Biodegradation of phthalic acid esters by a novel marine bacterial strain RL-BY03: Characterization, metabolic pathway, bioaugmentation and genome analysis.

Biodegradation is recognized as the main route for the decomposition of phthalic acid esters (PAEs) in nature, but the fate of PAEs in marine ecosystems is not well understood. Herein, a novel marine bacterium, Gordonia sihwaniensis RL-BY03, was identified and analyzed for its ability to degrade PAEs. Furthermore, the metabolic mechanism of di-(2-ethylhexyl) phthalate (DEHP) was examined through UPLC-MS/MS and genomic analysis. RL-BY03 could rely solely on several types of PAEs as its sole carbon source. Initial pH and temperature for DEHP degradation were optimized as 8.0 and 30 °C, respectively. Surprisingly, RL-BY03 could simultaneously degrade ethyl acetate and DEHP and they could increase the cell surface hydrophobicity. DEHP degradation kinetics fitted well with the first-order decay model. The metabolic pathway of DEHP was deduced following the detection of five metabolic intermediates. Further, genes that are related to DEHP degradation were identified through genomic analysis and their expression levels were validated through RT-qPCR. A co-related metabolic pathway at biochemical and molecular level indicated that DEHP was turned into DBP and DEP by ß-oxidation, which was further hydrolyzed into phthalic acid. Phthalic acid was utilized through catechol branch of ß-ketoadipate pathway. Additionally, RL-BY03 exhibited excellent bioremediation potential for DEHP-contaminated marine samples. In general, these findings have the potential to enhance our understanding of the fate of PAEs in marine ecosystems.

Genome-Wide Analysis of the Histone Modification Gene (HM) Family and Expression Investigation during Anther Development in Rice (Oryza sativa L.).

Histone modification plays a crucial role in chromatin remodeling and regulating gene expression, and participates in various biological processes, including plant development and responses to stress. Several gene families related to histone modification have been reported in various plant species. However, the identification of members and their functions in the rice (Oryza sativa L.) histone modification gene family (OsHM) at the whole-genome level remains unclear. In this study, a total of 130 OsHMs were identified through a genome-wide analysis. The OsHM gene family can be classified into 11 subfamilies based on a phylogenetic analysis. An analysis of the genes structures and conserved motifs indicates that members of each subfamily share specific conserved protein structures, suggesting their potential conserved functions. Molecular evolutionary analysis reveals that a significant number of OsHMs proteins originated from gene duplication events, particularly segmental duplications. Additionally, transcriptome analysis demonstrates that OsHMs are widely expressed in various tissues of rice and are responsive to multiple abiotic stresses. Fourteen OsHMs exhibit high expression in rice anthers and peaked at different pollen developmental stages. RT-qPCR results further elucidate the expression patterns of these 14 OsHMs during different developmental stages of anthers, highlighting their high expression during the meiosis and tetrad stages, as well as in the late stage of pollen development. Remarkably, OsSDG713 and OsSDG727 were further identified to be nucleus-localized. This study provides a fundamental framework for further exploring the gene functions of HMs in plants, particularly for researching their functions and potential applications in rice anthers' development and male sterility.

Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean.

Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.

Bioremediation of PAEs-contaminated saline soil: The application of a marine bacterial strain isolated from mangrove sediment.

Phthalic acid esters (PAEs) are known as the most widely used plasticizer as well as one of the ubiquitously distributed emerging pollutants. Biodegradation and bioremediation via application of PAEs-degrading microbes is promising. In this study, a novel marine microbe, Gordonia hongkongensis RL-LY01, was isolated from mangrove sediment showing high di-(2-ethylhexyl) phthalate (DEHP) degradation capacity. Strain RL-LY01 could degrade a wide range of PAEs and the degradation kinetics of DEHP followed the first-order decay model. Meanwhile, good environmental adaptability, preference to alkaline conditions and good tolerance to salinity and metal ions was shown. Further, metabolic pathway of DEHP in strain RL-LY01 was proposed, with di-ethyl phthalate, phthalic acid, benzoic acid and catechol as intermediates. Additionally, one known mono-alkyl phthalate hydrolase gene (mehpH) was identified. Finally, the excellent performance during bioremediation of artificial DEHP-contaminated saline soil and sediment indicated strain RL-LY01 employs great application potential for the bioremediation of PAE-contaminated environments.

