The Plant Microbiota: Systems-Level Insights and Perspectives

Müller, Daniel B.; Vogel, Christine; Bai, Yang; Vorholt, Julia A.

doi:10.1146/annurev-genet-120215-034952

Cited by 672 publications

(562 citation statements)

References 160 publications

(258 reference statements)

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“…THE LEGUME PHYTOMICROBIOME Investigations on phytomicrobiomes, particularly the phyllosphere and rhizosphere microbiota have uncovered considerable information, particularly in Arabidopsis, using metagenomic, transcriptomic, proteomic, and metabolomic analyses (reviewed by Müller et al 2016). Also well-studied are the Arabidopsis phytomicrobiome responses to biotic and abiotic stresses as well as the changes that occur during a plant's development from seedling stage to maturity (Chaparro et al 2014) and flowering (Wagner et al 2014).…”

Section: Do Nonrhizobial Bacteria Residing Within the Nodule Influencmentioning

confidence: 99%

The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

Martínez‐Hidalgo

Hirsch

2017

Phytobiomes Journal

245

163

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For decades, rhizobia were thought to be the only nitrogen-fixing inhabitants of legume nodules, and biases in culture techniques prolonged this belief. However, other bacteria, which are not typical rhizobia, are often detected within nodules obtained from soil, thus revealing the existence of a phytomicrobiome where the interaction among the individuals is not only complex, but also likely to affect the behavior and fitness of the host plant. Many of these nonrhizobial bacteria are nitrogen fixers, and some also induce nitrogen-fixing nodules on legume roots. Even more striking is the incredibly diverse population of bacteria residing within nodules that elicit neither nodulation nor nitrogen fixation. Yet, this community exists within the nodule, albeit clearly out-numbered by nitrogen-fixing rhizobia. Few studies of the function of these nodule-associated bacteria in nodules have been performed, and to date, it is not known whether their presence in nodules is biologically important or not. Do they confer any benefits to the Rhizobium-legume nitrogen-fixing symbiosis, or are they parasites/saprophytes, contaminants, or commensals? In this review, we highlight the lesser-known bacteria that dwell within nitrogen-fixing nodules and discuss their possible role in this enclosed community as well as any likely benefits to the host plant or to the rhizobial inhabitants of the nodule. Although many of these nodule inhabitants are not capable of nitrogen fixation, they have the potential to enhance legume survival especially under conditions of environmental stress. This knowledge will be useful in defining strategies to employ these bacteria as bioinoculants by themselves or combined with rhizobia. Such an approach will enhance rhizobial performance or persistence as well as decrease the usage of chemical fertilizers and pesticides.

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Section: Do Nonrhizobial Bacteria Residing Within the Nodule Influencmentioning

confidence: 99%

The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

Martínez‐Hidalgo

Hirsch

2017

Phytobiomes Journal

245

163

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“…Proving the mode of transmission and determining transmission rates are technically challenging, as many members of the seed microbiota overlap with microorganisms that are also commonly detected in rhizosphere soils, bulk soils, plant systemic tissue, and air [10,39,[48][49][50][51]. Thus, analysis of overlap among microbiota members across plant compartments or generations planted in the field is not sufficient to prove vertical transmission, even if seeds are specifically investigated.…”

Section: Current Opinion In Microbiologymentioning

confidence: 99%

“…To date many studies have investigated the composition and structure of microbiota associated with the phyllosphere and rhizosphere (Box 1) of numerous plant species during their vegetative or reproductive stages [10]. In contrast, analyses of microbiota associated with other plant habitats such as the anthosphere [11], the carposphere [12][13][14][15], the seed habitat [16] and the spermosphere [17 ,18] have been relatively less studied.…”

Section: Introductionmentioning

confidence: 99%

Ecological patterns of seed microbiome diversity, transmission, and assembly

Shade

Martin

Barret

2017

Current Opinion in Microbiology

342

280

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Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined.

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“…Beneficial endophytic bacteria play important roles that positively affect directly or indirectly plant growth and development [19]. In this study we selected 15 putative bacterial endophytes isolated from Venezuelan rice because they were IAA producers.…”

Section: Isolation Of Putative Endophytic Bacteria Determination Ofmentioning

confidence: 99%

“…Microbial bioinoculants face competition with the native soil microbiota and also need to withstand the natural abiotic conditions of soil and weather. A reductionist approach using simplified communities as models could facilitate the understanding of the microbial and plant-microbes interactions that occur in the soil [19].…”

Section: Introductionmentioning

confidence: 99%

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Moronta-Barrios¹,

Gionechetti²,

Pallavicini³

et al. 2017

Preprint

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Abstract:Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of hundreds bacterial isolates obtained from endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.

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The Plant Microbiota: Systems-Level Insights and Perspectives

Cited by 672 publications

References 160 publications

The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

Ecological patterns of seed microbiome diversity, transmission, and assembly

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

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The Plant Microbiota: Systems-Level Insights and Perspectives

Cited by 672 publications

References 160 publications

The Nodule Microbiome: N2-Fixing Rhizobia Do Not Live Alone

The Nodule Microbiome: N2-Fixing Rhizobia Do Not Live Alone

Ecological patterns of seed microbiome diversity, transmission, and assembly

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

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Product

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The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone

The Nodule Microbiome: N₂-Fixing Rhizobia Do Not Live Alone