Response of Soil Microbial Carbon Allocation Patterns to Induction of Viral Lysis in Aggregate Size Fractions DOI
Aubrey K. Fine, Sean M. Schaeffer, Mark Radosevich

et al.

Published: Jan. 1, 2023

Viral lysis exerts control on microbial mortality and dissolved organic matter production in oceans. In contrast, virus-microbe dynamics have rarely been experimentally observed soils, with their complex physical structure cross-scale heterogeneity habitat properties. Much of this comes from soil aggregates, which are often operationally classified into size fractions reflecting differences physicochemical biological characteristics. incubation study, Mitomycin C (MMC) was directly applied to induce viral-mediated cell three aggregate (large macro-, small micro-) under slurry conditions. Treatment MMC shifted mortality, substrate availability, viral production, the effects were studied over time relative a non-induced using fully factorial experimental design. Destructive sampling performed days 0, 3, 7, 14, 28 for common biogeochemical measurements activity inorganic N combined particle bacterial abundances determined epifluorescence microscopy. Using multiple statistical approaches, results indicate potential aggregate-scale variability interactions that is strongly dependent time. After an initial six day stress response, induction associated hot spot increased control. Mid-incubation characterized by active growth, enzyme activities, high predation pressure. By 28, altered carbon allocation patterns along net negative interpreted reflect shift towards lysogenic reproduction. These findings point toward dynamic nature possible links between functions, free abundance, aggregation processes contribute stabilization.

Language: Английский

Enumerating soil biodiversity DOI Creative Commons
Mark Anthony, S. Franz Bender, Marcel G. A. van der Heijden

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(33)

Published: Aug. 7, 2023

Soil is an immense habitat for diverse organisms across the tree of life, but just how many live in soil surprisingly unknown. Previous efforts to enumerate biodiversity consider only certain types (e.g., animals) or report values groups without partitioning species that versus other habitats. Here, we reviewed literature show likely home 59 ± 15% on Earth. We therefore estimate approximately two times greater than previous estimates, and include representatives from simplest (microbial) most complex (mammals) organisms. Enchytraeidae have greatest percentage (98.6%), followed by fungi (90%), Plantae (85.5%), Isoptera (84.2%). Our results demonstrate biodiverse singular habitat. By using this biodiversity, can more accurately quantitatively advocate organismal conservation restoration as a central goal Anthropocene.

Language: Английский

Citations

188
Incorporating viruses into soil ecology: A new dimension to understand biogeochemical cycling DOI
Xiaolong Liang, Mark Radosevich, Jennifer M. DeBruyn

et al.

Critical Reviews in Environmental Science and Technology, Journal Year: 2023, Volume and Issue: 54(2), P. 117 - 137

Published: June 16, 2023

Viruses, with an estimated abundance of 1031 on Earth, are important component soil ecosystems. As obligate parasites that entirely depend hosts for reproduction and survival, viruses have been linked to microbial community diversity metabolic activities in soil. Emerging evidence indicates influence a broad-spectrum processes sustain biodiversity, biogeochemical cycling, fertility, plant health. Research is its early stages. Even observational assessments viral ecology such as abundance, diversity, distribution, life strategies, ecological relevance, functions, only just beginning be revealed. In this review, we summarize the state knowledge concerning potential function(s) how they likely composition, nutrient cycles, carbon dynamics example. major drivers mortality functioning across wide range spatial temporal scales, appear key regulators cellular metabolism properties well critical ecosystem function. We conclude indispensable demanding further investigation. Defining abiotic interactions within environment, revealing virus-host interaction networks, elucidating roles cycling but few many aspects worthy future A more complete view participation food webs face changing climate will lead improved management services environmental sustainability.

