Unlocking the genomic repertoire of a cultivated megaphage DOI Creative Commons

A. Buchan,

Stephanie Wiedman,

Kevin Lambirth

и другие.

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

Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities DOI

Xiaolei Zhao,

Xiaolong Liang, Zhenke Zhu

и другие.

Environmental Science & Technology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 21, 2025

Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on metabolism the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active inactive bacteriophages (phages) soil DOM with original incubated them at 18 or 23 °C for 35 days. Phages initially (1–4 days) reduced CO2 efflux rate by 13-21% 3–30% but significantly (p < 0.05) increased 4–29% 9–41% after 6 days, raising cumulative emissions 14% 21% °C. decreased dominant taxa community diversity (consistent a "cull-the-winner" dynamic), thus altering predicted microbiome functions. Specifically, phages enriched some (such as Pseudomonas, Anaerocolumna, Caulobacter) involved in degrading complex compounds consequently promoted functions related C cycling. Higher temperature facilitated phage-bacteria interactions, diversity, enzyme activities, boosting 16%. Collectively, impact shifting microbial functions, moderate changes modulating magnitude these processes not qualitatively behavior.

Язык: Английский

Процитировано

1
Meeting report: International soil virus conference 2024 DOI
María Touceda‐Suárez, Melissa Perry,

Riccardo Frizzo

и другие.

Virus Research, Год журнала: 2025, Номер unknown, С. 199544 - 199544

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

0
Distance to the water table shapes the diversity and activity of DNA and RNA viruses in a subalpine peatland DOI Creative Commons
Z. Xiong, Xuan Qiu, Xing Xiang

и другие.

Environment International, Год журнала: 2025, Номер 197, С. 109363 - 109363

Опубликована: Март 1, 2025

Peatlands are essential reservoirs of carbon and critical zones for the cycling greenhouse gases on Earth. Their ecological functions primarily governed by microbial communities inhabiting them, which vary with hydrological conditions. However, roles viruses in peatland ecosystems remain poorly understood despite their abundance ubiquity. To address this gap, viral communities, roles, responses to environmental factors were explored using viromics, metatranscriptomics, physicochemical property analyses nine peat sediments collected from various layers three profiles different water table levels Dajiuhu Peatland, central China. This study revealed that distance (DWT) significantly influenced composition function altering redox potential total organic carbon, turn affected methane (CH4) concentrations pore water. Furthermore, a notable putative auxiliary metabolic genes associated methane, nitrogen, sulfur metabolism was identified DNA viruses, community strongly regulated DWT. Additionally, functional related oxidative phosphorylation cysteine synthesis detected first time RNA viruses. advances our comprehension how conditions affect peatlands, provides new insights into impact CH4 cycle, serves as crucial reference future investigations

Язык: Английский

Процитировано

0
Les virus des bactéries à l’ère de l’Anthropocène : amis ou ennemis de leurs hôtes ? DOI Creative Commons
Mireille Ansaldi, Claire Le Marrec

médecine/sciences, Год журнала: 2025, Номер 41(2), С. 160 - 165

Опубликована: Фев. 1, 2025

Les virus de bactéries, ou bactériophages, sont les plus abondants sur Terre, et leurs hôtes organismes vivants répandus dans la biosphère. Ils retrouvés à l’état libre, sous forme virions, aussi très génomes prophages. bactériophages présents tous biotopes colonisés par eaux, sols, environnements extrêmes, microbiotes humains, animaux végétaux, où ils participent aux échanges génétiques. Tous facteurs qui impactent ces ont donc des conséquences importantes dynamique populations bactéries virus.

Процитировано

0
Soil is alive – how does soil biota influence soil mechanical properties? A perspective review DOI Creative Commons
А. Д. Железова,

Gregorio Sorrentino,

Gerald Innocent Otim

и другие.

Biogeotechnics, Год журнала: 2025, Номер unknown, С. 100175 - 100175

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Soil biodiversity and function under global change DOI Creative Commons
Manuel Delgado‐Baquerizo, David J. Eldridge, Yu‐Rong Liu

и другие.

