Biology subjects

Hazard, C.

Publications and source records attributed to Hazard, C..

9 recordsLinked to original sources

bioRxiv2024

Phosphate amendment drives bloom of RNA viruses after soil wet-up

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting--while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2,190 RNA viral populations were identified across five phyla, with 37% of these predicted to infect bacteria (26%) or fungi (11%). Only 1.2% of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages, particularly Leviviricetes, proliferated significantly. Notably, 60% of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 107-109 bacteria per gram of soil, aligning with the total bacterial population (107-1010 g-1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect. HighlightsO_LISoil wet-up influences RNA virus dynamics for over a week C_LIO_LIThe majority of hosts predicted for RNA viruses were bacteria and fungi C_LIO_LIPhosphate amendment preferentially supports Lenarviricota over other RNA viruses C_LIO_LI60% of vOTUs that responded to phosphate were from unknown bacteriophage clades C_LIO_LIMost soil bacteria are predicted to be infected by RNA bacteriophages within a week C_LI

microbiology↗

bioRxiv2024

Soil pH influences the composition of bacteriophage communities infecting individual hosts

Bacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection of host communities across ecological gradients and co-evolutionary processes may influence both the distribution of phages and the susceptibility of individual hosts through virus interactions and local adaptation within distinct ecological niches. Metagenomic-based analyses have revealed that soil pH selects for distinct populations and community structures for both phage and hosts at local and global scales. However, whether contrasting soil pH represents a selective barrier for phages capable of infecting an individual host is unknown. To examine the influence of pH on individual host-virus interactions, two closely related Bacillus strains were isolated and characterized from pH 7.5 soil associated with a long-term contiguous pH gradient (pH 4.5 to 7.5). Phages infecting each strain were subsequently enriched from soils across the pH gradient (pH 4.5, 5.5, 6.5 and 7.5), enumerated using a plaque assay, and characterized via metagenomic analysis. Phages infecting each strain were cultivated from all soils but their community composition and abundance varied with pH. Phage populations infecting each of the two strains were distinct despite the close relatedness of the two hosts, indicating relatively narrow host ranges for each virus. These results suggest that while phage community structures vary substantially across an ecological gradient, soil pH alone does not represent a barrier for the distribution of phages capable of infecting an individual host.

ecology↗

bioRxiv2024

Acidotolerant soil nitrite oxidiser 'Candidatus Nitrobacter laanbroekii' NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidisers

Nitrobacter strain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacterium Nitrosospira AHB1, a consortium that nitrifies under acidic conditions. Here we characterise the growth of isolated Nitrobacter strain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA) in co-culture. NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2- concentrations of 500 {micro}M. However, the optimum decreases to pH 5.0 at lower initial NO2- concentrations closer to those found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2- with an apparent-half-saturation constant (54 {micro}M) one order of magnitude lower than its closest relative, the neutrophilic strain Nitrobacter hamburgensis X14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically, Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2 are sensitive to NO2--derived compounds and only oxidise [~]200-300 {micro}M ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by [~]0.5 pH units and both strains could oxidise up to 2.7-2.9 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3 and utilising AOA-derived NO2-. Removal of NO2- is likely crucial for nitrifier growth in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals that NHB1 is distinct from validated species and the name Nitrobacter laanbroekii is proposed.