Language: Английский

Citations

25
Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils DOI
Samuel E. Barnett, Ashley Shade

Soil Biology and Biochemistry, Journal Year: 2025, Volume and Issue: unknown, P. 109741 - 109741

Published: Feb. 1, 2025

Language: Английский

Citations

1
Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes DOI Creative Commons
Ling-Yi Wu, Nikolaos Pappas, Yasas Wijesekara

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 28, 2023

ABSTRACT As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting in metagenomic data not trivial. In past few years, many bioinformatic identification tools have been developed this task, making it challenging to choose right tools, parameters, and cutoffs. all these measure different biological signals, use algorithms training/reference databases, imperative conduct an independent benchmarking give users objective guidance. We compared performance of ten state-of-the-art thirteen modes on eight paired viral microbial datasets from three distinct biomes, including a new complex dataset Antarctic coastal waters. The had highly variable true positive rates (0 – 68%) false 15%). PPR-Meta best distinguished contigs, followed by DeepVirFinder, VirSorter2, VIBRANT. Different identified subsets except Sourmash, found unique contigs. Tools could be improved with adjusted parameter cutoffs, indicating that adjustment cutoffs before usage should considered. Together, our provides guidance choices gives suggestions adjustments viromics researchers.

Language: Английский

Citations

7
Locally heterogeneous soil viral and prokaryotic responses to prescribed burn correspond with patchy burn severity in a mixed conifer forest DOI Open Access
Sara E. Geonczy, Luke S. Hillary, Christian Santos‐Medellín

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 31, 2024

ABSTRACT Prescribed burning, a strategy to mitigate wildfires, imparts physicochemical and biological changes soil. The effects of burns on soil viruses virus-host dynamics are largely unexplored, despite known viral prokaryotic contributions biogeochemical processes. Using viromic (<0.2 µm size fraction metagenomic) approach, we assessed how communities responded spring prescribed burn in mixed conifer forest whether chemical properties and/or host could explain the observed patterns. From 120 samples (two per depth at 0-3 3-6 cm from four burned two control plots five timepoints, before three after burn), 91 viromes 115 16S rRNA gene amplicon libraries were sequenced. Plot location had greatest effect explaining variance communities, over treatment (burned or not), depth, timepoint. Viral exhibited locally heterogenous responses fire, with some resembling unburned controls. This was attributed patchy severity (defined by chemistry). Low DNA yields indicated substantial loss biomass high-severity locations. relative abundances Firmicutes, Actinobacteria, predicted infect them significantly increased along gradient, suggesting survival spore formers infection these abundant, fire-responsive taxa. Our analyses highlight importance nuanced view community not just overall, but specific degree experienced each patch soil, which differed for nearby soils same fire.

Language: Английский

Citations

2
Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology DOI Creative Commons
James C. Kosmopoulos,

Katherine M. Klier,

Marguerite V. Langwig

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 17, 2023

ABSTRACT Background Viruses, the majority of which are uncultivated, among most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses fundamental members microbiomes. While number studies leveraging viral metagenomics (viromics) for studying uncultivated is growing, standards viromics research lacking. Viromics can utilize computational discovery from total metagenomes all (hereafter metagenomes) or use physical separation virus-specific fractions viromes). However, differences in recovery and interpretation viromes obtained same samples remain understudied. Results Here, we compare communities paired 60 diverse across human gut, soil, freshwater, marine ecosystems. Overall, were more species rich than those metagenomes, although there some exceptions. Despite this, still contained many genomes not detected viromes. We also found notable predicted lytic state vs at time sequencing. Other forms variation observed include genome presence/absence, quality, encoded protein content between but magnitude these varied by environment. Conclusions our results show that choice method lead differing interpretations ecology. suggest whether target a metagenome virome study should be dependent environmental context ecological questions being asked. overall recommendation researchers investigating ecology evolution pair both approaches maximize their respective benefits.

