Biology subjects

Carlson, H. K.

Publications and source records attributed to Carlson, H. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Chemical stressors differentially induce prophage replication in Acinetobacter baumannii strains

Prophages are prevalent genomic elements that profoundly shape microbial communities by controlling host bacterial populations through lysis or enabling genetic recombination via transduction. Standard induction protocols rely heavily on DNA-damaging agents like mitomycin C, failing to capture the complex chemical landscapes bacteria encounter in natural and clinical settings where diverse environmental insults trigger excision. Furthermore, the regulatory variations governing polylysogenic hosts containing multiple co-habiting prophages under identical stressors remain largely uncharacterized. In this study, we surveyed a panel of five clinical Acinetobacter baumannii strains containing zero to four resident prophages against a library of 57 diverse chemical stressors. We demonstrate that chemical treatments, including distinct classes of antibiotics, drive differential prophage induction patterns across different host backgrounds. This could lead to a greater understanding of the importance of prophages in antibiotic treatment regimes.

microbiology↗

bioRxiv2026

Genome-wide fitness profiling reveals flagellar rotation as an energetic liability during anaerobic maintenance in Pseudomonas aeruginosa

Bacteria in nature and disease frequently spend time in non-growing states, yet the genes that allow cells to survive without growing remain poorly understood. Using Pseudomonas aeruginosa strain PA14 as a model system to study non-growth powered by anaerobic phenazine cycling, we employed randomly barcoded transposon-insertion sequencing (RB-TnSeq) to identify the genes required for this maintenance state using a platform that sustains anaerobic survival via continuous phenazine reoxidation. We found 167 genes whose disruption altered survival, including genes involved in transcription, translation, protein quality control, and cell envelope maintenance. Comparing our results to published TnSeq data from other forms of energy-limited growth arrest (conditions where electron acceptor or carbon availability constrains energy conservation below that required for cell growth/division) in PA14 revealed that while a subset of genes are fitness determinants across distinct growth-arrested states, most are condition-specific. Notably, genes involved in flagellar regulation and assembly were broadly detrimental to survival under this maintenance condition. Leveraging a high-throughput electrochemical system that allows for quantitative and mechanistic dissection of the phenazine cycling-dependent maintenance state, we found that flagellar abundance influences cells survival, metabolic rate, and ATP levels. Moreover, removing the flagellar stator proteins MotAC, which are required for flagellar rotation but not assembly, reversed these defects, indicating that the energetic cost of flagella comes from their rotation rather than construction under these conditions. These results show that in a low-powered maintenance state, limiting energy-dissipating processes, such as proton-motive force loss through flagellar rotation, supports cell survival.

microbiology↗

bioRxiv2026

Redirecting carbon and electron flow in methanogenic laboratory scale anaerobic digestors with hypophosphite

In anaerobic digestion, formate is a central electron carrier linking primary and secondary fermentation to methanogenesis. Efforts to alter methane production have largely focused on directly targeting methanogens, while disruption of other trophic levels is underexplored. We recently demonstrated that hypophosphite is a naturally occurring inhibitor of formate exchange in syntrophic methanogenic systems. Here, we investigated whether intercepting formate exchange using hypophosphite can modulate methane production in a complex fermentative methanogenic system and what the longer-term consequences are for the structure and function of the microbiome. Using continuous up-flow anaerobic sludge blanket (UASB) columns fed with whey, we found that 100 M hypophosphite resulted in a transient (17 days) reduction in methane production by 20% to 50%, while carbon and electron flow was redirected towards hydrogen and volatile fatty acids. Accumulation of propionate, butyrate, branched-chain fatty acids, and not acetate indicated disruption of syntrophic formate metabolism. Following recovery of methane production in hypophosphite treated columns, we increased hypophosphite concentrations to millimolar levels and saw no repeated suppression of methane production. 16S rDNA amplicon sequencing revealed that hypophosphite treatment did not cause significant changes to microbiome composition. Methanogenic activity assays revealed a loss of formatotrophic methanogenic capacity in hypophosphite treated columns. Together, these results show that specific inhibition of formate exchange between syntrophs and methanogens decouples fermentative and methanogenic processes without altering microbiome composition with carbon and electron flow to methane ultimately redirected through hydrogen or acetate. This work demonstrates that hypophosphite can intercept syntrophic formate exchange in an engineered system and that long- term treatment with hypophosphite redirects electron flow towards electron carriers other than formate.