Complete genome of Mycolicibacterium phocaicum RL-HY01, a PAEs-degrading marine bacterial strain isolated from Zhanjiang Bay, China.

Mycolicibacterium phocaicum RL-HY01, a marine bacterial strain with the capability to degrade phthalic acid esters (PAEs), was isolated from Zhanjiang Bay, China. Here, the complete genome sequence of strain RL-HY01 was presented. The genome of strain RL-HY01 contains one circular chromosome of 6,064,759 bp with a G + C content of 66.93 mol%. The genome contains 5681 predicted protein-encoding genes, 57 tRNA genes, and 6 rRNA genes. Genes and gene clusters potentially involved in the metabolism of PAEs were further identified. The genome Mycolicibacterium phocaicum RL-HY01 will be helpful for advancing our understanding of the fate of PAEs in marine ecosystem.

Effect of plant growth regulators DA-6 and COS on drought tolerance of pineapple through bromelain and oxidative stress.

BACKGROUND: Due to global warming, drought climates frequently occur on land, and despite being drought resistant, pineapples are still subjected to varying degrees of drought stress. Plant growth regulators can regulate the stress tolerance of plants through hormonal effects. This experiment aims to investigate the regulatory effects of different plant growth regulators on Tainong- 16 and MD-2 Pineapple when subjected to drought stress. RESULTS: In this experiment, we examined the regulatory effects of two different plant growth regulators, sprayed on two pineapple varieties: MD-2 Pineapple and Tainong-16. The main component of T1 was diethyl aminoethyl hexanoate (DA-6) and that of T2 is chitosan oligosaccharide (COS). An environment similar to a natural drought was simulated in the drought stress treatments. Then, pineapples at different periods were sampled and a series of indicators were measured. The experimental results showed that the drought treatments treated with T1 and T2 plant growth regulators had a decrease in malondialdehyde, an increase in bromelain and antioxidant enzyme indicators, and an increase in phenotypic and yield indicators. CONCLUSION: This experiment demonstrated that DA-6 and COS can enhance the drought resistance of pineapple plants to a certain extent through bromelain and oxidative stress. Therefore, DA-6 and COS have potential applications and this experiment lays the foundation for further research.

Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress.

Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.

Microbiome-metabolome analysis directed isolation of rhizobacteria capable of enhancing salt tolerance of Sea Rice 86.

Soil salinization has been recognized as one of the main factors causing the decrease of cultivated land area and global plant productivity. Application of salt tolerant plants and improvement of plant salt tolerance are recognized as the major routes for saline soil restoration and utilization. Sea rice 86 (SR86) is known as a rice cultivar capable of growing in saline soil. Genome sequencing and transcriptome analysis of SR86 have been conducted to explore its salt tolerance mechanisms while the contribution of rhizobacteria is underexplored. In the present study, we examined the rhizosphere bacterial diversity and soil metabolome of SR86 seedlings under different salinity to understand their contribution to plant salt tolerance. We found that salt stress could significantly change rhizobacterial diversity and rhizosphere metabolites. Keystone taxa were identified via co-occurrence analysis and the correlation analysis between keystone taxa and rhizosphere metabolites indicated lipids and their derivatives might play an important role in plant salt tolerance. Further, four plant growth promoting rhizobacteria (PGPR), capable of promoting the salt tolerance of SR86, were isolated and characterized. These findings might provide novel insights into the mechanisms of plant salt tolerance mediated by plant-microbe interaction, and promote the isolation and application of PGPR in the restoration and utilization of saline soil.

Transcriptomic analysis of Vigna radiata in response to chilling stress and uniconazole application.

