Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

In this very large-scale longitudinal field study of the maize rhizosphere microbiome, we identify heritable taxa. These taxa display variance in their relative abundances that can be partially explained by genetic differences between the maize lines, above and beyond the strong influences of field, plant age, and weather on the diversity of the rhizosphere microbiome. If these heritable taxa are associated with beneficial traits, they may serve as phenotypes in future breeding endeavors.

Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.

16S rDNA Profiling to Reveal the Influence of Seed-Applied Biostimulants on the Rhizosphere of Young Maize Plants

In an open field trial on two agricultural soils in NW Italy, the impact of two seed-applied biostimulants on the rhizosphere bacterial community of young maize plants was evaluated. The 16S rDNA profiling was carried out on control and treated plant rhizosphere samples collected at the 4-leaf stage and on bulk soil. In both soils, the rhizospheres were significantly enriched in Proteobacteria, Actinobacteria, and Bacteriodetes, while the abundances of Acidobacteria, Cloroflexi and Gemmatimonadetes decreased compared with bulk soil. Among the culturable bacteria genera that showed an increase by both biostimulants, most are known to be beneficial for nutrient uptake, such as Opitutus, Chryseolinea, Terrimonas, Rhodovastum, Cohnella, Pseudoduganella and the species Anaeromyxobacter dehalogenans; others are known to be involved in root growth, such as Niastella, Labrys, Chloroflexia and Thermomonas; or in plant defence, such as Ohtaekwangia, Quadrisphaera, Turneriella, and Actinoallomurus. Both biostimulants were also found to stimulate gen. Nannocystis, a potential biocompetitive agent against aflatoxigenic Aspergillus moulds. Under controlled conditions, both biostimulants enhanced the shoot and root biomass at the 4⁻5 leaf stage. We conclude that the biostimulants do not decrease the biodiversity of the microbial community rhizosphere of young maize plants, but stimulate rare bacterial taxa, some involved in plant growth and pathogen resistance, a result that may have implications in improving crop management.

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil

Exploiting native plant growth-promoting rhizobacteria (PGPR) in Cameroonian agro-ecosystems provides a means to improve plant-microbe interactions that may enhance ecosystem sustainability and agricultural productivity in an environmentally eco-friendly way. Consequently, we aimed to investigate the community structure and functional PGPR diversity of maize grown in Cameroon. Native bacteria isolated from Cameroon maize rhizosphere soil were identified by partial 16S rRNA gene sequencing and screened for traits particularly relevant for Cameroon low-fertility soil conditions, such as their abilities to tolerate high concentrations of salt, and their plant growth- promoting potential. Genetic and functional diversity was characterized according to their phylogenetic affiliation. A total of 143 bacteria were identified and assigned to 3 phyla (Actinobacteria, Firmicutes and Proteobacteria), 13 families and 20 genera. Bacillus (31.5%), Arthrobacter (17.5%), and Sinomonas (13.3%) were the most abundant genera identified among all the isolates. Based on their in vitro characterization, 88.1% were salt tolerant at 2% NaCl, but only 16.8% could tolerate 8% NaCl, 50.4% solubilized phosphate, 10.5% possessed the nifH gene, and 19.6% produced siderophores. Six isolates affiliated to the most abundant genera identified in this work, Bacillus and Arthrobacter, carrying multiple or only single tested traits were selected to evaluate their growth- promoting potential in an in vitro maize germination assay. Three strains possessing multiple traits induced significantly increased hypocotyl and root length of maize seeds compared to non-inoculated control seeds. Our results indicate the potential of selected indigenous Cameroon rhizobacteria to enhance maize growth.

The impact of the omics era on the knowledge and use of Lysobacter species to control phytopathogenic micro-organisms

Omics technologies have had a tremendous impact on underinvestigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture-independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics. Indeed, genomics has revealed that biocontrol Lysobacter strains share a vast number of genes involved in antagonism activities, and the molecular pathways underlying how Lysobacter spp. interact with the environment and other micro-organisms have been depicted through transcriptomic analysis. Furthermore, omics technologies shed light on the regulatory pathways governing cell motility and the biosynthesis of antibiotics. Overall, the results achieved so far through omics technologies confirm that the genus Lysobacter is a valuable source of novel biocontrol agents, paving the way for studies aimed at making their application in field conditions more reliable.