microbiology↗

bioRxiv2026

Metagenome-guided substrate selection enriches Terriglobus, reveals co-occurring taxa, and enables isolation of a novel species

Microbes that remain uncultivated occupy nearly every ecosystem on the planet; this is particularly true in soils, where despite their prevalence, the roles of rarely cultivated microbes in driving biogeochemical cycles and ecosystem function remain poorly explored. We combine metagenome-informed substrate selection with enrichment sub-communities to generate reduced-complexity communities that preserve co-occurrence and expand experimental access to underrepresented soil lineages without requiring prior isolation of each member. Carbohydrate-active enzyme (CAZyme) profiles from soil-derived genomes were used to select carbon compounds predicted to enrich difficult to culture taxa, including members of the phylum Acidobacteriota. Based on 16S rRNA amplicon sequencing, we reproducibly enriched Terriglobus (Acidobacteriota) on multiple metagenome-guided substrates. Select communities with consistent presence and varying abundance of Terriglobus were passaged in a longitudinal design to generate 89 metagenomes; genus-level profiling revealed that community composition varied between biological replicates but remained consistent within replicates over time, providing diverse Acidobacteriota-containing configurations for downstream analysis. Association network inference identified a core set of co-occurring taxa that positively tracked with Terriglobus across the longitudinal series. In parallel, the substrate-guided approach led to isolation of a novel Terriglobus species, the first cultured representative of its GTDB species cluster. Together, these results establish a generalizable strategy for generating communities enriched with rarely cultivated taxa, yielding tractable systems for studying microbial interactions and community assembly in soil.

microbiology↗

bioRxiv2026

Hypophosphite is a naturally-occurring selective inhibitor of syntrophic methanogenesis

Microbial methanogenesis is a major contributor to global warming and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still under-explored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with syntrophic electron exchange in methanogenic systems presents an additional target for methane control. Here we show that hypophosphite (H2PO2-), an inorganic formate analog, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively non-toxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate carbon cycling in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive, strategy for methane control in syntrophic methanogenic ecosystems.

microbiology↗

bioRxiv2025

Bioplastic Production Potential of Azospira suillum PS: Growth-Associated PHB Production Under Aerobic and Anaerobic Conditions

Plastics are indispensable in modern society, yet less than 10% of the 380 million tons produced annually are recycled. This accumulation of non-degradable waste has intensified the search for sustainable alternatives. Polyhydroxyalkanoates (PHAs), particularly polyhydroxybutyrate (PHB), are biodegradable polymers produced by microorganisms. Here, we investigate the capacity of Azospira suillum PS, a model facultative perchlorate-reducing bacterium, to synthesize PHB. We show that unlike most organisms, PHB production is growth-associated both aerobically, and anaerobically with perchlorate as an electron acceptor under moderate nitrogen deplete conditions. Genomic analysis revealed four phaC homologs, with one, phaC4, co-localized with phaB and phaR, suggesting a conserved operon. While three of the phaC genes were successfully deleted, phaC4 could not be disrupted, indicating an essential role for growth. Redox profiling revealed a positive correlation between PHB accumulation and NADPH/NADP+ ratios, supporting the role of cytoplasmic reducing equivalents in PHB synthesis. This study presents the first demonstration of PHA production under perchlorate-respiring conditions and one of the few documented cases of growth-associated PHA synthesis. It offers new insights into the genetic and metabolic basis of PHB production in A. suillum PS, underscoring its potential as a platform organism for sustainable, growth-coupled bioplastic production.