BACKGROUND: Chilling injury of mung bean (Vigna radiata (L.)) during the blooming and podding stages is a major agricultural threat in Northeast China. Uniconazole (UNZ) can alleviate water deficit stress in soybean and waterlogging stress in mung bean. However, there has been no report on the effect of UNZ application on the growth and transcriptomic profile of mung bean under chilling stress. RESULTS: UNZ application before chilling stress at the R1 stage alleviated the decline in mung bean yield. UNZ delayed the decrease in leaf chlorophyll content under chilling stress at the R1 stage and accelerated the increase in leaf chlorophyll content during the recovery period. Eighteen separate RNA-Seq libraries were generated from RNA samples collected from leaves exposed to six different treatment schemes. The numbers of DEGs specific for UNZ treatment between D1 + S vs. D1 and D4 + S vs. D4 were 708 and 810, respectively. GO annotations showed that photosynthesis genes were obviously enriched among the genes affected by chilling stress and UNZ application. KEGG pathway enrichment analysis indicated that 4 pathways (cutin, suberin and wax biosynthesis; photosynthesis; porphyrin and chlorophyll metabolism; and ribosome) were downregulated, while plant-pathogen interaction was upregulated, by chilling stress. UNZ application effectively prevented the further downregulation of the gene expression of members of these 4 KEGG pathways under chilling stress. CONCLUSIONS: UNZ application effectively delayed the decrease in photosynthetic pigment content under chilling stress and accelerated the increase in photosynthetic pigment content during the recovery period, thus effectively limiting the decline in mung bean yield. UNZ application effectively prevented the further downregulation of the gene expression of members of 4 KEGG pathways under chilling stress and increased mung bean tolerance to chilling stress.

Phthalic acid esters degradation by a novel marine bacterial strain Mycolicibacterium phocaicum RL-HY01: Characterization, metabolic pathway and bioaugmentation.

Phthalic acid esters (PAEs) are one of the most widely used plasticizers and the well-studied environmental pollutants with endocrine disrupting properties. Investigation about PAEs in terrestrial ecosystem has been extensively conducted while the fate of PAEs in marine environment remains underexplored. In this study, a novel di-(2-ethylhexyl) phthalate (DEHP) degrading marine bacterial strain, Mycolicibacterium phocaicum RL-HY01, was isolated and characterized from intertidal sediments. Strain RL-HY01 could utilize a range of PAE plasticizers as sole carbon source for growth. The effects of different environmental factors on the degradation of PAEs were evaluated and the results indicated that strain RL-HY01 could efficiently degrade PAEs under a wide range of pH (5.0 to 9.0), temperature (20 °C to 40 °C) and salinity (below 10%). Specifically, when Tween-80 was added as solubilizing agent, strain RL-HY01 could rapidly degrade DEHP and achieve complete degradation of DEHP (50 mg/L) in 48 h. The kinetics of DEHP degradation by RL-HY01 were well fitted with the modified Gompertz model. The metabolic intermediates of DEHP by strain RL-HY01 were identified by ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis and then the metabolic pathway of DEHP was deduced. DEHP was transformed into di-ethyl phthalate (DEP) via ß-oxidation and then DEP was hydrolyzed into phthalic acid (PA) by de-esterification. PA was further transformed into gentisate via salicylic acid and further utilized for cell growth. Bioaugmentation of strain RL-HY01 with marine samples was performed to evaluate its application potential and the results suggested that strain RL-HY01 could accelerate the elimination of DEHP in marine samples. The results have advanced our understanding of the fate of PAEs in marine ecosystem and identified an efficient bioremediation strategy for PAEs-polluted marine sites.

Complete Genome Sequence of Pantoea stewartii subsp. indologenes ZJ-FGZX1, a Lucky Bamboo Pathogen.

The phytopathogen Pantoea stewartii subsp. indologenes causes Stewart's wilt disease in lucky bamboo. Here, we report the complete genome of P. stewartii subsp. indologenes ZJ-FGZX1, which represents the first whole-genome sequence of an isolate from China. The assembled genome consisted of three contigs, with one circular chromosome of 4,550,072 bp and two circular plasmids of 326,337 and 106,454 bp. The complete genome will provide a valuable resource for further studies on bacterial blight worldwide.

Bioremediation of di-(2-ethylhexyl) phthalate contaminated red soil by Gordonia terrae RL-JC02: Characterization, metabolic pathway and kinetics.

Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer and a representative endocrine disrupting chemical. The toxicological effects of DEHP on environmental and human health have been widely investigated. In this study, the DEHP-degrading bacterial strain RL-JC02 was isolated from red soil with long-term usage of plastic mulch, and it was identified as Gordonia terrae by 16S rRNA gene analysis coupled with physiological and biochemical characterization. The biodegrading capacity of different phthalic acid esters and related intermediates was investigated as well as the performance of strain RL-JC02 under different environmental conditions, such as temperature, pH, salinity and DEHP concentration. Specifically, strain RL-JC02 showed good tolerance to low pH, with 86.6% of DEHP degraded under the initial pH of 5.0 within 72 h. The metabolic pathway of DEHP was examined by metabolic intermediate identification via a high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) analysis in which DEHP was hydrolyzed into phthalic acid (PA) and 2-ethylhexanol (2-EH) via mono (2-ethylhexyl) phthalate (MEHP). PA and 2-EH were further utilized through the protocatechuic acid metabolic pathway and ß-oxidation via protocatechuic acid and 2-ethylhexanoic acid, respectively. The application potential of strain RL-JC02 was confirmed through the bioremediation of artificial DEHP-contaminated red soil showing 91.8% DEHP degradation by strain RL-JC02 within 30 d. The kinetics analysis of DEHP degradation by strain RL-JC02 in soil demonstrated that the process followed the modified Gompertz model. Meanwhile, the cell concentration monitoring of strain RL-JC02 in soil with absolute quantification polymerase chain reaction (qPCR) suggested that strain RL-JC02 survived well during bioremediation. This study provides sufficient evidence of a robust degrader for the bioremediation of PAE-contaminated red soil.

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1.

The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

Regulatory effects of Shewanella putrefaciens isolated from shrimp Penaeus orientalis on the virulence factors of Vibrio parahaemolyticus and evaluation of the role of quorum sensing in virulence factors regulation.

As an aquatic pathogen widely present in aquatic food, Vibrio parahaemolyticus causes outbreaks of gastroenteritis across the globe. Virulence factors of V. parahaemolyticus increases with the amount of spoilage in aquatic organisms including shrimp, but mechanisms regulating its virulence factors are not well understood. In this study, five spoilage bacteria isolated from shrimp were investigated for their regulatory effects on the virulence factors including haemolysin and biofilm of V. parahaemolyticus. Among these isolates, Shewanella putrefaciens induced haemolytic activity in V. parahaemolyticus in a time-dose-temperature-dependent manner and we found the main component responsible for this effect to be the supernatant or cell-free extract of S. putrefaciens. Total haemolytic activity, expression of the thermostable direct haemolysin gene tdh and biofilm production of V. parahaemolyticus were significantly up-regulated by S. putrefaciens, but also by deletion of quorum-sensing luxM or luxS gene of V. parahaemolyticus. However, this regulation by S. putrefaciens was significantly impaired by deletion of the luxM gene, but not by deletion of the luxS gene. Further study showed that S. putrefaciens exhibited a strong degradation ability on the signalling molecule acylated homoserine lactone (AHL) synthesised by the LuxM enzyme. This study revealed a novel virulence regulatory mechanism that S. putrefaciens can significantly increase the virulence factors of V. parahaemolyticus via interfering with the luxM- type quorum-sensing signalling pathway through its AHL-degradation ability.

Regulation of Thermostable Direct Hemolysin and Biofilm Formation of Vibrio parahaemolyticus by Quorum-Sensing Genes luxM and luxS.

Vibrio parahaemolyticus is a seafood opportunistic pathogen. There are evidences suggesting that virulence skills, including hemolytic activity and biofilm formation, are regulated by the luxM/luxS-dependent quorum-sensing system in V. parahaemolyticus, and their regulatory mechanism is not well understood. To better understand the virulence regulatory mechanism of V. parahaemolyticus, the luxM deletion (△luxM) and luxS deletion (△luxS) mutants were constructed and their impacts on growth, hemolysin activity, and biofilm were investigated. Results show that both luxM and luxS are involved in the adaptation to environmental conditions in early adaptive-log phase growth of V. parahaemolyticus. Thermostable direct hemolysin gene (tdh) was negatively regulated by luxM and positively regulated by luxS. The biofilm formation was negatively regulated by both luxS and luxM. This study provides an insight into some aspects of V. parahaemolyticus virulence regulation by luxM/luxS-dependent quorum-sensing system.

Rhizospheric effects on atrazine speciation and degradation in laterite soils of Pennisetum alopecuroides (L.) Spreng.

