A panoramic view of the virosphere in three wastewater treatment plants by integrating viral‐like particle‐concentrated and traditional non‐concentrated metagenomic approaches DOI Creative Commons
Jiayu Zhang,

Aixi Tang,

Tao Jin

и другие.

iMeta, Год журнала: 2024, Номер 3(3)

Опубликована: Март 29, 2024

Abstract Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness largely depends on activity these microorganisms. Specifically, viruses play crucial role in altering microbial behavior metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral‐like particle‐concentrated (VPC, representing free particles) non‐concentrated (NC, cellular fraction), were employed to assess efficacy revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, functional genes across processing units three wastewater treatment plants (WWTPs). Our findings indicate each approach offers unique insights into viral community composition. Their combined use proved effective elucidating WWTP viromes. We identified nearly 50,000 contigs, with Cressdnaviricota Uroviricota being predominant phyla VPC NC fractions, respectively. Notably, two pathogenic families, Asfarviridae Adenoviridae, commonly found WWTPs. also observed significant differences viromes WWTPs different types wastewater. Additionally, various phage‐derived auxiliary (AMGs) active at RNA level, contributing metabolism community, particularly carbon, sulfur, phosphorus cycling. Moreover, we 29 virus‐carried antibiotic resistance (ARGs) potential for transfer, highlighting spreading ARGs environment. Overall, this study provides detailed integrated view virosphere through application approaches. enhance understanding communities, offering valuable optimizing operation regulation systems.

Язык: Английский

Soil viral diversity, ecology and climate change DOI
Janet Jansson, Ruonan Wu

Nature Reviews Microbiology, Год журнала: 2022, Номер 21(5), С. 296 - 311

Опубликована: Ноя. 9, 2022

Язык: Английский

Процитировано

115
Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes DOI Creative Commons
Xiaoxuan Zheng, Martin T. Jahn, Mingming Sun

и другие.

The ISME Journal, Год журнала: 2022, Номер 16(5), С. 1397 - 1408

Опубликована: Янв. 17, 2022

Viruses significantly influence local and global biogeochemical cycles help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched organochlorine pesticide (OCP) contaminated soil China if viral include linked OCP biodegradation. Using metagenomics, found that OCP-contaminated soils displayed a lower bacterial, but higher diversity viruses harbored relative abundance metabolism. Furthermore, the increased along severity contamination, several biodegradation were identified bioinformatically metagenomes. Functional assays conducted experimentally demonstrate virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for precursors, improving growth at sub-inhibitory concentrations. Taken together, these results metabolism biodegradation, being more abundant diverse pesticides. Moreover, our findings highlight importance accessory ecology stressful environments, providing novel avenue using bioremediation soils.

Язык: Английский

Процитировано

114
Diversity in the soil virosphere: to infinity and beyond? DOI Creative Commons
Simon Roux, Joanne Emerson

Trends in Microbiology, Год журнала: 2022, Номер 30(11), С. 1025 - 1035

Опубликована: Май 26, 2022

Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome metatranscriptome analyses offer unprecedented windows into the soil virosphere. Given emerging picture high viral activity, diversity, dynamics over short spatiotemporal scales, then outline eco-evolutionary processes hypothesize major diversity drivers for viruses. We argue a effort is needed to establish 'global virosphere atlas' can be used address roles viruses microbiomes terrestrial biogeochemical cycles across scales.

Язык: Английский

Процитировано

71
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting DOI Creative Commons
Hanpeng Liao, Chen Liu,

Chaofan Ai

и другие.

The ISME Journal, Год журнала: 2023, Номер 17(6), С. 916 - 930

Опубликована: Апрель 8, 2023

Abstract While decomposition of organic matter by bacteria plays a major role in nutrient cycling terrestrial ecosystems, the significance viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study mesophilic thermophilic their on during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics activity are tightly coupled, where specific track host densities, triggering microbial community succession via top-down control HTC. Moreover, encoded expressed several auxiliary metabolic genes (AMGs) linked carbon cycling, impacting turnover alongside bacteria. Nutrient correlated positively virus–host ratio, indicative positive relationship between ecosystem functioning, viral abundances, activity. These effects were predominantly driven DNA as most detected RNA associated eukaryotes not phase composting. findings suggest could drive HTC recycling bacterial biomass through cell lysis expressing key AMGs. Viruses hence potentially be used indicators functioning optimize productivity biotechnological agricultural systems.

Язык: Английский

Процитировано

56
PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations DOI Creative Commons

Ruo Han Wang,

Shuo Yang, Zhixuan Liu

и другие.

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D756 - D761

Опубликована: Окт. 30, 2023

Abstract Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems develop phage therapy strategies. However, existing databases short meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online database with comprehensive harbors a collection 873 718 sequences from various sources. Applying fifteen state-of-the-art tools perform systematic annotations analyses, provides on genome completeness, host range, lifestyle information, taxonomy classification, nine types structural functional genetic elements, three comparative studies for curated phages. Additionally, incorporates automatic analyses visualizations customized phages, serving as efficient platform study.

Язык: Английский

Процитировано

56
Biogeographic patterns and drivers of soil viromes DOI
Bin Ma, Yiling Wang, Kankan Zhao

и другие.