Language: Английский

Citations

4
Soil viral and prokaryotic communities shifted significantly after wildfire in chaparral and woodland habitats DOI Open Access
Sara E. Geonczy, Anneliek M. ter Horst, Joanne Emerson

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 16, 2024

ABSTRACT Increased wildfire activity warrants more research into fire-driven biotic changes in soil, given that soil microbes contribute to biogeochemical processes by way of organic matter decomposition, nutrient cycling, and promoting plant growth. Viruses prokaryotes apply pressure microbial communities, making their responses fire also important for understanding post-fire ecology. Leveraging viromes 16S rRNA gene amplicon sequencing, here we studied viral prokaryotic community woodland chaparral soils at five timepoints over one year following the California LNU Complex wildfire. We compared samples unburned controls final three timepoints, beginning months after fire. Viromic DNA yields were low-to-undetectable (indicative low particle abundances), particularly first timepoint, comparisons suggest a return baseline abundances within Viral composition chemistry differed significantly burned from both habitats. Compared controls, greater proportion ‘species’ (vOTUs) conifer forest detected habitats here, suggesting fire-associated habitat filtering. Published collected same sites nine pre-fire similar than viromes. Together, these results indicate significant communities due

Language: Английский

Citations

1
Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils DOI Creative Commons
Samuel E. Barnett, Ashley Shade

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 27, 2024

Abstract Viruses are important components of the soil microbiome, influencing microbial population dynamics and functions their hosts. However, relationships feedbacks between virus dynamics, host environmental disturbance is not understood. Centralia, PA, USA, site an underground coal seam fire that has been burning for over 60 years. As moves along seam, previously heated soils cool to ambient temperature, creating a gradient heat intensity recovery. We examined annual viral seven consecutive years in Centralia using untargeted metagenome sequencing. Viral communities changed time were distinct fire-affected reference sites. Dissimilarity was greater across sites (space) than within (time), cumulative diversity more rapidly stabilized year There also changes CRISPR investment as cooled, corresponding shifts diversity. Finally, there differences viral-encoded auxiliary metabolic genes These results indicate despite high site-to-site diversity, surprising community consistency shifting host-viral interactions recovering from disturbance. Together, these provide insights into how collectively respond unpredicted Highlights In seven-year study temperate affected by fire, displayed variability (spatial) (temporal). unheated throughout sampling. Soil bacterial composition correlated composition, though this relationship weakened when accounting edaphic properties temperature pH. may be less resilient press communities. Viral-host shift during recovery long-term heating.

Language: Английский

Citations

0
Meeting report: The first soil viral workshop 2022 DOI Open Access
Živilė Buivydaitė, Laxman Aryal, Felipe Borim Corrêa

et al.

Virus Research, Journal Year: 2023, Volume and Issue: 331, P. 199121 - 199121

Published: April 30, 2023

Language: Английский

Citations

1
Response of Soil Microbial Carbon Allocation Patterns to Induction of Viral Lysis in Aggregate Size Fractions DOI
Aubrey K. Fine, Sean M. Schaeffer, Mark Radosevich

et al.

Published: Jan. 1, 2023

Viral lysis exerts control on microbial mortality and dissolved organic matter production in oceans. In contrast, virus-microbe dynamics have rarely been experimentally observed soils, with their complex physical structure cross-scale heterogeneity habitat properties. Much of this comes from soil aggregates, which are often operationally classified into size fractions reflecting differences physicochemical biological characteristics. incubation study, Mitomycin C (MMC) was directly applied to induce viral-mediated cell three aggregate (large macro-, small micro-) under slurry conditions. Treatment MMC shifted mortality, substrate availability, viral production, the effects were studied over time relative a non-induced using fully factorial experimental design. Destructive sampling performed days 0, 3, 7, 14, 28 for common biogeochemical measurements activity inorganic N combined particle bacterial abundances determined epifluorescence microscopy. Using multiple statistical approaches, results indicate potential aggregate-scale variability interactions that is strongly dependent time. After an initial six day stress response, induction associated hot spot increased control. Mid-incubation characterized by active growth, enzyme activities, high predation pressure. By 28, altered carbon allocation patterns along net negative interpreted reflect shift towards lysogenic reproduction. These findings point toward dynamic nature possible links between functions, free abundance, aggregation processes contribute stabilization.

Language: Английский

Citations

0