Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Seeking Alfalfa Resistance to a Rhizophagous Pest, the Clover Root Curculio (Sitona hispidulus F.)

Since the cancellation of broad-spectrum soil-active insecticides in alfalfa (Medicago sativa L.) production, clover root curculio (Sitona hispidulus F.) (CRC) larval root damage has increased. Current CRC management practices are limited in their ability to suppress larval feeding belowground. First, we field screened developmental alfalfa populations for CRC damage. Subsequently, we developed a soil-less arena to observe nodule feeding and development (head capsule width) of larvae in the lab. This method was used to evaluate five alfalfa populations (two CRC-susceptible (control) and three CRC-resistant populations) against larvae. Further, one CRC-resistant population paired with its genetically similar susceptible population were tested against adult leaf consumption and oviposition in the greenhouse. Field screening revealed that the alfalfa populations selected for little or no larval root feeding damage were more resistant to CRC larval feeding than their corresponding unselected cultivars and significantly more resistant than populations selected for susceptibility. The development of a soil-less arena provided a useful method for evaluation of root-larva interactions. Although larval development was similar across susceptible and resistant alfalfa populations, one CRC-resistant population (NY1713) displayed overall increased nodulation and, thus, had a significantly lower proportion of nodules consumed by larvae. Adult feeding and oviposition aboveground were similar across all populations tested. These results provide possible candidates and screening method for the development and evaluation of alfalfa cultivars that may reduce the impacts of larval feeding and that offer an additional option for CRC management.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial.

The effects of clover and nitrogen fertiliser on the presence of pasture pests in dairy pastures

A comprehensive dataset obtained from sampling four trials investigating interactions between perennial ryegrass and white clover under two levels of applied nitrogen (N) has highlighted different effects of pasture composition and N use on pasture pests.• For swards with white clover, presence of clover root weevil, whitefringed weevil and grass grub increased under low N by 36%, 11% and 5%, respectively, compared with high N treatments.• High N increased the presence of both Argentine stem weevil and root aphid by 7%.• Unexpectedly, clover reduced the presence of two grass feeders, Argentine stem weevil and black beetle, by 7% and 11% respectively.• Presence of grass grub was 17-30% lower under tetraploid ryegrasses than under diploids.• More clover and reduced N fertiliser inputs could reduce the frequency of black beetle and Argentine stem weevil with environmental benefits.

Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches

BackgroundAgriculture is fundamental for food production, and microbiomes support agricultural through multiple essential ecosystem services. Despite the importance of individual (i.e. niche specific) agricultural microbiomes, microbiome interactions across niches are not well-understood. To observe the linkages between nearby agricultural microbiomes, multiple approaches (16S, 18S, and ITS) were used to inspect a broad coverage of niche microbiomes. Here we examined agricultural microbiome responses to 3 different nitrogen treatments (0 kg/ha/yr, 150kg/ha/yr and 300kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches (rumen, faecal, white clover leaf, white clover root, rye grass leaf, rye grass root)ResultsNitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive.ConclusionsNitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should to be considered when management is applied to a single agricultural niche.

Amplicons and isolates: Rhizobium diversity in fields under conventional and organic management

BackgroundThe influence of farming on plant, animal and microbial biodiversity has been carefully studied and much debated. Here, we compare an isolate-based study of 196 Rhizobium strains to amplicon-based MAUI-seq analysis of rhizobia from 17,000 white clover root nodules. We use these data to investigate the influence of soil properties, geographic distance, and field management on Rhizobium nodule populations.ResultsOverall, there was good agreement between the two approaches and the precise allele frequency estimates from the large-scale MAUI-seq amplicon data allowed detailed comparisons of rhizobium populations between individual plots and fields. A few specific chromosomal core-gene alleles were significantly correlated with soil clay content, and core-gene allele profiles became increasingly distinct with geographic distance. Field management was associated with striking differences in Rhizobium diversity, where organic fields showed significantly higher diversity levels than conventionally managed trials.ConclusionsOur results indicate that MAUI-seq is suitable and robust for assessing nodule Rhizobium diversity. We further observe possible profound effects of field management on microbial diversity, which could impact plant health and productivity and warrant further investigation.

Extracellular Synthesis and Characterization of Silver Nanoparticles from Alkaliphilic Pseudomonas sp.

Bio-nanotechnology offers eco-friendly processes for the synthesis of stable nanoparticles (NPs). We hypothesized that microorganisms isolated from the root nodules of leguminous plants would biosynthesize silver (Ag) bio-nanoparticles. Clover root nodules enriched with nutrient broth (NB) produced four distinct colonies on NA plates. Microbial colonies were purified by repeated streaking and designated as SS6, SS7, SS8, and SS9 for identification using 16S rRNA sequencing. Four species of Pseudomonas were identified with a similarity score of over 99% using the EZ Taxon search engine, and tested for extracellular biosynthesis of AgNPs. Microorganism Pseudomonas taiwanensis-SS8 with alkaliphilic growth characteristics reduced the AgNO3 solution into AgNPs in the shortest time period. AgNPs were characterized using UV-Vis spectrophotometry and electron and transmission electron microscopy. A number of physical (i.e., temperature and time) and chemical (i.e., pH and growth media) parameters were optimized. An efficient polydispersal biosynthesis of AgNPs at pH 8–9 after 48 hrs in NB growth medium was observed. In addition, the AgNPs showed antimicrobial properties against 16 commonly occurring pathogenic microorganisms.

Unraveling the Draft Genome Sequence of Paenibacillus sp. tmac-D7 a Non-Rhizobial Endophyte from Trifolium macraei Located in Bodega Bay, California

Paenibacillus sp. tmac-D7 was isolated from coastline growing Trifolium macraei (double-head clover) root nodules from Bodega Bay, California. The draft genome is 5,567,337 bp with a G+C% of 52.4%, an N50 of 114,261 bp, and 5,282 predicted protein-coding genes. Paenibacillus, while found in many other environments, is frequently isolated from root nodules, with many acting as plant pathogen antagonists. Paenibacillus sp. tmac-D7 is the first genome of a non-rhizobial endophyte isolate from wild Trifolium macraei (double-head clover).