Dataset Information

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession.

ABSTRACT: Proper quantification of the relative influence of soil and plant host on the root-associated microbiome can only be achieved by studying its distribution along an environmental gradient. Here, we used an undisturbed salt marsh chronosequence to study the bacterial communities associated with the soil, rhizosphere and the root endopshere of Limonium vulgare using 454-pyrosequencing. We hypothesize that the selective force exerted by plants rather than soil would regulate the dynamics of the root-associated bacterial assembly along the chronosequence. Our results showed that the soil and rhizosphere bacterial communities were phylogenetically more diverse than those in the endosphere. Moreover, the diversity of the rhizosphere microbiome followed the increased complexity of the abiotic and biotic factors during succession while remaining constant in the other microbiomes. Multivariate analyses showed that the rhizosphere and soil-associated communities clustered by successional stages, whereas the endosphere communities were dispersed. Interestingly, the endosphere microbiome showed higher turnover, while the bulk and rhizosphere soil microbiomes became more similar at the end of the succession. Overall, we showed that soil characteristics exerted an overriding influence on the rhizosphere microbiome, although plant effect led to a clear diversity pattern along the succession. Conversely, the endosphere microbiome was barely affected by any of the environmental measurements and very distinct from other communities.

SUBMITTER: Wang M

PROVIDER: S-EPMC4700203 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession.

Wang Miao M Yang Pu P Falcão Salles Joana J

Frontiers in plant science 20160105

Proper quantification of the relative influence of soil and plant host on the root-associated microbiome can only be achieved by studying its distribution along an environmental gradient. Here, we used an undisturbed salt marsh chronosequence to study the bacterial communities associated with the soil, rhizosphere and the root endopshere of Limonium vulgare using 454-pyrosequencing. We hypothesize that the selective force exerted by plants rather than soil would regulate the dynamics of the root ...[more]

PMID: 26779222

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Project description:Plant-associated bacteria are known for their high functional trait diversity, from which many are likely to play a role in primary and secondary succession, facilitating plant establishment in suboptimal soils conditions. Here we used an undisturbed salt marsh chronosequence that represents over 100 years of soil development to assess how the functional traits of plant associated bacteria respond to soil type, plant species and plant compartment. We isolated and characterized 808 bacterial colonies from the rhizosphere soil and root endosphere of two salt marsh plants, Limonium vulgare and Artemisia maritima, along the chronosequence. From these, a set of 59 strains (with unique BOX-PCR patterns, 16S rRNA sequence and unique to one of the treatments) were further screened for their plant growth promoting traits (siderophore production, IAA production, exoprotease production and biofilm formation), traits associated with bacterial fitness (antibiotic and abiotic stress resistance - pH, osmotic and oxidative stress, and salinity) and metabolic potential. An overall view of functional diversity (multivariate analysis) indicated that the distributional pattern of bacterial functional traits was driven by soil type. Samples from the late succession (Stage 105 year) showed the most restricted distribution, harboring strains with relatively low functionalities, whereas the isolates from intermediate stage (35 year) showed a broad functional profiles. However, strains with high trait performance were largely from stage 65 year. Grouping the traits according to category revealed that the functionality of plant endophytes did not vary along the succession, thus being driven by plant rather than soil type. In opposition, the functionality of rhizosphere isolates responded strongly to variations in soil type as observed for antibiotic resistance (P = 0.014). Specifically, certain Pseudomonas sp. and Serratia sp. strains revealed high resistance against abiotic stress and antibiotics and produce more siderophores, confirming the high plant-growth promoting activity of these two genera. Overall, this study contributes to a better understanding of the functional diversity and adaptation of the microbiome at typical salt marsh plant species across soil types. Specifically, soil type was influential only in the rhizosphere but not on the endosphere, indicating a strong plant-driven effect on the functionality of endophytes.

Project description:Background:The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier's retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods:The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results:nosZ-denitrifiers were more abundant and diverse in soils from successional years 20-60 compared to 0-5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40-60 years) than in younger soils (?20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0-20 years) and in the mature phase (40-60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).

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Project description:Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

Dataset Information

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession.

Publications

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession.

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