Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?

Qiu, Zhiguang; Wang, Juntao; Delgado‐Baquerizo, Manuel; Trivedi, Pankaj; Egidi, Eleonora; Zhang, Haiyang; Singh, Brajesh K.

doi:10.3389/fpls.2020.00993

Cited by 18 publications

(18 citation statements)

References 61 publications

(89 reference statements)

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“…Extracted DNA was quality checked by NanoDrop 2000 (Thermo Fisher Scientific), and PCR checked to confirm the amplifiability. Amplicon sequencing was performed using 799F/1193R targeting 16S rRNA for bacteria and ITS2 region FITS7‐ITS4R (Hamonts et al, 2018; H. Liu et al, 2019; Qiu et al, 2020) at the Next‐Generation Sequencing Facility, Western Sydney University, Richmond, NSW Australia.…”

Section: Methodsmentioning

confidence: 99%

Synthetic community improves crop performance and alters rhizosphere microbial communities

Kaur

Egidi

Qiu

et al. 2022

J of Sust Agri & Env

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Introduction Harnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐scale adoption by the farming community. Material & Methods In this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed. Results Results showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria. Conclusion Overall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity.

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Section: Methodsmentioning

confidence: 99%

Synthetic community improves crop performance and alters rhizosphere microbial communities

Kaur

Egidi

Qiu

et al. 2022

J of Sust Agri & Env

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“…For characterizing the bacterial communities, primers 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′) were used to amplify the V3 and V4 region of 16S rDNA gene ( Herlemann et al, 2011 ; Qiu et al, 2020 ). 25 μL PCR reactions were performed with 40 ng μL –1 template DNA, 12.5 μL Multiplex Master Mix (Qiagen, Mexico), 1.25 μL each primer, 6 μL MilliQ water.…”

Section: Methodsmentioning

confidence: 99%

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens

et al. 2021

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The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria, Bacillus spp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity of Mortierella sp., Fusarium spp., Lasiodiplodia sp. and Scytalidium sp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.

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“…The four DNA extraction kits tested in this study were chosen on the basis of previous studies that had yielded good sequencing results. Two of the kits were designed especially for soil samples (Kits 2 and 4) and had been previously used for extracting DNA from decomposing leaf litter (Kit 2; Tláskal et al, 2016) or in other studies that compared extraction procedures to minimize the introduction of bias (Kit 2, Qiu et al, 2020; Kit 4, Sare et al, 2020). Kit 3 was used to extract DNA from macrophyte leaf litter decomposition (Zhao et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…Here, we compare four commercial kits originally designed for water or soil. With the exception of the DNeasy PowerWater Kit, which is mainly used for DNA extraction from large water samples, the kits have been used in other studies focusing on plant microbiomes (Tláskal et al, 2016; Zhao et al, 2017; Qiu et al, 2020; Sare et al, 2020). The goal of our study is to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis.…”

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confidence: 99%

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

Janssen¹,

Low

Wang

et al. 2021

Appl Plant Sci

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Premise Within a broader study on leaf fossilization in freshwater environments, a long‐term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis. Methods We extracted surface‐associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits. Results Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition. Discussion The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram‐positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

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Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?

Abstract: data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.

Cited by 18 publications

References 61 publications

Synthetic community improves crop performance and alters rhizosphere microbial communities

Synthetic community improves crop performance and alters rhizosphere microbial communities

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

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