Rhizosphere Bacterial Composition Research Articles

The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease.

Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.

Effects of coastal saline-alkali soil on rhizosphere microbial community and crop yield of cotton at different growth stages.

Soil salinization is a global constraint that significantly hampers agricultural production, with cotton being an important cash crop that is not immune to its detrimental effects. The rhizosphere microbiome plays a critical role in plant health and growth, which assists plants in resisting adverse abiotic stresses including soil salinization. This study explores the impact of soil salinization on cotton, including its effects on growth, yield, soil physical and chemical properties, as well as soil bacterial community structures. The results of β-diversity analysis showed that there were significant differences in bacterial communities in saline-alkali soil at different growth stages of cotton. Besides, the more severity of soil salinization, the more abundance of Proteobacteria, Bacteroidota enriched in rhizosphere bacterial composition where the abundance of Acidobacteriota exhibited the opposite trend. And the co-occurrence network analysis showed that soil salinization affected the complexity of soil bacterial co-occurrence network. These findings provide valuable insights into the mechanisms by which soil salinization affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving soil salinization using beneficial microorganisms.

A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt

Abstract Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2−, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils.

Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of 'Valencia' sweet orange (Citrus × sinensis) trees grafted on 'US-812' (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.

Responses of wheat nitrogen uptake and utilization, rhizosphere bacterial composition and nitrogen-cycling functional genes to nitrogen application rate, planting density and their interactions

The nitrogen application rate and planting density affect soil physiochemical properties, plant physiological characteristics, and soil bacterial community composition. In this study, a two-factor randomized block design was adopted with two planting density levels (high density, HD and low density, LD), and three nitrogen application rate levels (no nitrogen application, N0, low nitrogen application, LN and high nitrogen application, HN). The results showed that the highest yield was produced by LDHN and HDLN, while HDLN had the highest nitrogen use efficiency. Root dry weight was highest in HDHN, followed by HDLN, LDHN and LDLN, while the root nitrogen content was highest in LDHN and HDLN. In the 0–20 cm soil, LDLN had the highest pH and lowest nitrate nitrogen content, HDHN had the lowest pH, and HDLN had the highest content of soluble organic nitrogen and free amino acids. In addition, compared to LDHN, the bacterial community in HDLN and LDLN had higher α diversity and a higher relative abundance of functional genes involved in nitrate reduction. However, HDHN was the opposite. Additionally, correlation analysis also found that the abundance of some bacterial modules was significantly correlated with wheat nitrogen partial factor productivity. Overall, nitrogen application rates and planting density, through changing the physicochemical properties of rhizosphere soil, bacterial composition and function, and wheat root physiological properties, changed the nitrogen utilization and yield of wheat.

Effects of grazing intensity on diversity and composition of rhizosphere and non-rhizosphere microbial communities in a desert grassland.

Overgrazing-induced grassland degradation has become a serious ecological problem worldwide. The diversity and composition of soil microbial communities are sensitive to grazing disturbances. However, our understanding is limited with respect to the effects of grazing intensity on bacterial and fungal communities, especially in plant rhizosphere. Using a long-term grazing experiment, we evaluated the diversity and composition of microbial communities in both rhizosphere and non-rhizosphere soils under three grazing intensities (light, moderate, and heavy grazing) in a desert grassland and examined the relative roles of grazing-induced changes in some abiotic and biotic factors in affecting the diversity and composition of microbial communities. Our results showed that soil bacteria differed greatly in diversity and composition between rhizosphere and non-rhizosphere zones, and so did soil fungi. Moderate and heavy grazing significantly reduced the rhizosphere bacterial diversity. Grazing intensity substantially altered the bacterial composition and the fungal composition in both zones but with different mechanisms. While root nitrogen and soil nitrogen played an important role in shaping the rhizosphere bacterial composition, soil-available phosphorus greatly affected the non-rhizosphere bacterial composition and the fungal composition in both soils. This study provides direct experimental evidence that the diversity and composition of microbial communities were severely altered by heavy grazing on a desert grassland. Thus, to restore the grazing-induced, degraded grasslands, we should pay more attention to the conservation of soil microbes in addition to vegetation recovery.

Genotype-Specific Recruitment of Rhizosphere Bacteria From Sandy Loam Soil for Growth Promotion of Cucumis sativus var. hardwickii.