microbiology↗

bioRxiv2025

Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture

The anaerobic conversion of organic matter to methane and carbon dioxide typically relies on obligate syntrophic interactions between bacteria and methanogenic archaea, where interspecies hydrogen (H2) transfer enables thermodynamically constrained reactions to proceed near equilibrium. Syntrophs couple the oxidation of fermentation products such as fatty acids and alcohols to the reduction of protons to form H2. These reactions can only proceed if low H2 concentrations are maintained by H2-consuming syntrophic partners. Here, we describe "lithosyntrophy," a novel mode of syntrophic interaction in which electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates. Candidatus Phosphitivorax anaerolimi strain Phox-21 oxidizes phosphite (HPO32-, oxidation state +3) to phosphate coupled to hydrogenogenesis in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Physiology experiments, thermodynamic calculations, genomic annotation, and metaproteomics analysis collectively revealed a mechanism for syntrophic phosphite oxidation in Phox-21, which requires phosphite, acetate, and CO2 as co-substrates. In this pathway, electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase. Unlike previously characterized acetogenic phosphite oxidizers that grow without exogenous acetate, Phox-21 requires acetate to regenerate AMP, a cofactor required by the phosphite dehydrogenase, PtdF. Lithosyntrophic phosphite oxidizers may play important roles both in transferring reducing equivalents as well as biologically available phosphorus to other members of their surrounding microbial communities. We infer that lithosyntrophic DPO emerged before acetoclastic methanogenesis and was a major sink for acetate in the Archaean when phosphite was more abundant. Significance statementDissimilatory phosphite-oxidizing microorganisms (DPOM) use phosphite as an energy source, producing phosphate. While the two previously isolated DPOM couple phosphite oxidation to carbon fixation via the Wood-Ljungdahl pathway, Candidatus Phosphitivorax anaerolimi strain Phox-21 instead performs lithosyntrophic metabolism, coupling DPO to proton reduction in obligate partnership with a hydrogenotrophic methanogen. This establishes a novel link between phosphorus and carbon redox cycles: like organosyntrophy, DPO can fuel methanogenesis. Lithosyntrophy expands our understanding of syntrophic interactions and suggests similar processes may occur with other inorganic substrates in anoxic ecosystems. We propose lithosyntrophic DPO predates acetoclastic methanogenesis, serving as an early acetate sink during the Archaean. Following Earths oxygenation, phosphite depletion likely reduced competition for acetate, enabling the later evolution of acetoclastic methanogenesis.

microbiology↗

bioRxiv2025

Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria

Rice paddies naturally host aerobic methanotrophic bacteria, due to the production of methane in flooded soils. However, relatively little is known about how the activity of methanotrophs impacts the structure of the broader microbial community in this globally important agricultural environment. To address this question, we passaged 51 aerobic microbial enrichment cultures from rice rhizosphere, root, and stem samples in a chemically-defined medium with methane as the primary carbon source and electron donor. We profiled the cultures over time by 16S rRNA gene amplicon sequencing and sequenced the genomes of 40 isolates from the enrichments to gain functional insights. Taxa whose relative abundance increased during community growth on methane represented more than a dozen families, many of which are not known to utilize methane or other one-carbon substrates. Despite the selective pressure imposed by the culture condition, the final community structures were taxonomically varied rather than converging to a common composition. Genomic analysis of the sequenced isolates revealed considerable variation in likely carbon source utilization repertoires, as well as the capacity for nitrogen fixation or denitrification. Taken together, these findings support the view that methanotrophy represents a key link in the microbial food web of rice fields, with the potential for downstream effects on the abundance and activity of a wide range of community members. ImportanceRice paddies produce the primary staple food for more than half of the worlds population, but are also a major source of methane emissions. Methane-oxidizing bacteria known as methanotrophs naturally occur in rice paddies, where they consume methane that would otherwise escape to the atmosphere. Enhancing the activity of native methanotrophs could improve the sustainability of rice cultivation. However, large gaps remain in our knowledge of how increased methanotrophic activity could impact other members of rice paddy microbial communities, leaving open the possibility of unintended effects on other important microbial ecosystem functions, such as nitrogen cycling. This study sheds light on the taxonomic range and metabolic capacities of rice-associated bacteria that can benefit from the activity of native methanotrophs, laying the foundation for a broader understanding of how methanotrophs impact microbiome assembly and nutrient cycling in rice paddies.

microbiology↗

bioRxiv2025

Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes

Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC- preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC preference can be leveraged for predicting and engineering greenhouse gas fluxes and understanding bacterial population dynamics and trait evolution across redox gradients.

microbiology↗

bioRxiv2024

Microbes display broad diversity in cobamide preferences

Cobamides, the vitamin B12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli, Sinorhizobium meliloti, and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms, but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function.

