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1.
Sci Total Environ ; 943: 173831, 2024 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-38866152

RESUMO

The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.


Assuntos
Fertilizantes , Microbiota , Nitrogênio , Microbiologia do Solo , Sorghum , Sorghum/microbiologia , Nitrogênio/análise , Bactérias/classificação , Fungos/fisiologia , Rizosfera , RNA Ribossômico 16S , Raízes de Plantas/microbiologia
2.
Sci Total Environ ; 863: 160986, 2023 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-36528948

RESUMO

Soil-borne fungal pathogens pose a major threat to global agricultural production and food security. Pathogen-suppressive bacteria and plant beneficial protists are important components of soil microbiomes and essential to plant health and performance, but it remains largely unknown regarding how agricultural management practices influence the relative importance of protists and bacteria in plant disease suppression. Here, we characterized soil microbiomes (including fungi, protists, and bacteria) in bulk and sorghum rhizosphere soils with various long-term inorganic and organic fertilization regimes, and linked the changes in fungal plant pathogens with the protistan and bacterial communities. We found that the relative abundances of fungal pathogens were significantly decreased by organic fertilization regimes, and there was a significant difference in the community composition of fungal pathogens between inorganic and organic fertilization regimes. Organic fertilization significantly enhanced predatory protists but reduced the proportions of protistan phototrophs. Co-occurrence network analysis revealed more intensive connections between fungal plant pathogens with protists, especially predatory protists, than with bacterial taxa, which was further supported by stronger associations between the community structure of fungal pathogens and predatory protists. We identified more protist consumer taxa than bacterial taxa as predictors of fungal plant pathogens, and structural equation modelling revealed a more important impact of protist consumers than bacteria on fungal pathogens. Altogether, we provide new evidence that the disease inhibitory effects of long-term organic fertilization regimes could be best explained by the potential predation pressure of protists. Our findings advance the mechanistic understanding of the role of predator-prey interactions in controlling fungal diseases, and have implications for novel biocontrol strategies to mitigate the consequences of fungal infections for plant performance.


Assuntos
Comportamento Predatório , Solo , Animais , Solo/química , Microbiologia do Solo , Eucariotos , Bactérias , Fertilização
3.
J Hazard Mater ; 442: 130111, 2023 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-36209605

RESUMO

Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.


Assuntos
Solo , Vírus , Ecossistema , Virulência/genética , Microbiologia do Solo , Vírus/genética
4.
Environ Microbiome ; 17(1): 6, 2022 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-35130971

RESUMO

BACKGROUND: Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. RESULTS: Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. CONCLUSIONS: The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.

5.
Sci Total Environ ; 812: 152217, 2022 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-34890674

RESUMO

Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.


Assuntos
Microbiota , Solo , Ecossistema , Cadeia Alimentar , Microbiologia do Solo , Viroma
6.
Environ Microbiol ; 23(2): 588-599, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32249528

RESUMO

Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro-ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate-binding modules. These results demonstrate that virus-encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil.


Assuntos
Biodiversidade , Microbiologia do Solo , Vírus/isolamento & purificação , Agricultura , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Ecossistema , Concentração de Íons de Hidrogênio , Filogenia , Rizosfera , Solo/química , Vírus/classificação , Vírus/genética
7.
Microb Ecol ; 75(2): 375-386, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28825127

RESUMO

A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.


Assuntos
Biodiversidade , Vírus de DNA/isolamento & purificação , Microbiologia do Solo , China , Vírus de DNA/classificação , Vírus de DNA/genética , Ecossistema , Filogenia , Salinidade , Solo/química
8.
Sci Rep ; 7: 45142, 2017 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-28327667

RESUMO

Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem "phages, prophages, transposable elements, and plasmids". Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.


Assuntos
Vírus de DNA/classificação , Vírus de DNA/genética , DNA Viral , Variação Genética , Microbiologia do Solo , Agricultura , Sequência de Aminoácidos , Proteínas do Capsídeo/química , Proteínas do Capsídeo/genética , China , Vírus de DNA/ultraestrutura , Genoma Viral , Genômica/métodos , Filogenia , Análise de Sequência de DNA
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