Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest

Haas, Julia Christa; Street, Nathaniel R.; Sjödin, Andreas; Lee, Natuschka; Högberg, Mona N.; Näsholm, Torgny; Hurry, Vaughan

doi:10.1016/j.soilbio.2018.07.005

Cited by 57 publications

(53 citation statements)

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“…These studies have revealed the importance of soil characteristics, management, and plant developmental stage on the assembly of the rhizosphere microbiome. Fewer studies have addressed the rhizosphere microbiota in perennial plants, where each growing season represents a small part of the plant's lifetime, and in particular, the bacterial communities are understudied (Wagner et al, 2016;Haas et al, 2018;Li et al, 2018). Perennial tree crops, including several conifers, are a source of products of economic importance, for example, wood, paper, and Christmas trees.…”

Section: Introductionmentioning

confidence: 99%

“…The tree crops are furthermore responsible for important ecosystem services such as carbon sequestration (Mercado-Blanco et al, 2018). Conifer tree crops are abundant in the Boreal regions, where low soil nitrogen (N) often limits plant growth (Haas et al, 2018). This limitation makes plants more dependent on interactions with microorganisms involved in the provision of N such as N-fixing bacteria and ectomycorrhizal (EM) fungi (Mercado-Blanco et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

et al. 2020

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Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growthpromoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the Frontiers in Microbiology | www.frontiersin.org March 2020 | Volume 11 | Article 198 Garcia-Lemos et al.Under the Christmas Tree greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

et al. 2020

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“…As the novelty of our method lies in the recovery of proteins from the phenol phase, typically discarded in the protocol of Griffiths et al (), we further demonstrate that our biomolecule co‐extraction is suitable for metaproteomics analysis of other soil types with varying clay contents. Indeed, the DNA and RNA co‐extraction protocol from Griffiths et al () has been cited to date by over 1,250 papers including many reporting on downstream high‐throughput sequencing, including 16SrRNA and ITS amplicon analysis (Haas et al, ; Morawe et al, ; Sayer et al, ; Whitman et al, ), metagenomics (Malik, Thomson, Whiteley, Bailey, & Griffiths, ; Soares et al, ; Wilhelm, Hanson, Chandra, & Madsen, ) and metatranscriptomics (Alessi et al, ; de Menezes, Clipson, & Doyle, ; Hesse et al, ). Here, 16S rRNA profiling from DNA and cDNA was performed on three samples corresponding to three biological replicates from one soil type (with a clay content of 11.1%) while metaproteomics was conducted for nine samples corresponding to three biological replicates from three soil types (with clay content of 11.1%, 19.4% and 35.1%).…”

Section: Introductionmentioning

confidence: 99%

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures

Thorn

Bergesch

Joyce

et al. 2019

Molecular Ecology Resources

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The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co‐recovered from the same biological samples. Commercial kits are currently available for the co‐extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol–chloroform‐based methods for nucleic acids co‐extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost‐effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high‐throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co‐extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram‐positive and Gram‐negative pure cultures.

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“…In the litter, Acinetobacter and Legionella (Proteobacteria phylum) were associated with E. uncinatum and P. apiculatum, respectively. These bacterial genera have been constantly detected in the phyllosphere and litter of several plants (Tláskal et al, 2016;Haas et al, 2018), even though we did not observe these bacterial genera as phyllosphere indicators of tree species. Our data suggest that these bacterial genera might be members of both bacteriomes, without necessarily being associated to a specific plant species.…”

Section: Discussioncontrasting

confidence: 76%

Microbiomes of the Amazon forest: bacterial diversity and community structure in the phyllosphere, litter and soil

Moreira¹

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Interações planta-bactéria 2. Florestas tropicais 3. 16S rRNA 4. Biodiversidade 5. Seca I. Título ACKNOWLEDGMENTS Special thanks to my parents, Terezinha and Elviro and my brother, Augusto, who supported and advised my journey. My fiancee Ellen, thank you a lot for everything, you were my support to overcome every hard moment, thank you for all your affection and dedication. I love you so much! I would like to acknowledge the College of Agriculture "Luiz de Queiroz", University of Sao Paulo (ESALQ/USP) for the knowledge and support. Thanks for the Molecular Microbiology Laboratory group under the coordination of Dr. Marcio Rodrigues Lambais. Prof. Dr. Marcio Lambais, I'm grateful for the opportunity to be part of this great group, thanks also for all the advises and time that you spent with me, mostly guiding me to achieve this degree. I would like to thank Prof. Dr. Jorge Luiz Mazza Rodrigues, for helping me at the University of California-Davis, where I have conducted part of my PhD. Thank you for the valuable time that you have spent for the development of my work.

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Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest

Cited by 57 publications

References 120 publications

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures

Microbiomes of the Amazon forest: bacterial diversity and community structure in the phyllosphere, litter and soil

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