microbiology↗

bioRxiv2024

Insights into the role of dopamine in rhizosphere microbiome assembly

Dopamine plays a critical role in animal physiology and interactions with gut microbes. In plants, dopamine is known to function in plant defense and abiotic stress tolerance; however, its role in mediating plant-microbiome interactions remains unexplored. In this study, we observed that dopamine is one of the most abundant exometabolites with natural variation in root exudates across diverse Brachypodium distachyon lines, suggesting a potential role in rhizosphere microbial assembly. To further investigate this, we colonized ten natural B. distachyon lines with a 16-member bacterial synthetic community (SynCom), collected paired metabolomic and 16S rRNA sequencing data, and performed an association analysis. Our results revealed that dopamine levels in root exudates were significantly associated with the abundance of six SynCom members in a hydroponic system. In vitro growth studies demonstrated that dopamine had a significant effect on the growth of the same six bacterial isolates. Additionally, treating soil directly with dopamine enriched Actinobacteria, consistent with both the SynCom-dopamine correlations and the isolate growth results. Collectively, our study underscores the selective influence of dopamine on rhizosphere microbial communities, with implications for precision microbiome management.

plant biology↗

bioRxiv2024

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly-barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we provide the first evidence that M. maripaludis can utilize the nitrogen sources L-glutamine, D-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP, group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale dataset that can be used as a resource to further understand gene function and metabolism in the archaeal domain. Significance StatementArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly-barcoded transposon libraries (RB-TnSeq) to the model archaeon Methanococcus maripaludis. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This dataset encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy; thus, providing an extensive dataset for the archaeal community to mine for characterizing additional genes of unknown function.

microbiology↗

bioRxiv2024

Vitamin B12 variants structure soil microbial communities despite soil's vast reservoir of B12.

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

microbiology↗

bioRxiv2024

Niche exclusion of a lung pathogen in mice with designed probiotic communities

For years, the airway microbiota have been theorized to be gatekeepers of respiratory health, as pathogens entering the airway make contact with resident microbes prior to or coincident with their interaction with host cells. Thus, modification of the native airway community may serve as a means of altering the local environment in favor of health. In this work, we hypothesize that synthetic bacterial communities introduced into the airway can serve as prophylactic countermeasures against infection by Burkholderia thailandensis in mice. We demonstrate that understanding of antagonistic interactions between a pathogen and airway microbiota in vitro can guide identification of probiotics with protective capabilities in vivo. Specifically, we show that niche overlap between the probiotic and pathogen is indicative of probiotic performance in vivo. This work serves as a foundation for the rational design of probiotic communities for protection against and treatment of respiratory infections.

microbiology↗

bioRxiv2023

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids--the vitamin B12 family of cofactors--are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microbes involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1,000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

microbiology↗

bioRxiv2023

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.

microbiology↗

bioRxiv2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

plant biology↗

bioRxiv2023

Geochemical constraints on bacteriophage infectivity in terrestrial environments

Lytic phages can be potent and selective inhibitors of microbial growth and can have profound impacts on microbiome composition and function. However, there is uncertainty about the biogeochemical conditions under which phage predation can proceed and modulate microbial ecosystem function, particularly in terrestrial systems. Ionic strength is known to be critical for infection of bacteria by many phages, but there is limited quantitative data on ion thresholds for phage infection that can be compared with environmental ion concentrations. Similarly, while carbon composition varies in terrestrial environments, we know little of which carbon sources favor or disfavor phage infection and how these higher order interactions impact microbiome function. Here, we measured the half-maximal effective concentrations (EC50) of 80 different inorganic ions for the infection of E. coli with two canonical dsDNA and ssRNA phages, T4 and MS2, respectively. We found that many alkaline earth metals and alkali metals enabled successful lytic infection but that the ionic strength thresholds varied for different ions between phages. Additionally, using a freshwater nitrate reducing microbiome, we found that the ability of lytic phage to influence nitrate reduction end-products was dependent on the carbon source as well as the ion concentration. For all phage:host pairs we tested, the ion EC50s for phage infection we measured exceed the ion concentrations found in many terrestrial freshwater systems. Thus, our findings support a model where the influence of phages on terrestrial microbial functional ecology is greatest in hot spots and hot moments such as metazoan guts, drought influenced soils, or biofilms where ion concentration is locally or transiently elevated and carbon source composition is of a sufficiently low complexity to enrich for a dominant phage susceptible population. SignificanceViral-prokaryote dynamics greatly influence microbial ecology and the earths biogeochemical cycles. Thus, identifying the key environmental controls on phage predation is critical for predictive microbial ecology. Here we conduct laboratory experiments that implicate ionic strength and carbon composition as major controls on phage interactions with bacterial hosts in terrestrial microbiomes. We propose a model in which terrestrial phage predation is most favored in drought impacted soils and in higher ionic strength environments such as metazoan guts or between adjacent cells in biofilms.

microbiology↗