Root rot alters the root-associated microbiome of field pea in commercial crop production systems

Hossain, Zakir; Hubbard, Michelle; Gan, Yantai; Bainard, Luke D.

doi:10.1007/s11104-020-04779-8

Cited by 13 publications

(4 citation statements)

References 74 publications

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“…Some genera were only found in either declined or healthy samples and could be identified as indicator genera. The number of indicator genera was slightly higher in healthy trees than in declined trees, as found in other studies (Hossain et al, 2021). On the one hand, regarding genera exclusive to healthy samples, Phoma and Periconia are known to have a plant-pathogenic lifestyle.…”

Section: Discussionsupporting

confidence: 80%

Health condition and mycobiome diversity in Mediterranean tree species

Díez-Hermano¹,

Ahmad²,

Niño-Sanchez³

et al. 2022

Front. For. Glob. Change

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IntroductionMediterranean forests are currently facing a surge in abiotic stressors such as droughts and massive fires as a result of climate crisis and human pressure. Susceptibility to biotic stressors has also increased, including a variety of pests and pathogens capable of weakening and potentially killing forest flora. Biodiversity of microbiome protects forests against declines as it increases trees’ resilience and adaptability.ObjectivesWith the objective of analyzing the relationship between health status and fungal diversity, in the present work the mycobiota of declined and healthy specimens of keystone Mediterranean tree species is described and compared.MethodsTo this end, bark and wood from declining Spanish forests of Castanea sativa (chestnut), Quercus ilex (holm oak), Quercus suber (cork oak), and Quercus pyrenaica (pyrenean oak) were sampled and the Internal Transcribed Spacer (ITS1) genomic region was sequenced.ResultsResults showed a predominance of Ascomycota, Basidiomycota, and Mucoromycota in all samples. Alpha diversity at genus level was not affected by health status and was characterized by uneven, poorly distributed fungal communities dominated by a few genera. Differentially abundant (DA) genera between healthy and declined samples were found in chestnut (15), holm oak (6), and pyrenean oak (4) trees, but not in cork oak. Some genera known for their plant protection potential, such as Trichoderma, were found exclusively in healthy trees. Functional profiles revealed a predominance of phytopathogens and saprobes in all tree species, irrespective of their health status.DiscussionThis study emphasizes the importance of Mediterranean forests as biodiversity refuges and highlights the value of above-ground tissues as a valid approach to assess shifts in forests’ microbiome diversity in response to biotic and abiotic stressors.

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Section: Discussionsupporting

confidence: 80%

Health condition and mycobiome diversity in Mediterranean tree species

Díez-Hermano¹,

Ahmad²,

Niño-Sanchez³

et al. 2022

Front. For. Glob. Change

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“…Bacterial alpha diversity metrics, in particular the Shannon Index and number of observed features, were higher in diseased samples of soil and rhizosphere (but not root) compared to healthy ones. Previous results highlighted the presence of higher bacterial diversity in samples associated with different microhabitats of diseased plants ( Hossain et al, 2021 ; Obieze et al, 2023 ). In addition, root samples had a lower richness (in terms of observed features) compared to both the rhizosphere and soil, which also aligned with previous observations of bacterial populations in plants ( Bulgarelli et al, 2012 ; Lundberg et al, 2012 ; Mukhtar et al, 2021 ; Yuan et al, 2022 ).…”

Section: Discussionmentioning

confidence: 89%

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease

Guaschino,

Garello,

Nari

et al. 2024

Front. Microbiol.

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Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.

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“…) and the root rot infected pea (Hossain et al 2021). On the contrary, we found that the ACE and Chao 1 were higher in rhizosphere soil of healthy seedlings compared to the rhizosphere soil of seedlings infected with F. solani isolate F2P2Rg and F. graminearum isolateF4P5Rk.…”

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confidence: 99%

Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species

Uwaremwe,

Bao,

Daoura

et al. 2023

Int Microbiol

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BackgroundRoot rot disease caused by soilborne pathogens is a threat to agriculture, affecting plant survival and leading to yield losses. The soil in which plants grow is inhabited by bene cial microbiome playing essential roles in various aspects of host functionality and tness. However, this microbiome composition may change based on plant health status. MethodsIn the current study, we tested the pathogenicity of pathogenic fungi isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess fungal community shifts in the rhizosphere of P. volubilis after root rot infection. ResultsFour Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents in P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on pathogen and functional taxonomic classi cation. ConclusionsBased on our results, we concluded that Fusarium spp. and Rhizopus spp. cause root rot infection of P. volubilis. In root rot infected P. volubilis, the response of the rhizosphere fungal community was pathogen dependent. These ndings may serve as a key point for a future study on biocontrol of root rot in P. volubilis.

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Root rot alters the root-associated microbiome of field pea in commercial crop production systems

Cited by 13 publications

References 74 publications

Health condition and mycobiome diversity in Mediterranean tree species

Health condition and mycobiome diversity in Mediterranean tree species

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease

Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species

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