Brachiaria Grasses (Brachiaria spp.) harbor a diverse bacterial community with multiple attributes beneficial to plant growth and development

Endophytic and plant-associated bacteria were isolated from plants and rhizoplane soil of naturally grown Brachiaria grasses at International Livestock Research Institute in Nairobi, Kenya. Eighty-four bacterial strains were isolated from leaf tissues, root tissues, and rhizoplane soil on nutrient agar and 869 media. All bacterial strains were identified to the lowest possible taxonomic unit using 16S rDNA primers and were characterized for the production of Indole-3-acetic acid, hydrogen cyanide, and ACC deaminase; phosphate solubilization; siderophore production; antifungal properties; and plant biomass production. The 16S rDNA-based identification grouped these 84 bacterial strains into 3 phyla, 5 classes, 8 orders, 12 families, 16 genera, and 50 unique taxa. The four most frequently isolated genera were Pseudomonas (23), Pantoea (17), Acinetobacter (9), and Enterobacter (8). The functional characterization of these strains revealed that 41 of 84 strains had a minimum of three plant beneficial properties. Inoculation of maize seedlings with Acinetobacter spp., Microbacterium spp., Pectobacterium spp., Pseudomonas spp., and Enterobacter spp. showed positive effects on seedling biomass production. The ability of Brachiaria grasses to host genetically diverse bacteria, many of them with multiple plant growth-promoting attributes, might have contributed to high biomass production and adaptation of Brachiaria grasses to drought and low fertility soils.

Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing

In this study, we designed a microcosm experiment to explore the composition of the bacterial community in the rhizosphere of maize and bulk soil by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina system. 978–1239 OTUs (cut off level of 3%) were found in rhizosphere and bulk soil samples. Rhizosphere shared features with the bulk soil, such as predominance of Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes and TM7. At genus level, many of the dominant rhizosphere genera (Chitinophaga, Nitrospira, Flavobacterium, etc.) displayed different patterns of temporal changes in the rhizosphere as opposed to the bulk soil, showing rhizosphere has more impact on soil microorganisms. Besides, we found that significant growth-related dynamic changes in bacterial community structure were mainly associated with phylum Bacteroidetes, Proteobacteria and Actinobacteria (mainly genera Burkholderia, Flavisolibacter and Pseudomonas), indicating that different growth stages affected the bacterial community composition in maize soil. Furthermore, some unique genera in especial Plant-Growth Promoting Rhizobacteria (PGPR) such as Nonomuraea, Thiobacillus and Bradyrhizobium etc., which were beneficial for the plant growth appeared to be more abundant in the rhizosphere than bulk soil, indicating that the selectivity of root to rhizosphere microbial is an important mechanism leading to the differences in the bacteria community structure between rhizosphere and bulk soil.

Simplified and representative bacterial community of maize roots

Plant-associated microbes are important for the growth and health of their hosts. As a result of numerous prior studies, we know that host genotypes and abiotic factors influence the composition of plant microbiomes. However, the high complexity of these communities challenges detailed studies to define experimentally the mechanisms underlying the dynamics of community assembly and the beneficial effects of such microbiomes on plant hosts. In this work, from the distinctive microbiota assembled by maize roots, through host-mediated selection, we obtained a greatly simplified synthetic bacterial community consisting of seven strains (Enterobacter cloacae, Stenotrophomonas maltophilia, Ochrobactrum pituitosum, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum, and Chryseobacterium indologenes) representing three of the four most dominant phyla found in maize roots. By using a selective culture-dependent method to track the abundance of each strain, we investigated the role that each plays in community assembly on roots of axenic maize seedlings. Only the removal of E. cloacae led to the complete loss of the community, and C. pusillum took over. This result suggests that E. cloacae plays the role of keystone species in this model ecosystem. In planta and in vitro, this model community inhibited the phytopathogenic fungus Fusarium verticillioides, indicating a clear benefit to the host. Thus, combined with the selective culture-dependent quantification method, our synthetic seven-species community representing the root microbiome has the potential to serve as a useful system to explore how bacterial interspecies interactions affect root microbiome assembly and to dissect the beneficial effects of the root microbiota on hosts under laboratory conditions in the future.

Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida

Pseudomonas putida strains are frequent inhabitants of soil and aquatic niches and they are occasionally isolated from hospital environments. As the available iron sources in human tissues, edaphic, and aquatic niches are different, we have analyzed iron-uptake related genes in different P. putida strains that were isolated from all these environments. We found that these isolates can be grouped into different clades according to the genetics of siderophore biosynthesis and recycling. The pyoverdine locus of the six P. putida clinical isolates that have so far been completely sequenced, are not closely related; three strains (P. putida HB13667, HB3267, and NBRC14164T) are grouped in Clade I and the other three in Clade II, suggesting possible different origins and evolution. In one clinical strain, P. putida HB4184, the production of siderophores is induced under high osmolarity conditions. The pyoverdine locus in this strain is closely related to that of strain P. putida HB001 which was isolated from sandy shore soil of the Yellow Sea in Korean marine sand, suggesting their possible origin, and evolution. The acquisition of two unique TonB-dependent transporters for xenosiderophore acquisition, similar to those existing in the opportunistic pathogen P. aeruginosa PAO, is an interesting adaptation trait of the clinical strain P. putida H8234 that may confer adaptive advantages under low iron availability conditions.

