuhrman, Jed A.; Ahlgren, Nathan A. (February 2023, Viruses)

   Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage–host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle—virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage–host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models. 

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4. Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters

   https://doi.org/10.3389/fmars.2021.764383  

   Giebel, Helge-Ansgar; Arnosti, Carol; Badewien, Thomas H.; Bakenhus, Insa; Balmonte, John Paul; Billerbeck, Sara; Dlugosch, Leon; Henkel, Rohan; Kuerzel, Birgit; Meyerjürgens, Jens; et al (December 2021, Frontiers in Marine Science)

   The Pacific Ocean constitutes about half of the global oceans and thus microbial processes in this ocean have a large impact on global elemental cycles. Despite several intensely studied regions large areas are still greatly understudied regarding microbial activities, organic matter cycling and biogeography. Refined information about these features is most important to better understand the significance of this ocean for global biogeochemical and elemental cycles. Therefore we investigated a suite of microbial and geochemical variables along a transect from the subantarctic to the subarctic Pacific in the upper 200 m of the water column. The aim was to quantify rates of organic matter processing, identify potential controlling factors and prokaryotic key players. The assessed variables included abundance of heterotrophic prokaryotes and cyanobacteria, heterotrophic prokaryotic production (HPP), turnover rate constants of amino acids, glucose, and acetate, leucine aminopeptidase and β-glucosidase activities, and the composition of the bacterial community by fluorescence in situ hybridization (FISH). The additional quantification of nitrate, dissolved amino acids and carbohydrates, chlorophyll a , particulate organic carbon and nitrogen (POC, PON) provided a rich environmental context. The oligotrophic gyres exhibited the lowest prokaryotic abundances, rates of HPP and substrate turnover. Low nucleic acid prokaryotes dominated in these gyres, whereas in temperate and subpolar regions further north and south, high nucleic acid prokaryotes dominated. Turnover rate constants of glucose and acetate, as well as leucine aminopeptidase activity, increased from (sub)tropical toward the subpolar regions. In contrast, HPP and bulk growth rates were highest near the equatorial upwelling and lowest in the central gyres and subpolar regions. The SAR11 clade, the Roseobacter group and Flavobacteria constituted the majority of the prokaryotic communities. Vertical profiles of the biogeochemical and microbial variables markedly differed among the different regions and showed close covariations of the microbial variables and chlorophyll a , POC and PON. The results show that hydrographic, microbial, and biogeochemical properties exhibited distinct patterns reflecting the biogeographic provinces along the transect. The microbial variables assessed contribute to a better and refined understanding of the scales of microbial organic matter processing in large areas of the epipelagic Pacific beyond its well-studied regions. 

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5. Multispecies biofilm architecture determines bacterial exposure to phages

   https://doi.org/10.1371/journal.pbio.3001913  

   Winans, James B.; Wucher, Benjamin R.; Nadell, Carey D. (December 2022, PLOS Biology)

   Barr, Jeremy J. (Ed.)

   Numerous ecological interactions among microbes—for example, competition for space and resources, or interaction among phages and their bacterial hosts—are likely to occur simultaneously in multispecies biofilm communities. While biofilms formed by just a single species occur, multispecies biofilms are thought to be more typical of microbial communities in the natural environment. Previous work has shown that multispecies biofilms can increase, decrease, or have no measurable impact on phage exposure of a host bacterium living alongside another species that the phages cannot target. The reasons underlying this variability are not well understood, and how phage–host encounters change within multispecies biofilms remains mostly unexplored at the cellular spatial scale. Here, we study how the cellular scale architecture of model 2-species biofilms impacts cell–cell and cell–phage interactions controlling larger scale population and community dynamics. Our system consists of dual culture biofilms ofEscherichia coliandVibrio choleraeunder exposure to T7 phages, which we study using microfluidic culture, high-resolution confocal microscopy imaging, and detailed image analysis. As shown previously, sufficiently mature biofilms ofE.colican protect themselves from phage exposure via their curli matrix. Before this stage of biofilm structural maturity,E.coliis highly susceptible to phages; however, we show that these bacteria can gain lasting protection against phage exposure if they have become embedded in the bottom layers of highly packed groups ofV.choleraein co-culture. This protection, in turn, is dependent on the cell packing architecture controlled byV.choleraebiofilm matrix secretion. In this manner,E.colicells that are otherwise susceptible to phage-mediated killing can survive phage exposure in the absence of de novo resistance evolution. While co-culture biofilm formation withV.choleraecan confer phage protection toE.coli, it comes at the cost of competing withV.choleraeand a disruption of normal curli-mediated protection forE.colieven in dual species biofilms grown over long time scales. This work highlights the critical importance of studying multispecies biofilm architecture and its influence on the community dynamics of bacteria and phages. 

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