Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 14, 2024

Abstract Background Wet tropical forest soils store a vast amount of organic carbon and cycle over third terrestrial net primary production. The microbiomes these have global impact on greenhouse gases tolerate remarkably dynamic redox environment—driven by high availability reductant, soil moisture, fine-textured that limit oxygen diffusion. Yet microbiomes, particularly virus-host interactions, remain poorly characterized, we little understanding how they will shape future cycling as high-intensity drought precipitation events make conditions less predictable. Results To investigate the effects shifting active viral communities virus-microbe conducted 44-day manipulation experiment using from Luquillo Experimental Forest, Puerto Rico, amended with 13 C-enriched plant biomass. We sequenced 10 bulk metagenomes 85 stable isotope probing targeted generated extracting whole community DNA, performing density fractionation, conducting shotgun sequencing. Viral microbial genomes were assembled resulting in 5,420 populations (vOTUs) 927 medium-to-high-quality metagenome-assembled across 25 bacterial phyla. Notably, half (54%) vOTUs C-enriched, highlighting their role degradation litter. These primarily infected phyla Pseudomonadota , Acidobacteriota Actinomycetota 57% unique to particular treatment. anoxic samples exhibited most distinct communities, an increased potential for modulating host metabolism carrying redox-specific glycoside hydrolases. However, present all conditions, suggesting selection cosmopolitan viruses occurs naturally experience conditions. Conclusions Our study demonstrates interactions soils. By applying different DNA assembly methods incubating under various regimes, identified observed significant variations composition function. findings highlight specialized roles diverse environmental providing important insights into contributions broader implications climate change.

Язык: Английский

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Element cycling by environmental viruses

National Science Review, Год журнала: 2024, Номер 11(12)

Опубликована: Ноя. 14, 2024

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High Throughput Viral Enumeration of Aquatic Ecosystems via Flow Cytometry

Опубликована: Окт. 21, 2024

Abstract For the past 25 years, flow cytometry has been a gold standard for direct measurement of viral-like particles (VLP) in aquatic ecosystems. Flow allows higher throughput and costs less than alternative enumeration methods, leading to its broad usage viral ecology. A major challenge associated with is degradation VLPs over time, making use high plates not possible, thus lowering overall throughput. It also difficult maintain method low contamination, signal-to-noise ratios, observations real vs. fake particles. these reasons, rapidly declined years due advent massively parallel sequencing. Here, we describe 96 well plate format that provides hands-free approach enumeration. Our limits particles, noise levels, cross-sample contamination. In run, 60 samples can be measured within 2.25 hours, which ∼1 hour faster single tube ∼1.5 hours epifluorescence microscopy (EFM). Direct still window into viral-host interactions ecosystems, resolved manner.

Язык: Английский

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Unlocking the genomic repertoire of a cultivated megaphage

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 20, 2024

Abstract Megaphages are bacteriophages (i.e., phages) with exceptionally large genomes that ecosystem cosmopolitans, infect various bacterial hosts, and have been discovered across metagenomic datasets globally. To date, almost all megaphages evaded cultivation, only phage G being in active culture for over 50 years. We examined multiomics this five decades long cultivated history from nine different laboratories lab variants to the modern era. In work, we resolved complete genomes, particle proteome, de novo methylome, used artificial intelligence (AI) annotate genome of G. Phage is one largest phages a size >0.6 µm, about half width host cell, 499 kbp, non-permuted, linear has, uniquely among known phages, two pairs ends. Its closest relative Moose W30-1 which was metagenomically assembled without cultivation moose rumen sample. has >650 protein-coding open reading frames (ORFs), >65% hypothetical proteins no function, rest geared towards nucleic acid replication (e.g., helicases, polymerases, endonucleases) structural nature capsid, tail, portal, terminase). The encodes 35 kbp stretch 66 ORFs any functional homology, cryptic genomic region roughly lambda. an expansive repertoire auxiliary metabolic genes (AMGs) acquired its host, including phoH , ftsZ UvsX/RecA-like, gyrA, gyrB ,and DHFR . Furthermore, AMGs could manipulate sporulation ( sspD, RsfA, spoK ) antiviral escape anti-CBass nuclease Anti-Pycsar protein). proteomics found >15% protein were present either wild-type or mutant G, involved UvsX/RecA-like ), sporulation, as well portal). methylome localized limited supervised machine learning HMMs) unable resolve region, but AI. This hot spot methylation at 32%, where many functions ORF still unknown. Our study represents doorway into complexity megaphage, highlighting continuous first time.

Язык: Английский

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