The composition and structure of the rhizosphere microbiome is affected by many factors, including soil type, genotype, and cultivation time of the plant. However, the interaction mechanisms among these factors are largely unclear. We use culture-independent 16S rRNA amplicon sequencing to investigate the rhizosphere bacterial composition and the structure of cultivated cucumber Xintaimici (XT) and wild-type cucumber Cucumis sativus var. hardwickii (HD) in four kinds of soils. We found that soil type, cultivation time, and genotype affected the composition and structure of cucumber rhizosphere bacterial communities. Notably, HD showed better physiological features in sandy soil and sandy loam soil than it did in black soil and farm soil at 50 days post-sowing, which was due to its stronger recruitment ability to Nitrospira, Nocardioides, Bacillus, and Gaiella in sandy soil, and more Tumebacillus, Nitrospira, and Paenibacillus in sandy loam soil. Meanwhile, we also found that HD showed a better recruiting capacity for these bacterial genera than XT in both sandy soil and sandy loam soil. Functional predictions indicated that these bacteria might have had stronger root colonization ability and then promoted the growth of cucumbers by enhancing nitrogen metabolism and active metabolite secretion. In this study, our findings provided a better insight into the relationship between cucumber phenotype, genotype, and the rhizosphere bacterial community, which will offer valuable theoretical references for rhizosphere microbiota studies and its future application in agriculture.

Host genomic influence on bacterial composition in the switchgrass rhizosphere.

Host genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range. Here, we compared 383 switchgrass accessions in a common garden to determine the host genotypic influence on rhizosphere bacterial composition. We hypothesized that the composition and diversity of rhizosphere bacterial assemblages would differentiate due to genotypic differences between hosts (potentially due to root phenotypes and associated life history variation). We observed higher alpha diversity of bacteria associated with upland ecotypes and tetraploids, compared to lowland ecotypes and octoploids, respectively. Alpha diversity correlated negatively with flowering time and plant height, indicating that bacterial composition varies along switchgrass life history axes. Narrow-sense heritability (h2 ) of the relative abundance of 21 core bacterial families was observed. Overall compositional differences among tetraploids, due to genetic variation, supports widespread genotypic influence on the rhizosphere microbiome. Tetraploids were only considered due to complexities associated with the octoploid genomes. Lastly, a genome-wide association study identified 1861 single-nucleotide polymorphisms associated with 110 families and genes containing them related to potential regulatory functions. Our findings suggest that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments.

Untangling the Rhizosphere Bacterial Community Composition and Response of Soil Physiochemical Properties to Different Nitrogen Applications in Sugarcane Field

Minimizing the use of chemical fertilizers and investigating an appropriate ecofriendly level of nitrogen fertilizer is the key to sustainable agriculture. Sugarcane is the main cash crop of China, especially in the Guangxi region. Information regarding the effect of different nitrogen levels on sugarcane rhizosphere microbiota is still limited. In this study, we evaluated the effect of four different levels of nitrogen fertilizers on rhizosphere bacterial composition using high throughput sequencing, along with soil physiochemical properties, sugarcane agronomic and yield performance. The four treatment combinations were CK (no fertilizers), L (Low, 100 kg ha–1), M (Medium, 150 kg ha–1), and H (High, 200 kg ha–1). The results showed that M nitrogen application significantly altered the rhizosphere bacterial community, soil properties, and sugarcane yield. The richness and evenness of the bacterial community were higher in M treatment than CK. In M treatment important bacterial phyla Acidobacteria and Proteobacteria increased by 47 and 71%, respectively; and at genus level, Acidothermus and Bradyrhizobium increased by 77.2 and 30.3%, respectively, compared to CK. Principal component analysis (PCA) and cluster analysis further confirmed the level of differences among the treatments. The PCA analysis explained 80% of the total variation among the treatments. Spearmen correlation heatmap showed that environmental factors such as pH, AP (available phosphorous), AK (available potassium), and SCAT (soil catalase) were the key factors impacting sugarcane rhizosphere microbiome composition. The H and L nitrogen application alter the bacterial community and sugarcane performance but the M nitrogen application appears to be ecofriendly, productive, and an appropriate nitrogen application rate that could be further used in the Guangxi region.

Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

Invasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions.

Investigation of soil nutrients and associated rhizobacterial communities in different sugarcane genotypes in relation to sugar content