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome

Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches

Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing

Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize intercropped with bur clover, and Gp4, Subdivision3 genera incertae sedis of phylum Verrucomicrobia, Gp6 and Rhodoferax were the main genera in the rhizosphere of maize plants. Taken together, our results suggest that bur clover produces specific changes in rhizospheric bacterial diversity of amilaceous maize plants.

Influences of Land Use/Cover Types on Nitrous Oxide Emissions during Freeze-Thaw Periods from Waterlogged Soils in Inner Mongolia

Nitrous oxide emissions during freeze/thaw periods contribute significantly to annual soil N₂O emissions budgets in middle- and high-latitude areas; however, the freeze/thaw-related N₂O emissions from waterlogged soils have hardly been studied in the Hulunber Grassland, Inner Mongolia. For this study, the effects of changes in land use/cover types on N₂O emissions during freeze–thaw cycles were investigated to more accurately quantify the annual N₂O emissions from grasslands. Soil cores from six sites were incubated at varying temperature (ranging from −15 to 10°C) to simulate freeze–thaw cycles. N₂O production rates were low in all soil cores during freezing periods, but increased markedly after soil thawed. Mean rates of N₂O production differed by vegetation type, and followed the sequence: Leymus chinensis (LC) and Artemisia tanacetifolia (AT) steppes > LC steppes ≥ Stipa baicalensis (SB) steppes. Land use types (mowing and grazing) had differing effects on freeze/thaw-related N₂O production. Grazing significantly reduced N₂O production by 36.8%, while mowing enhanced production. The production of N₂O was related to the rate at which grassland was mowed, in the order: triennially (M3) > once annually (M1) ≥ unmown (UM). Compared with the UM control plot, the M3 and M1 mowing regimes enhanced N₂O production by 57.9% and 13.0% respectively. The results of in situ year-round measurements showed that large amounts of N₂O were emitted during the freeze–thaw period, and that annual mean fluxes of N₂O were 9.21 μg N₂O-N m^-2 h^-1 (ungrazed steppe) and 6.54 μg N₂O-N m^-2 h^-1 (grazed steppe). Our results further the understanding of freeze/thaw events as enhancing N₂O production, and confirm that different land use/cover types should be differentiated rather than presumed to be equivalent, regarding nitrous oxide emission. Even so, further research involving multi-year and intensive measurements of N₂O emission is still needed.

Field trial on removal of petroleum-hydrocarbon pollutants using a microbial consortium for bioremediation and rhizoremediation

Petroleum waste sludges are toxic and dangerous that is why environmental protection agencies have declared their treatment top priority. Physicochemical treatments are expensive and environmentally unfriendly, while alternative biological treatments are less costly but, in general, work at a slower pace. An in situ bioremediation and rhizoremediation field scale trial was performed in an area contaminated with oil refinery sludge under semiarid climate. The bioremediation and rhizoremediation treatments included the use of an artificial consortium made up of plant growth-promoting rhizobacteria and polycyclic aromatic hydrocarbon-degrading bacteria,and the combined use of the mentioned consortium along with pasture plants respectively. Rhizoremediation revealed that the development of vegetation favoured the evolution of indigenous microbiota with potential to remove petroleum wastes. This was inferred as the decline of total petroleum hydrocarbons 7 months after the biological treatment.

Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site

We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.

Host signature effect on plant root-associated microbiomes revealed through analyses of resident vs. active communities

Plant roots create specific microbial habitat in the soil - the rhizosphere. In this study, we characterized the rhizosphere microbiome of four host plant species to get insight into the impact of the host (host signature effect) on resident vs. active communities. Results show a distinct plant host specific signature found among wheat, maize, tomato and cucumber, based on the following three parameters: (i) each plant promoted the activity of a unique suite of soil bacterial populations; (ii) significant variations were observed in the number and the degree of dominance of active populations; and (iii) the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants, a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This study demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations.

In vivo gene expression of Pseudomonas putida KT2440 in the rhizosphere of different plants

Pseudomonas putida KT2440 has the ability to colonize the rhizosphere of a wide range of plants and can reach cell densities in the range of 10⁵–10⁶ cfu g soil⁻¹. Using the IVET technology we investigated which KT2440 genes were expressed in the rhizosphere of four different plants: pine, cypress, evergreen oak and rosemary. We identified 39 different transcriptional fusions containing the promoters of annotated genes that were preferentially expressed in the rhizosphere. Six of them were expressed in the rhizosphere of all the plant types tested, 11 were expressed in more than one plant and the remaining 22 fusions were found to be expressed in only one type of plant. Another 40 fusions were found to correspond to likely promoters that encode antisense RNAs of unknown function, some of which were isolated as fusions from the bacteria recovered in the rhizosphere from all of the plants, while others were specific to one or several of the plants. The results obtained in this study suggest that plant-specific signals are sensed by KT2440 in the rhizosphere and that the signals and consequent gene expression are related to the bacteria's successful establishment in this niche.