PLoS Biology, Год журнала: 2025, Номер 23(3), С. e3003093 - e3003093

Опубликована: Март 27, 2025

Soil organisms represent the most abundant and diverse on planet support almost every ecosystem function we know, thus impact our daily lives. Some of these impacts have been well-documented, such as role soil in regulating fertility carbon sequestration; processes that direct implications for essential services including food security climate change mitigation. Moreover, biodiversity also plays a critical supporting other aspects from One Health—the combined health humans, animals, environment—to conservation historic structures monuments. Unfortunately, is highly vulnerable to growing number stressors associated with global environmental change. Understanding how when supports functions, it will adapt changing conditions, crucial conserving soils maintaining future generations. In this Essay, discuss fundamental importance multiple Health, further highlight knowledge gaps need be addressed conserve next

Язык: Английский

Процитировано

0
Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater DOI
Xiaojie Yan, Yuan Xin, Liying Zhu

и другие.

Water Research, Год журнала: 2025, Номер unknown, С. 123627 - 123627

Опубликована: Апрель 1, 2025

Язык: Английский

Процитировано

0
Potential Roles of Soil Viruses in Karst Forest Soil Carbon and Nitrogen Cycles DOI Open Access
Hanqing Wu, Nan Wu,

Qiumei Ling

и другие.

Forests, Год журнала: 2025, Номер 16(5), С. 735 - 735

Опубликована: Апрель 25, 2025

Soil viruses, ubiquitous and abundant biological entities that are integral to microbial communities, exert pivotal impacts on ecosystem functionality, particularly within carbon (C) nitrogen (N) cycles, through intricate interactions with bacteria, archaea, fungi, other taxa. While their contributions soil dynamics increasingly elucidated, the specific roles of viruses in karst forest remain largely underexplored. Karst ecosystems (covering 15% global terrestrial surface) characterized by unique geological formations, thin patchy layers, high pH Ca2+, rapid hydrological dynamics, collectively fostering environmental conditions may shape viral ecology modulate C N cycling. This perspective synthesizes existing knowledge functions distinctive characteristics soil, proposing potential mechanisms which could influence cycling such fragile ecosystems. regulate cycles both directly indirectly via hosts, mainly including shaping community structure, mediating horizontal gene transfer metabolism, increasing availability alleviating nutrient limitations, promoting sequestration, mitigating climate change. work aims bridge biogeochemical providing insights into sustainable stewardship resilience. We delineate critical gaps propose future perspectives, advocating for targeted metagenomic long-term experimental studies diversity, virus–host-environment interactions, temporal dynamics. Specifically, we advocate following research priorities advance our understanding studies: (I) abundance, activity: characterizing activity forests using metagenomics complementary molecular approaches; (II) virus–host interactions: investigating between key taxa involved cycling; (III) impacts: quantifying lysis fluxes soil; (IV) modeling cycles: developing integrative models incorporate virus-mediated processes frameworks at different spatial scales. Such efforts essential validate hypothesized underlying mechanisms, offering a foundation nature-based solutions facilitate support ecological restoration vulnerable regions amid

Язык: Английский

Процитировано

0
Impact of Viruses on Prokaryotic Communities and Greenhouse Gas Emissions in Agricultural Soils DOI Creative Commons
Xing Huang, Lucas P. P. Braga,

Chenxiao Ding

и другие.

Advanced Science, Год журнала: 2024, Номер 11(48)

Опубликована: Окт. 7, 2024

Abstract Viruses are abundant and ubiquitous in soil, but their importance modulating greenhouse gas (GHG) emissions terrestrial ecosystems remains largely unknown. Here, various loads of viral communities introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role viruses regulating prokaryotic communities. The results showed that addition has strong impact on methane (CH 4 ) nitrous oxide (N 2 O) and, minor extent, carbon dioxide (CO emissions, along dissolved nitrogen pools, depending soil history. high load resulted decrease microbial biomass (MBC) by 31.4%, changes relative abundance 16.6% dominant amplicon sequence variants (ASVs) comparison control treatments. More specifically, large effects pressure observed some specific decreased prokaryotes dissimilate sulfur compounds increased Nanoarchaea . Structural equation modeling further highlighted differential direct indirect CO , N O, CH emissions. These findings underpin understanding complex microbe‐virus interactions advance current knowledge virus ecology.

Язык: Английский

Процитировано

3
Unveiling the top-down control of soil viruses over microbial communities and soil organic carbon cycling: a review DOI Creative Commons
Shuo Wang,

Dong Yu Zhu,

Tida Ge

и другие.

Climate smart agriculture., Год журнала: 2024, Номер 1(2), С. 100022 - 100022

Опубликована: Окт. 17, 2024

Язык: Английский

Процитировано

2