BackgroundPlant microbiomes and soil are bridged by rhizobacteria, maintaining and improving plant health and growth in different aspects. This study was conducted in the field station of the Guangxi University, Fusui, China. We investigated soil nutrients, root morphology and rhizosphere bacterial composition, and community structures in 18 sugarcane genotypes concerning sugar content under the same environmental condition.ResultsMost of the rhizosphere microbiomes of these genotypes exhibited similar bacterial compositions. However, the evaluated genotypes harbored a significant effect and difference in the abundance of operational taxonomic units and bacterial composition in the rhizosphere compartments. Alpha diversity analysis on the rhizosphere microbiome showed a significant difference in the bacterial diversity (Shannon index, p < 0.001) and OTU richness (Chao1, p < 0.001). The principal coordinate analysis (PCoA) and hierarchical cluster analysis revealed that the genotype replicated samples grouped, indicating their similarity. Besides, these genotypes also differed significantly in terms of root structure and soil properties. A significant genotypic effect (p < 0.05) was found in the root traits except for rooting depth. The soil chemical properties were significantly different among the evaluated genotypes. Furthermore, sucrose content was strongly correlated with the total root length (TRL) and rooting depth. Genotypes (FN-1702, GUC-3, ZZ-13, ZZ-10, ZZ-6) were the best performing and distinct in bacterial diversity, root structure, soil parameters and sucrose content.ConclusionThe results showed a closely related and highly conserved bacterial community of the rhizosphere microbiome. The rhizosphere microbiome diversity and related bacterial communities were highly associated with the relevant plant taxa, probably at the order level. As a result, it is possible to conclude that the host genotype and the same environmental condition influenced the rhizosphere microbiome via root phenes. Future research regarding plant phenes and microbiome functional groups could be considered an essential factor.Graphic abstract

Effects of mancozeb on citrus rhizosphere bacterial community

Multiple and consecutive application of fungicide might damage the rhizosphere bacterial community of citrus. In order to evaluated effect of mancozeb on the chemical properties of citrus-cultivated soil and the richness and diversity of rhizosphere bacterial community. The abundance response of rhizosphere bacterial groups without application or with application of 1.333 g mg−1 mancozeb for 2, 4, 6 and 8 times were investigated, and further studied the relationship between the rhizosphere bacterial community and chemical properties of citrus-cultivated soil. We found the rhizosphere bacterial composition and diversity were distinct between soil planted with citrus and without citrus, in addition, the abundance of rhizosphere-associated bacterial species in the soil planted with citrus increased significantly. Meanwhile, the chemical properties and the richness and diversity of rhizosphere bacterial community of the soil planted with citrus did not significantly change among different application frequence of mancozeb. Moreover, with the increased applying times of mancozeb, the relative abundance of Candidatus, Saccharibacteria, Parcubacteria, and Proteobacteria increased but the abundance of Nitrospirae decreased. In our one-year trial, there were less adverse effects of mancozeb on the citrus-cultivated rhizosphere by the repeated application of mancozeb. Therefore, mancozeb, as a fungicide, could be used multiple times to control citrus disease.

Induced secretion system mutation alters rhizosphere bacterial composition in Sorghum bicolor (L.) Moench

Main conclusionA novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623.Favorable plant–microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.

Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica.

Elytrigia atherica is a native invasive plant species whose expansion on salt marshes is attributed to genotypic and phenotypic adaptations to non-ideal environmental conditions, forming two ecotypes. It is unknown how E. atherica–microbiome interactions are contributing to its adaptation. Here we investigated the effect of sea-water flooding frequency and associated soil (a)biotic conditions on plant traits and root-associated microbial community composition and potential functions of two E. atherica ecotypes. We observed higher endomycorrhizal colonization in high-elevation ecotypes (HE, low inundation frequency), whereas low-elevation ecotypes (LE, high inundation frequency) had higher specific leaf area. Similarly, rhizosphere and endosphere bacterial communities grouped according to ecotypes. Soil ammonium content and elevation explained rhizosphere bacterial composition. Around 60% the endosphere amplicon sequence variants (ASVs) were also found in soil and around 30% of the ASVs were ecotype-specific. The endosphere of HE-ecotype harbored more unique sequences than the LE-ecotype, the latter being abundant in halophylic bacterial species. The composition of the endosphere may explain salinity and drought tolerance in relation to the local environmental needs of each ecotype. Overall, these results suggest that E. atherica is flexible in its association with soil bacteria and ecotype-specific dissimilar, which may enhance its competitive strength in salt marshes.

The response of arsenic bioavailability and microbial community in paddy soil with the application of sulfur fertilizers