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a worldwide-used herbicide and often detected in agricultural soils and groundwater at concentrations above the permitted limit, because of its high mobility, persistence, and massive application. This study applied pot experiments to investigate the atrazine contents and speciation during the phytoremediation process by Pennisetum alopecuroides (L.) Spreng. in laterite soils. From the change of the total atrazine and bioavailable atrazine measured by diffusive gradients in thin film (DGT), P. alopecuroides significantly improved atrazine degradation efficiency from 15.22 to 51.46%, attributing to the increasing bioavailable atrazine in rhizosphere. Only a small amount of atrazine was taken up by P. alopecuroides root and the acropetal translocation from roots to shoots was limited. The atrazine speciation was significantly different between rhizosphere and non-rhizosphere, attributing to the declining pH and organic matters in rhizosphere. The relationship between pH and soil-bound/humus-fixed atrazine illustrated the pH-dependant release of the atrazine from soils and the competition between humus adsorption and uptake by P. alopecuroides. The present study reveals the important roles of soil pH and organic matters in atrazine speciation and availability in laterite soils, and provides new insights in the rhizospheric effects on effective phytoremediation of atrazine.

Effects of two ecological earthworm species on atrazine degradation performance and bacterial community structure in red soil.

Vermicomposting is an effective and environmentally friendly approach for eliminating soil organic contamination. Atrazine is one of the most commonly applied triazinic herbicides and frequently detected in agricultural soils. This study investigated the roles and mechanisms of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) in microbial degradation of atrazine. Both earthworms accelerated atrazine degradation performance from 39.0% in sterile soils to 94.9%-95.7%, via neutralizing soil pH, consuming soil humus, altering bacterial community structure, enriching indigenous atrazine degraders and excreting the intestinal atrazine-degrading bacteria. Rhodoplanes and Kaistobacter were identified as soil indigenous degraders for atrazine mineralization and stimulated by both earthworm species. A. robustus excreted the intestinal Cupriavidus and Pseudomonas, whereas Flavobacterium was released by E. foetida. This study provides a comprehensive understanding of the distinct effects of two earthworm species on soil microbial community and atrazine degradation, offering technical supports to apply vermicomposting in effective soil bioremediation.

Bacteria-mediated phthalic acid esters degradation and related molecular mechanisms.

Phthalic acid esters (PAEs) have long been known as the most widely used plasticizer with a broad range of industrial application. PAEs are ubiquitous in different environments and our daily life due to their large and widespread application. Recent PAEs research mainly focused on their environmental fate (including leaching, migration, transformation) and toxicology and risk assessment. With the comprehensive recognition of their potential hazard, the elimination of PAEs has attracted worldwide concerns. Although many factors may contribute to the degradation of PAEs, the dominant role of biodegradation was widely reported. Many PAEs-degrading bacteria were isolated, metabolites and metabolic pathways were proposed, and enzymes involved in the degradation were identified. The current paper presents an overview of available reports about PAEs-degrading bacteria and related molecular mechanisms. The metabolic pathways deduced from the identified intermediates were presented. The upstream and downstream pathways of PAEs metabolism were summarized, including the aerobic and anaerobic pathways of phthalic acid (PA) degradation. Known enzymes involved in the hydrolysis of ester bonds were characterized according to their properties. Based on phylogenetic analysis, all these enzymes were distributed in four families of esterases and one unknown family. For these five families, conserved sequence motifs were identified and the biological properties of these motifs were characterized. Challenges and emerging opportunities are also discussed.

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils.

The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively.

The Pik-p resistance to Magnaporthe oryzae in rice is mediated by a pair of closely linked CC-NBS-LRR genes.

The blast resistance gene Pik-p, mapping to the Pik locus on the long arm of rice chromosome 11, was isolated by map-based in silico cloning. Four NBS-LRR genes are present in the target region of cv. Nipponbare, and a presence/absence analysis in the Pik-p carrier cv. K60 excluded two of these as candidates for Pik-p. The other two candidates (KP3 and KP4) were expressed in cv. K60. A loss-of-function experiment by RNAi showed that both KP3 and KP4 are required for Pik-p function, while a gain-of-function experiment by complementation test revealed that neither KP3 nor KP4 on their own can impart resistance, but that resistance was expressed when both were introduced simultaneously. Both Pikp-1 (KP3) and Pikp-2 (KP4) encode coiled-coil NBS-LRR proteins and share, respectively, 95 and 99% peptide identity with the two alleles, Pikm1-TS and Pikm2-TS. The Pikp-1 and Pikp-2 sequences share only limited homology. Their sequence allowed Pik-p to be distinguished from Pik, Pik-s, Pik-m and Pik-h. Both Pikp-1 and Pikp-2 were constitutively expressed in cv. K60 and only marginally induced by blast infection.