Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

Soil microbes play pivotal roles in global carbon cycling; however, the fundamental interactions between microbes and their infecting viruses remain unclear. This is exacerbated with soil depth, where the patterns of viral dispersal, ecology, and evolution are markedly underexplored. To investigate viral communities throughout the soil depth profile, we leveraged a publicly available metagenomic data set sampled from grassland soil in Northern California. In total, 10,196 non-redundant viral operational taxonomic units were recovered from soil between 20 cm and 115 cm below the surface. Viral prevalence was high throughout the soil depth profile, with viruses infecting dominant soil hosts, including Actinomycetia . Contrary to leading hypotheses, lysogeny did not dominate in the soil viral communities. Viral diversity was assessed at both the population level (i.e., macrodiversity) and strain level (i.e., microdiversity) to reveal diverse ecological and evolutionary patterns of virus-host interactions in surface and subsurface soils. Investigating viral microdiversity uncovered potential patterns of antagonistic co-evolution across both surface and subsurface soils. Furthermore, we have provided evidence for the potential of soil viruses to augment the remineralization of soil carbon. While we continue to yield a more comprehensive understanding of soil viral ecology, our work appeals to future researchers to further investigate subsurface viral communities. IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems

The human gut phageome : origins and roles in the human gut microbiome

The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease

Isolation and Characterization of Klebsiella Phages for Phage Therapy

Introduction: Klebsiella is a clinically important pathogen causing a variety of antimicrobial resistant infections in both community and nosocomial settings, particularly pneumonia, urinary tract infection, and sepsis. Bacteriophage (phage) therapy is being considered a primary option for the treatment of drug-resistant infections of these types. Methods: We report the successful isolation and characterization of 30 novel, genetically diverse Klebsiella phages. Results: The isolated phages span six different phage families and nine genera, representing both lysogenic and lytic lifestyles. Individual Klebsiella phage isolates infected up to 11 of the 18 Klebsiella capsule types tested, and all 18 capsule-types were infected by at least one of the phages. Conclusions: Of the Klebsiella-infecting phages presented in this study, the lytic phages are most suitable for phage therapy, based on their broad host range, high virulence, short lysis period and given that they encode no known toxin or antimicrobial resistance genes. Phage isolates belonging to the Sugarlandvirus and Slopekvirus genera were deemed most suitable for phage therapy based on our characterization. Importantly, when applied alone, none of the characterized phages were able to suppress the growth of Klebsiella for more than 12 h, likely due to the inherent ease of Klebsiella to generate spontaneous phage-resistant mutants. This indicates that for successful phage therapy, a cocktail of multiple phages would be necessary to treat Klebsiella infections.Peer reviewe

A many-analysts approach to the relation between religiosity and well-being

The relation between religiosity and well-being is one of the most researched topics in the psychology of religion, yet the directionality and robustness of the effect remains debated. Here, we adopted a many-analysts approach to assess the robustness of this relation based on a new cross-cultural dataset (N=10,535 participants from 24 countries). We recruited 120 analysis teams to investigate (1) whether religious people self-report higher well-being, and (2) whether the relation between religiosity and self-reported well-being depends on perceived cultural norms of religion (i.e., whether it is considered normal and desirable to be religious in a given country). In a two-stage procedure, the teams first created an analysis plan and then executed their planned analysis on the data. For the first research question, all but 3 teams reported positive effect sizes with credible/confidence intervals excluding zero (median reported β=0.120). For the second research question, this was the case for 65% of the teams (median reported β=0.039). While most teams applied (multilevel) linear regression models, there was considerable variability in the choice of items used to construct the independent variables, the dependent variable, and the included covariates

A Many-analysts Approach to the Relation Between Religiosity and Well-being

The relation between religiosity and well-being is one of the most researched topics in the psychology of religion, yet the directionality and robustness of the effect remains debated. Here, we adopted a many-analysts approach to assess the robustness of this relation based on a new cross-cultural dataset (N = 10, 535 participants from 24 countries). We recruited 120 analysis teams to investigate (1) whether religious people self-report higher well-being, and (2) whether the relation between religiosity and self-reported well-being depends on perceived cultural norms of religion (i.e., whether it is considered normal and desirable to be religious in a given country). In a two-stage procedure, the teams first created an analysis plan and then executed their planned analysis on the data. For the first research question, all but 3 teams reported positive effect sizes with credible/confidence intervals excluding zero (median reported β = 0.120). For the second research question, this was the case for 65% of the teams (median reported β = 0.039). While most teams applied (multilevel) linear regression models, there was considerable variability in the choice of items used to construct the independent variables, the dependent variable, and the included covariates

Unearthing the ecological roles of microbial viruses across soil microbiomes

Viruses are abundant, diverse, and ubiquitous across soil habitats. By regulating microbial dynamics through host cell lysis, and augmenting host metabolism through the expression of auxiliary metabolic genes, bacteriophages (phages) are integral members of the marine food web. Critically, this has highlighted the knowledge gap in our understanding of viruses in soil ecosystems. The advent and accessibility of next-generation sequencing has uncoupled the investigation of soil viruses from their lab cultivation with hosts. This approach was subsequently taken here to address the following questions: 1) What is most prevalent infection strategy of soil viruses, and what drives the shifts between virulence and lysogeny? 2) What are the ecological drivers of spatial variation in soil viral diversity? 3) How do soil viruses influence soil biogeochemistry? In Chapter 2, a multi-‘omic approach was taken to investigate the influence of crop rotation on the composition and spatiotemporal activity of soil viral communities. This was the first time that ssRNA phages were described at the root surface, which in turn expanded the number of Leviviricetes genomes by more than five times. Chapter 2 also provides seminal evidence of crop rotation-driven impacts on microbial communities extending to viruses, such that the novel principal of “viral priming” was presented. In Chapter 3, a publicly available metagenomic data set was leveraged to describe virushost interactions throughout the soil depth profile. This uncovered evidence of viruses augmenting the remineralisation of soil carbon across the markedly underexplored niches of subsurface soil. Furthermore, by investigating viral micro diversity across the soil depth profile for the first time, subsurface soil was found to host distinctive antagonistic co-evolution between viruses and their hosts. In summary, this thesis extends our understanding of the ecological roles of microbial viruses across soil microbiomes. The further characterisation of these roles across spatial, temporal, and trophic scales could inform global actions to mitigate climate change, promote bioremediation, and support sustainable agriculture. Most importantly, this work implores that future soil microbiome studies integrate viruses and recognise their interactions with microbes, higher plants, and even humans

Virus-host interactions along a grassland soil depth profile

This repository contains data used in Muscatt et al. 2022 (preprint). c1.ntw.gz = vConTACT2 network output file DNAP_plus_ref.faa.gz = fasta amino acid file containing DNA polymerase protein sequences used for phylogenetic tree DNAP_tree.gz = tree file for jumbo phage phylogenetic tree based on DNA polymerase gene edges.csv.gz = edges for drawing vConTACT2 network gene_to_genome.csv.gz = viral gene to genome index used as input to vConTACT2 genome_by_genome.csv.gz = viral cluster statuses outputted by vConTACT2 MAG_bins.fna.gz = fasta nucleotide file containing 285 microbial MAG bins previously assembled by Sharrar et al. 2020 nodes.csv.gz = nodes for drawing vConTACT2 network rpS3.fna.gz = fasta nucleotide file containing 1516 rpS3 sequences vOTU_prediction.csv.gz = stats on viral scaffold prediction vOTU_proteins.faa.gz = fasta amino acid file containing XXX dsDNA vOTU genes vOTUs.fna.gz = fasta nucleotide file containing 10,196 dsDNA vOTUs</p

DNA and RNA viruses in the rhizosphere

This repository contains data used in Muscatt et al. 2022  Futher details on analysis can be found here  https://github.com/GeorgeMuscatt/RhizosphereVirome   Data is stored in the file RhizosphereVirome.tar  The following files are stored. See the README for full details: c1.ntw.gz = vConTACT2 network output file  core_protein_concatenation_tree = ssRNA phage phylogenetic tree based on aligned core protein concatenations  CP.faa.gz = fasta amino acid file containing coat protein sequences for 11,222 near-complete ssRNA phage vOTUs CP_ref_Leviviricetes.faa.gz = fasta amino acid file containing coat protein sequences for 1,868 reference Leviviricetes genomes dsDNA_gene_annotations.csv.gz = annotations for 20,746 dsDNA vOTU genes dsDNA_vOTUs.faa.gz = fasta amino acid file containing 20,267 dsDNA vOTU genes dsDNA_vOTUs.fna.gz = fasta nucleotide file containing 1,059 dsDNA vOTUs edges.csv.gz = edges for drawing vConTACT2 network gene_2_genome.csv.gz = input file for vConTACT2 containing gene-to-genome index for 1,059 dsDNA vOTUs and 16,540 ssRNA phage vOTUs  MP.faa.gz = fasta amino acid file containing maturation protein sequences for 11,222 near-complete ssRNA phage vOTUs MP_ref_Leviviricetes.faa.gz = fasta amino acid file containing maturation protein sequences for 1,868 reference Leviviricetes genomes nodes.csv.gz = nodes for drawing vConTACT2 network RdRp.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 11,222 near-complete ssRNA phage vOTUs RdRp_ref_Leviviricetes.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 1,868 reference Leviviricetes genomes ssRNA_vOTUs.faa.gz = fasta amino acid file containing 52,700 ssRNA phage vOTU genes ssRNA_vOTUs.fna.gz = fasta nucleotide file containing 16,541 ssRNA phage vOTUs viral_cluster_overview.csv = output file from vConTACT2 containing viral cluster information</p

A many-analysts approach to the relation between religiosity and well-being

The relation between religiosity and well-being is one of the most researched topics in the psychology of religion, yet the directionality and robustness of the effect remains debated. Here, we adopted a many-analysts approach to assess the robustness of this relation based on a new cross-cultural dataset (N = 10, 535 participants from 24 countries). We recruited 120 analysis teams to investigate (1) whether religious people self-report higher well-being, and (2) whether the relation between religiosity and self-reported well-being depends on perceived cultural norms of religion (i.e., whether it is considered normal and desirable to be religious in a given country). In a two-stage procedure, the teams first created an analysis plan and then executed their planned analysis on the data. For the first research question, all but 3 teams reported positive effect sizes with credible/confidence intervals excluding zero (median reported beta = 0.120). For the second research question, this was the case for 65% of the teams (median reported beta = 0.039). While most teams applied (multilevel) linear regression models, there was considerable variability in the choice of items used to construct the independent variables, the dependent variable, and the included covariates