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(4), С. 717 - 728

Опубликована: Фев. 21, 2024

Язык: Английский

Процитировано

26
A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts DOI Creative Commons
Emily Graham, Antônio Pedro Camargo, Ruonan Wu

и другие.

Nature Microbiology, Год журнала: 2024, Номер 9(7), С. 1873 - 1883

Опубликована: Июнь 20, 2024

Historically neglected by microbial ecologists, soil viruses are now thought to be critical global biogeochemical cycles. However, our understanding of their distribution, activities and interactions with the microbiome remains limited. Here we present Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced metagenomes composed 616,935 uncultivated viral genomes 38,508 unique operational taxonomic units. Rarefaction curves Atlas indicate that most diversity unexplored, further underscored high spatial turnover low rates shared units across samples. By examining genes associated functions, also demonstrate potential impact carbon nutrient cycling. This study represents an extensive characterization provides foundation for developing testable hypotheses regarding role virosphere in biogeochemistry.

Язык: Английский

Процитировано

23
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations DOI Creative Commons
Anneliek M. ter Horst, Christian Santos‐Medellín, Jackson W. Sorensen

и другие.

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Ноя. 26, 2021

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due climate change, leading increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions these processes in peatlands underlain with permafrost, little is known about viruses other peatlands. More generally, soil biogeography its potential drivers poorly understood at both local global scales. Here, 87 metagenomes five size-fraction (viromes) from a boreal peatland northern Minnesota (the SPRUCE whole-ecosystem warming experiment surrounding bog) were analyzed dsDNA community ecological patterns, the recovered populations (vOTUs) compared our curated PIGEON database of 266,125 vOTUs diverse ecosystems. Results Within experiment, composition was significantly correlated peat depth, water content, carbon chemistry, including CH 4 CO 2 concentrations, but not temperature during first years treatments. Peat aquatic-like signatures (shared predicted protein content marine and/or freshwater vOTUs) enriched more waterlogged surface depths. Predicted host ranges relatively narrow, generally within single bacterial genus. Of 4326 vOTUs, 164 previously detected soils, mostly None identified 202,371 peat, 0.4% 80,714 clusters (VCs, grouped by content) shared between aquatic environments. On per-sample basis, vOTU recovery 32 times viromes total metagenomes. Conclusions suggest strong “species” boundaries terrestrial ecosystems some extent differences less pronounced taxonomic levels. The significant enrichment suggests that may also exhibit niche partitioning on These patterns presumably driven part ecology, consistent narrow ranges. Although samples sequencing depth improved metagenomes, substantially after particle highlights utility viromics.

Язык: Английский

Процитировано

90
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation DOI Creative Commons
Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A. Zayed

и другие.

PeerJ, Год журнала: 2021, Номер 9, С. e11447 - e11447

Опубликована: Июнь 14, 2021

Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing roles across diverse ecosystems, its analyses differ in many ways from those used microbes. To date, viromics benchmarking covered read pre-processing, assembly, relative abundance, mapping thresholds estimation, but other steps would benefit standardization. Here we use silico-generated datasets an extensive literature survey to evaluate highlight how dataset composition (i.e., viromes vs bulk metagenomes) assembly fragmentation impact (i) contig identification tool, (ii) virus taxonomic classification, (iii) curation auxiliary metabolic genes (AMGs).The silico five commonly tools show that gene-content-based consistently performed well long (≥3 kbp) contigs, while k-mer- blast-based were uniquely able detect viruses short (≤3 contigs. Notably, however, the performance increase contigs was obtained at cost increased false positives (sometimes up ∼5% virome ∼75% samples), particularly when eukaryotic or mobile genetic element sequences included test datasets. For variously sized genome fragments assessed using gene-sharing network analytics quantify drop-offs assignments, which revealed correct assignations ranging ∼95% (whole genomes) down ∼80% (3 kbp fragments). A similar trend also observed classification such as VPF-class, ViPTree VIRIDIC, suggesting caution is warranted classifying not full genomes. Finally, fragmented assemblies can lead erroneous AMGs outline a best-practices workflow curate candidate genomes assembled metagenomes.Together, these experiments annotation guidelines should aid researchers seeking best detect, classify, characterize myriad 'hidden' sequence

Язык: Английский

Процитировано

89
Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers DOI
Mo-Lian Chen,

Xin‐Li An,

Hu Liao

и другие.

Environmental Science & Technology, Год журнала: 2021, Номер 55(20), С. 13881 - 13890

Опубликована: Окт. 1, 2021

Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little known about contribution viruses dissemination genes (ARGs) in this context. Here, we profiled viral communities and virus-associated ARGs long-term (over 10 years) fertilized field by metagenomic analysis. A total 61,520 populations (viral operational taxonomic units, vOTUs) were retrieved, which 21,308 assigned at family level. The community structures significantly correlated with bacterial (P < 0.001) dosage applied sewage sludge (r2 = 0.782). 16 unique detected soil viromes, number ARG subtypes was higher treatments (except for 1 SS) than others. network analysis showed that application fertilizer increased bacteria-virus interactions, suggesting chances exchange between their hosts may increase. Overall, our results provide novel understanding factors affecting profile soil.

Язык: Английский

Процитировано

83