microbiology↗

bioRxiv2023

Diverse viruses infect nitrifying archaea and bacteria communities in soil

Soil virus communities are diverse and dynamic but contributions to specific processes, such as nitrification, are largely uncharacterised. Chemolithoautotrophic nitrifiers perform this essential component of the nitrogen cycle and are established model groups for linking phylogeny, evolution and ecophysiology due to limited taxonomic and functional diversity. Ammonia-oxidising bacteria (AOB) dominate the first step of ammonia oxidation at high supply rates, with ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) often active at lower supply rates or when AOB are inactive, and nitrite-oxidising bacteria (NOB) completing canonical nitrification. Here, the diversity and genome content of dsDNA viruses infecting different nitrifier groups were characterised after in situ enrichment via differential host inhibition, a selective approach that alleviates competition for non-inhibited populations to determine relative activity. Microcosms were incubated with urea to stimulate nitrification and amended with 1-octyne or 3,4-dimethylpyrazole phosphate (AOB inhibited), acetylene (all ammonia oxidisers inhibited), or no inhibitor (AOB stimulated), and virus-targeted metagenomes characterised using databases of host genomes, reference (pro)viruses and hallmark genes. Increases in the relative abundance of nitrifier host groups were consistent with predicted inhibition profiles and concomitant with increases in the relative abundance of their viruses, represented by 200 viral operational taxonomic units. These included 61 high-quality/complete virus genomes 35-173 kb in length and possessing minimal similarity to validated families. Most AOA viruses were placed within a unique lineage and viromes were enriched in AOA multicopper oxidase genes. These findings demonstrate that focussed incubation studies facilitate characterisation of host-virus interactions associated with specific functional processes.

microbiology↗

bioRxiv2022

Viruses of soil ammonia oxidising archaea identified using a novel DNA stable isotope probing approach for low GC mol% genomes

Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived 13C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of 13C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of 13C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in 13C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.

microbiology↗

bioRxiv2021

Soil viral communities are structured by pH at local and global scales

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 - 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

ecology↗

bioRxiv2020

Methane-derived carbon flow through host-virus trophic networks in soil

The concentration of atmospheric methane continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of organisms regulating methane production and consumption, the frequency and impact of interactions with viruses on their activity in soil is unknown. Metagenomic sequencing of soil microbial communities has enabled identification of linkages between viruses and hosts. However, determining host-virus linkages through sequencing does not determine whether a virus or a host are active. In this study, we identified active individual interactions in situ by following the transfer of assimilated carbon from active hosts to viruses. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized methane-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilisers of carbon, together with the recent transfer of methane-derived carbon to viruses. Sixty-three percent of viral contigs from replicated soil incubations contained genes associated with known methanotrophic bacteria. Genomic sequences from 13C-enriched viruses were present in clustered regularly interspaced short palindromic repeats (CRISPR) arrays of multiple, closely-related Methylocystis populations, revealing differences in their history of viral interaction. Viruses infecting non-methanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with methane-fueled microbial food networks.

microbiology↗

bioRxiv2020

Use and abuse of potential rates in soil microbiology

Potential rate assays are used in soil microbial ecology to determine the rates of a functional process in environmental samples under a defined set of conditions. While they can be used appropriately to provide mechanistic insights, potential rates are also often used to estimate the abundance of specific taxonomic groups and their in situ activity. These estimates incorrectly assume that all contributing organisms in a community are active at a maximum rate under one set of optimal incubation conditions and that potential rates reflect activity in the soil. While investigators now recognise that populations within communities are physiologically diverse, they often ignore the consequent suboptimal activity, or even inactivity, of the majority of community members performing that function. In this short perspective article, we discuss when potential assays can be informative and highlight the underlying conceptual problems under circumstances where potential assays are misused, using potential nitrification rate (PNR) as an example. PNR was originally developed to estimate the size of active ammonia oxidising communities in environmental samples. It is routinely determined in short-term shaken slurry incubations by measuring assumed maximum rates of nitrate or nitrite production under optimal, non-substrate-limiting conditions. As with other functional processes, it is now recognised that a broad diversity of organisms contribute to aerobic ammonia oxidation in terrestrial and other habitats, and this diversity represents a substantial range of physiologies, including variation in substrate affinity, ammonia tolerance, cell specific activity and substrate preference. Despite this, PNR, and other potential rate assays, are often inappropriately used in an attempt to determine an ecologically relevant measurement of activity in soil. As with any potential assay, PNR has inherent biases towards particular functional groups and its use in investigating the ecology of ammonia oxidisers in natural systems should be carefully considered.

microbiology↗

bioRxiv2020

Cropping systems that improve richness convey increased resistance and resilience to fungal, but not prokaryote, communities.

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species- rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.

microbiology↗