Arsenic (As) has been recognized as one of the most toxic metalloids present in the surface soil contaminating food chain and posing threat to human life. Sulfur (S) fertilizer is often supplied in paddy soil for rice growth, but its impact on As mobility and related bacteria remains poorly understood. In this study, a pot experiment was set up with two different types of sulfur treatments (element sulfur and Na2SO4) to evaluate the effect of sulfur fertilizers on As speciation in porewater, As fractions in soil, As accumulation in rice plants. Besides, rhizosphere bacterial composition and functional genes that might influence As mobility were also studied. The results revealed that the addition of 150 mg/kg Na2SO4 decreased As(III) and As(V) concentrations in soil porewater at maturation stage by 77% and 64%, respectively. With the same sulfur content, Na2SO4 was more effective than element sulfur. The addition of sulfur fertilizers promoted rice growth and reduced As accumulation in shoots, further reduced As translocation from root to above-ground parts by 39–59%. The addition of sulfur fertilizers had little effect on genes involved in As metabolism. However, the relative abundance of Fe(III) and sulfate reduction related genera increased with the addition of 150 mg/kg Na2SO4, consistent with the increase of Fe(III) reducing bacteria Geobacteraceae and sulfate reducing gene dsrA. The phenomenon likely influenced the decrease of As concentrations in soil porewater and rice uptake. The outcomes indicate that promoting Fe- and S- reducing bacteria in the rhizosphere by sulfur fertilizers may be one way to reduce As risk in the soil-rice system.

Rhizosphere Bacterial Composition of the Sugar Beet Using SDS-PAGE Methodology

Rhizosphere Bacterial Composition of the Sugar Beet Using SDS-PAGE Methodology

Influence of metal contamination in soil on metabolic profiles of Miscanthus x giganteus belowground parts and associated bacterial communities

Miscanthus x giganteus is well known for its ability to grow on metal contaminated soils. However, little is known concerning its metabolic changes including secondary metabolites under metal pressure. These changes might impact the diversity and function of associated bacterial populations. Thus, this study focused on evaluating the modifications of secondary metabolism production of M. x giganteus belowground parts (i.e. roots and rhizomes), and of rhizosphere bacterial communities under diverse contaminated conditions. Samples of M. x giganteus roots and rhizomes were collected from 3 sites exhibiting a gradient of metal pollution and extracted with MeOH:H2O. Secondary metabolic profiles of root and rhizome extracts were analyzed by UHPLC/DAD/ESI-QTOF. The structure and diversity of rhizosphere communities were studied using high-throughput sequencing. The results showed out the modification of the secondary metabolic profiles of M. x giganteus belowground parts, when they are grown on diversely contaminated soils. Major increased metabolites were identified as 3- and 5-feruloylquinic acid whereas decreased compound was 4-feruloylquinic acid. Metal contamination also led to a shift in rhizosphere bacterial composition and structure as well as the selection of some opportunistic pathogenic genera such as Pseudomonas or Stenotrophomonas but there was only a weak effect on the bacterial diversity and richness. In the context of a moderate metal contamination in agricultural soil slight changes were seen in the secondary metabolic profiles of M. x giganteus roots and rhizomes and their associated bacterial communities. Whether the metal-induced changes allow plants to recruit beneficial microbes that favor the adaptation process to this stress need to be further investigated.

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem

Although rice cultivated under water-saturated conditions as opposed to submerged conditions has received considerable attention with regard to reducing As levels in rice grain, the rhizosphere microbiome potentially influencing As-biotransformation and bioavailability in a rice ecosystem has rarely been studied. In this study, the impacts of flooded, non-flooded and alternate wetting and drying (AWD) practices on rhizosphere bacterial composition and activities that could potentially impact As speciation and accumulation in rhizosphere soil and pore water, As fractions in rhizosphere soil and As speciation and distribution in plant parts were assessed. The results revealed that in addition to pore water As concentration, non-specifically sorbed As fraction, specifically sorbed As fraction and amorphous iron oxide bound As fraction in soil were bio-available to rice plants. In the flooded treatment, As(III) in the pore water was the predominant As species, accounting for 87.3–93.6% of the total As, whereas in the non-flooded and AWD treatments, As(V) was the dominant As species, accounting for 89.6–96.2% and 73.0–83.0%, respectively. The genera Ohtaekwangia, Geobacter, Anaeromyxobacter, Desulfuromonas, Desulfocapsa, Desulfobulbus, and Lacibacter were found in relatively high abundance in the flooded soil, whereas the genera Acinetobacter, Ignavibacterium, Thiobacillus, and Lysobacter were detected in relatively high abundance in the non-flooded soil. Admittedly, the decrease in As level in rice cultivated under the non-flooded and AWD conditions was mostly linked to a relatively high soil redox potential, low As(III) concentration in the soil pore water, a decrease in the relative abundance of As-, Fe- and sulfur-reducing bacteria and an increase in the relative abundance of As-, Fe- and sulfur-oxidizing bacteria in the rhizosphere soil of the rice. This study demonstrated that with substantial reduction in grain As levels and higher water productivity, AWD practice in rice cultivation should be favored over the non-flooded and continuously flooded rice cultivations in As-contaminated sites.

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

BackgroundMangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants.Methodology/Principal FindingsA barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment.Conclusions/SignificanceIn as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments.