Colonization Of Rice Roots Research Articles

DIAZOTROPHIC ENDOPHYTE Klebsiella sp. N5 FROM SORGHUM SHOWS CROSS-COLONIZATION AND PLANT GROWTH PROMOTION IN RICE

Rice necessitates the highest levels of N fertilizers during its cultivation increasing demand for nitrogen fertilizers as well as negatively affecting the environment. Endophytic diazotrophic bacteria were isolated from sorghum, out of 35 isolates Klebsiella sp. N5 showed maximum potential for biological nitrogen fixation. Primary screening of strain N5 was done with acetylene reduction assay indicating dry root activity of 638.55 nmol C2H4 h-1 g-1. That was further confirmed by nifH gene amplification. The strain was identified morphologically, biochemically and 16S rDNA sequencing analysis and identified as Klebsiella sp. strain N5. This strain exhibited other plant growth-promoting (PGP) traits, such as phosphate solubilization, production of indole acetic acid, siderophore activity, ACC deaminase activity, and anti-fungal activity. PGP endophyte N5 was inoculated into rice seedlings to investigate its interaction under axenic conditions and to characterize its ability to colonize non-native host plant rice. Extensive colonization of rice roots was corroborated by Scanning electron microscopy. In-planta experiments with rice seeds inoculated with Klebsiella sp. N5 showed significant improvements in various agronomic traits such as increase in shoot length, root length, fresh and dry weight of root and shoot, chlorophyll content, and nitrogen content of the plant and soil compared to the untreated plants. Klebsiella sp. N5, a cross colonizer from sorghum (C4 plant) to rice (C3 plant) plays a crucial role in facilitating the acquisition of essential resources such as nitrogen, phosphorus, and iron through direct mechanisms. This study expands the horizon for its potential as a valuable bioinoculant for sustainable agricultural practices, particularly in non-native host rice, paving the way for future field trials.

Effect of Arbuscular Mycorrhizal Fungi on Lowland Rice Growth and Yield (Oryza sativa L.) under Different Farming Practices

In this study, a field experiment was conducted to evaluate the growth and yield responses of Sri Lankan lowland rice (Oryza sativa L.) with the application of beneficial Arbuscular mycorrhizal fungi (AMF) inoculum and intercropping with highly mycorrhizal-dependent vetiver grass (Chrysopogon zizanioides L.) under two different soil nutrient management systems (NMSs): conventional/chemical (CNMS) and organic (ONMS). The experiment was designed as a split plot with three blocks. Each CNMS and ONMS experiment included an untreated control (T0) and three treatments—AMF inoculation (T1), vetiver intercropping (T2), and the combination of AMF and vetiver (T3). According to the results, the colonization of rice roots with AMF was not affected significantly by the treatments and ranged from 0–15.8%. The effect was very low or absent in the early stage and then higher in the later stages of the rice plant. Furthermore, plant growth was not significantly different between the two NMSs, although grain yield was significantly higher (p < 0.05) in ONMS than for the respective controls (T0), with the order T1 (0.45 kg/m2) > T2 (0.42 kg/m2) > T3 (0.41 kg/m2) in CNMS and T2 (0.44 kg/m2) > T1 (0.41 kg/m2) > T3 (0.40 kg/m2), thus suggesting the utilization of AMF and vetiver in a lowland rice farming system is beneficial.

Serendipita indica chitinase protects rice from the blast and bakanae diseases.

Serendipita indica, a multifunctional and useful endophyte fungus, has been intensively investigated in promoting plant growth and resistance towards biotic and abiotic stress. Multiple chitinases from microorganisms or plants have been identified to have a high antifungal activity as a biological control. However, chitinase of S. indica still needs to be characterized. We functionally characterized a chitinase (SiChi) in S. indica. The result showed that the purified SiChi protein confers high chitinase activity; importantly, SiChi inhibits the conidial germination of Magnaporthe oryzae and Fusarium moniliforme. After the successful colonization of rice roots by S. indica, both the rice blast disease and bakanae disease were significantly reduced. Interestingly, the purified SiChi could promptly induce rice disease resistance towards M. oryzae and F. moniliforme pathogens when sprayed on rice leaves. Like S. indica, SiChi could upregulate rice pathogen-resistant proteins and defense enzymes. In conclusion, chitinase of S. indica has direct antifungal activity and indirect induced resistance activity, implying an efficient and economic strategy for rice disease control by applying S. indica and SiChi.

Engineering D-glucose utilization in Azospirillum brasilense Sp7 promotes rice root colonization.

Bacteria of the genus Azospirillum include several plant associated bacteria which often promote the growth of their host plants. Although the host range of Azospirillum brasilense Sp7 is much wider than its close relative Azospirillum lipoferum 4B, it lacks the ability to efficiently utilize D-glucose for its growth. By comparing the genomes of both the species, the genes of A. lipoferum 4B responsible for conferring D-glucose utilization ability in A. brasilese Sp7 were identified by cloning individual or a combination of genes in a broad host range expression vector, mobilizing them in A. brasilense Sp7 and examining the ability of exconjugants to use D-glucose as sole carbon source for growth. These genes also included the homologs of genes involved in N-acetyl glucosamine utilization in Pseudomonas aeruginosa PAO1. A transcriptional fusion of the 5 genes encoding glucose-6-phosphate dehydrogenase and 4 components of glucose phosphotransferase system were able to improve D-glucose utilization ability in A. brasilense Sp7. The A. brasilense Sp7 strain engineered with D-glucose utilization ability showed significantly improved root colonization of rice seedling. The improvement in the ability of A. brasilense Sp7 to colonize rice roots is expected to bring benefits to rice by promoting its growth. KEY POINTS: • Genes required for glucose utilization in Azospirillum lipoferum were identified. • A gene cassette encoding glucose utilization was constructed. • Transfer of gene cassette in A. brasilense improves glucose utilization and rice root colonization..

Comparative Genomics of Three Aspergillus Strains Reveals Insights into Endophytic Lifestyle and Endophyte-Induced Plant Growth Promotion.

Aspergillus includes both plant pathogenic and beneficial fungi. Although endophytes beneficial to plants have high potential for plant growth promotion and improving stress tolerance, studies on endophytic lifestyles and endophyte-plant interactions are still limited. Here, three endophytes belonging to Aspergillus, AS31, AS33, and AS42, were isolated. They could successfully colonize rice roots and significantly improved rice growth. The genomes of strains AS31, AS33, and AS42 were sequenced and compared with other Aspergillus species covering both pathogens and endophytes. The genomes of AS31, AS33, and AS42 were 36.8, 34.8, and 35.3 Mb, respectively. The endophytic genomes had more genes encoding carbohydrate-active enzymes (CAZymes) and small secreted proteins (SSPs) and secondary metabolism gene clusters involved in indole metabolism than the pathogens. In addition, these endophytes were able to improve Pi (phosphorus) accumulation and transport in rice by inducing the expression of Pi transport genes in rice. Specifically, inoculation with endophytes significantly increased Pi contents in roots at the early stage, while the Pi contents in inoculated shoots were significantly increased at the late stage. Our results not only provide important insights into endophyte-plant interactions but also provide strain and genome resources, paving the way for the agricultural application of Aspergillus endophytes.

Piriformospora indica and Azotobacter chroococcum Consortium Facilitates Higher Acquisition of N, P with Improved Carbon Allocation and Enhanced Plant Growth in Oryza sativa.

The soil microbiome contributes to nutrient acquisition and plant adaptation to numerous biotic and abiotic stresses. Numerous studies have been conducted over the past decade showing that plants take up nutrients better when associated with fungi and additional beneficial bacteria that promote plant growth, but the mechanisms by which the plant host benefits from this tripartite association are not yet fully understood. In this article, we report on a synergistic interaction between rice (Oryza sativa), Piriformospora indica (an endophytic fungus colonizing the rice roots), and Azotobacter chroococcum strain W5, a free-living nitrogen-fixing bacterium. On the basis of mRNA expression analysis and enzymatic activity, we found that co-inoculation of plant roots with the fungus and the rhizobacterium leads to enhanced plant growth and improved nutrient uptake compared to inoculation with either of the two microbes individually. Proteome analysis of O. sativa further revealed that proteins involved in nitrogen and phosphorus metabolism are upregulated and improve nitrogen and phosphate uptake. Our results also show that A. chroococcum supports colonization of rice roots by P. indica, and consequentially, the plants are more resistant to biotic stress upon co-colonization. Our research provides detailed insights into the mechanisms by which microbial partners synergistically promote each other in the interaction while being associated with the host plant.

The endophytic bacterium Bacillus koreensis 181-22 promotes rice growth and alleviates cadmium stress under cadmium exposure.

Recently, cadmium (Cd) contamination in paddy soils has become a highly concerning pollution problem. Endophytic microbes in rice not only affect the plant growth but also contribute to ion absorption by the roots. Therefore, they are a promising, ecologically sound means of reducing the Cd transport from soils to shoots and grains of the plant. In this study, a Cd-resistant endophytic bacterium, named 181-22, with high Cd absorption capacity (90.8%) was isolated from the roots of rice planting in heavily Cd-contaminated paddy soils and was identified as Bacillus koreensis CGMCC 19,468. The strain significantly increased fresh weight of roots and shoots (44.4% and 42.7%) and dry weight of roots and shoots (71.3% and 39.9%) and decreased Cd content in the rice roots (12.8%), shoots (34.3%), and grains (39.1%) under Cd stress compared to uninoculated plant by colonizing rice roots via seed inoculation. Moreover, colonization of 181-22 reprogrammed rice physiology to alleviate Cd stress by increasing pigment and total protein content, regulating Cd-induced oxidative stress enzymes such as superoxide dismutase and catalase and reducing malondialdehyde. Thus, B. koreensis 181-22 has the potential to protect rice against Cd stress and can be used as a biofertilizer to bioremediate paddy soils contaminated with Cd. KEY POINTS: • Bacillus koreensis 181-22 colonized the inside of rice roots at high numbers via seed inoculation. • B. koreensis 181-22 promoted rice growth and decreased Cd accumulation in grains. • B. koreensis 181-22 regulated the physiological response to alleviated Cd stress in rice.

Bioprospecting aerobic rice (Oryza sativa) and mycorrhizal interaction for nutrient uptake and plant growth

With the growing concern of water scarcity in agriculture, aerobic rice (Oryza sativa L.) is a promising mode of cultivation for reducing water use, although the reduced optimal plant growth and yield are major constraints. Arbuscular mycorrhiza (AM) are known to readily colonize rice roots under aerobic conditions, however, the response of upland and lowland rice genotypes has not been investigated. This study was carried out during 2018-19 at ICAR-IARI, New Delhi, using a mycorrhizal consortium and percent colonization was observed to be higher by 58% in upland rice genotypes. AM- upland plants also showed 20% higher plant biomass. AM colonization significantly enhanced rice growth under aerobic conditions, with the upland rice genotypes. Pyari and Satyabhama showed higher response upon AM inoculation. AM colonization increased the total chlorophyll by 54% and the upland rice genotypes showed 51% enhanced nitrogenase activity in their root zones, with highest recorded for Satyabhama. The AM plants showed enhanced activities of nitrate reductase (NR) and glutamine synthetase (GS), and interestingly, the rice genotypes with higher NR and GS (Pyari, Satyabhama) also exhibited more (20%) biomass production and plant N content (36%). Significant varietal differences were recorded in terms of accumulation of antioxidant compounds such as ascorbate, glutathione and proline in AM inoculated plants, which helped to alleviate negative effects of water stress in rice plants under aerobic cultivation.

Molecular Programming of Drought-Challenged Trichoderma harzianum-Bioprimed Rice (Oryza sativa L.)

Trichoderma biopriming enhances rice growth in drought-stressed soils by triggering various plant metabolic pathways related to antioxidative defense, secondary metabolites, and hormonal upregulation. In the present study, transcriptomic analysis of rice cultivar IR64 bioprimed with Trichoderma harzianum under drought stress was carried out in comparison with drought-stressed samples using next-generation sequencing techniques. Out of the 2,506 significant (p < 0.05) differentially expressed genes (DEGs), 337 (15%) were exclusively expressed in drought-stressed plants, 382 (15%) were expressed in T. harzianum-treated drought-stressed plants, and 1,787 (70%) were commonly expressed. Furthermore, comparative analysis of upregulated and downregulated genes under stressed conditions showed that 1,053 genes (42%) were upregulated and 733 genes (29%) were downregulated in T. harzianum-treated drought-stressed rice plants. The genes exclusively expressed in T. harzianum-treated drought-stressed plants were mostly photosynthetic and antioxidative such as plastocyanin, small chain of Rubisco, PSI subunit Q, PSII subunit PSBY, osmoproteins, proline-rich protein, aquaporins, stress-enhanced proteins, and chaperonins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis states that the most enriched pathways were metabolic (38%) followed by pathways involved in the synthesis of secondary metabolites (25%), carbon metabolism (6%), phenyl propanoid (7%), and glutathione metabolism (3%). Some of the genes were selected for validation using real-time PCR which showed consistent expression as RNA-Seq data. Furthermore, to establish host–T. harzianum interaction, transcriptome analysis of Trichoderma was also carried out. The Gene Ontology (GO) analysis of T. harzianum transcriptome suggested that the annotated genes are functionally related to carbohydrate binding module, glycoside hydrolase, GMC oxidoreductase, and trehalase and were mainly upregulated, playing an important role in establishing the mycelia colonization of rice roots and its growth. Overall, it can be concluded that T. harzianum biopriming delays drought stress in rice cultivars by a multitude of molecular programming.

Motility, Adhesion and c-di-GMP Influence the Endophytic Colonization of Rice by Azoarcus sp. CIB.

Proficient crop production is needed to ensure the feeding of a growing global population. The association of bacteria with plants plays an important role in the health state of the plants contributing to the increase of agricultural production. Endophytic bacteria are ubiquitous in most plant species providing, in most cases, plant promotion properties. However, the knowledge on the genetic determinants involved in the colonization of plants by endophytic bacteria is still poorly understood. In this work we have used a genetic approach based on the construction of fliM, pilX and eps knockout mutants to show that the motility mediated by a functional flagellum and the pili type IV, and the adhesion modulated by exopolysaccarides are required for the efficient colonization of rice roots by the endophyte Azoarcus sp. CIB. Moreover, we have demonstrated that expression of an exogenous diguanylate cyclase or phophodiesterase, which causes either an increase or decrease of the intracellular levels of the second messenger cyclic di-GMP (c-di-GMP), respectively, leads to a reduction of the ability of Azoarcus sp. CIB to colonize rice plants. Here we present results demonstrating the unprecedented role of the universal second messenger cyclic-di-GMP in plant colonization by an endophytic bacterium, Azoarcus sp. CIB. These studies pave the way to further strategies to modulate the interaction of endophytes with their target plant hosts.

Effects of crop rotation on enhanced occurrence of arbuscular mycorrhizal fungi and soil carbon stocks of lowland paddy fields in seasonaly dry tropics

The impacts of crop rotation systems on the arbuscular mycorrhizal fungal (AMF) spore density, mycorrhizal colonization of rice roots, soil C fractions and C stocks in seasonally dry climatic zone of Sri Lanka were examined in Rice–Soybean (RS) and Rice–Onion (RO) crop rotation systems during the subsequent rice cultivation season and, compared these with a rice monoculture, i.e. Rice–Rice (RR). The study also examined the correlations between AMF occurrence and soil carbon stocks. Results revealed that RS crop rotation system significantly enhances the occurrence of AMF spores in soil with a higher fraction of large sized spores, the total organic C (TOC), microbial biomass C (MBC), water soluble C (WSC), labile C and a high AMF colonization in rice roots in the subsequent rice cultivation season. The diversity of AMF morphospecies were also the highest in RS. Reduction in AMF density in the soil in RR crop rotation system may be due to prolonged anaerobic conditions prevailed. The growth of onion has drastically reduced the AMF colonization in rice and soil C contents. Soil carbon stocks showed positive correlations with % root colonization and AMF spore number in soil. Thus, the study confirmed that C stocks in paddy soils can be improved by intercropping with AMF supporting plants like soya bean. This is the first report that shows positive correlations of AMF sporulation and % root colonization in lowland rice with soil carbon stocks.

Bradyrhizobium sp. strain ORS278 promotes rice growth and its quorum sensing system is required for optimal root colonization.

Many Gram-negative bacteria communicate by using homoserine lactones (HSLs) as quorum sensing (QS) signals in a cell density-dependent manner. In addition to fatty acyl-HSL (acyl-HSL) signals, certain strains, most of them associated with plants, produce non-canonical aryl-HSLs such as cinnamoyl-HSL. However, the role of aryl-HSL in endophytic associations remained elusive. Bradyrhizobium sp. strain ORS278 possesses a LuxI-LuxR type QS system and produces cinnamoyl-HSL as a QS signal. Here, we report that strain ORS278 promotes growth of domesticated rice (Oryza sativa). QS mutants unable to produce cinnamoyl-HSL exhibited reduced plant-growth promoting activity in comparison to the parent strain ORS278. Likewise, the QS mutants were impaired in their ability to colonize rice roots. These findings suggest that genes controlled by cinnamoyl-HSL play an important role in the association between rice and ORS278. However, biofilm production was not visibly altered in these mutants. In conclusion, our study highlights the importance of aryl-HSLs in endophytic plant-bacteria interactions.

Bacillus pumilus LZP02 Promotes Rice Root Growth by Improving Carbohydrate Metabolism and Phenylpropanoid Biosynthesis.

Elucidation of the underlying mechanisms of plant growth promotion of rhizobacteria is very important. This study explored the mechanism by which Bacillus pumilus LZP02 promotes growth in rice roots through proteomic, transcriptomic, and metabolomic techniques. The results showed that B. pumilus LZP02 promoted the absorption of phosphorous, calcium, and magnesium ions by colonization of rice roots and enhanced peroxidase, catalase, superoxide dismutase, and Ca2+Mg2+ adenosine triphosphatase activities and chlorophyll contents in rice. The proteomic results showed that most of the differentially expressed proteins were involved in carbohydrate metabolism and that the biosynthesis of other secondary metabolites was also increased. According to RNA-seq and reverse transcription-quantitative PCR analyses, expression of some genes involved in carbohydrate metabolism and phenylpropanoid biosynthesis was upregulated in rice roots. Regarding metabolomics, phenylpropanoid biosynthesis, starch and sucrose metabolism, the pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism were increased. The results indicated that B. pumilus LZP02 promoted the growth of rice roots by enhancing carbohydrate metabolism and phenylpropanoid biosynthesis.

Standardization of spore load for AMF inoculation and its effect on rice root colonization and root system architecture in vitro

Arbuscular Mycorrhizal Fungi (AMF) can form symbiotic relationship with rice, preferably in the modern rice production systems such as System of Rice Intensification (SRI), aerobic and upland conditions. Their association with rice roots under in vitro conditions was investigated in this study. A suspension containing one lakh (1, 00,000) spores of Rhizophagus irregularis was employed to standardize optimum AMF spore load/seedling and evaluate its effect on Root System Architecture (RSA). The results indicated that different spore loads of AMF inoculated with rice seedlings, under in vitro conditions, modified most of the traits of RSA of rice at early stages significantly better than the uninoculated Control. The in vitro study clearly showed that the seedlings of rice with AMF inoculated with a dose of 14 µl/seedling (31 spores/ seedling) recorded maximum root colonization of 100 per cent by AMF in rice..

Type 3 Secretion System (T3SS) of Bradyrhizobium sp. DOA9 and Its Roles in Legume Symbiosis and Rice Endophytic Association.

The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod, nif, and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod-box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (ΩrhcN) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four (Arachis hypogea, Vigna radiata, Crotalaria juncea, and Macroptilium atropurpureum) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one (Stylosanthes hamata) responded negatively (fewer nodules and less nitrogen fixation) and four species (Aeschynomene americana, Aeschynomene afraspera, Indigofera tinctoria, and Desmodium tortuosum) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice.

The Regulatory Network Controlling Ethanol-Induced Expression of Alcohol Dehydrogenase in the Endophyte Azoarcus sp. Strain BH72.

The habitat of the nitrogen-fixing endophyte Azoarcus sp. strain BH72 is grass roots grown under waterlogged conditions that produce, under these conditions, ethanol. Strain BH72 is well equipped to metabolize ethanol, with eight alcohol dehydrogenases (ADHs), of which ExaA2 and ExaA3 are the most relevant ones. exaA2 and exaA3 cluster and are surrounded by genes encoding two-component regulatory systems (TCSs) termed ExaS-ExaR and ElmS-GacA. Functional genomic analyses revealed that i) expression of the corresponding genes was induced by ethanol, ii) the genes were also expressed in the rhizoplane or even inside of rice roots, iii) both TCSs were indispensable for growth on ethanol, and iv) they were important for competitiveness during rice root colonization. Both TCSs form a hierarchically organized ethanol-responsive signal transduction cascade with ExaS-ExaR as the highest level, essential for effective expression of the ethanol oxidation system based on ExaA2. Transcript and expression levels of exaA3 increased in tcs deletion mutants, suggesting no direct influence of both TCSs on its ethanol-induced expression. In conclusion, this underscores the importance of ethanol for the endophytic lifestyle of Azoarcus sp. strain BH72 and indicates a tight regulation of the ethanol oxidation system during root colonization.

PiHOG1, a stress regulator MAP kinase from the root endophyte fungus Piriformospora indica, confers salinity stress tolerance in rice plants.

In this study, yeast HOG1 homologue from the root endophyte Piriformospora indica (PiHOG1) was isolated and functionally characterized. Functional expression of PiHOG1 in S. cerevisiae ∆hog1 mutant restored osmotolerance under high osmotic stress. Knockdown (KD) transformants of PiHOG1 generated by RNA interference in P. indica showed that genes for the HOG pathway, osmoresponse and salinity tolerance were less stimulated in KD-PiHOG1 compared to the wild-type under salinity stress. Furthermore, KD lines are impaired in the colonization of rice roots under salinity stress of 200 mM NaCl, and the biomass of the host plants, their shoot and root lengths, root number, photosynthetic pigment and proline contents were reduced as compared to rice plants colonized by WT P. indica. Therefore, PiHOG1 is critical for root colonisation, salinity tolerance and the performance of the host plant under salinity stress. Moreover, downregulation of PiHOG1 resulted not only in reduced and delayed phosphorylation of the remaining PiHOG1 protein in colonized salinity-stressed rice roots, but also in the downregulation of the upstream MAP kinase genes PiPBS2 and PiSSK2 involved in salinity tolerance signalling in the fungus. Our data demonstrate that PiHOG1 is not only involved in the salinity response of P. indica, but also helping host plant to overcome salinity stress.

A rhamnose-deficient lipopolysaccharide mutant of Rhizobium sp. IRBG74 is defective in root colonization and beneficial interactions with its flooding-tolerant hosts Sesbania cannabina and wetland rice.

Rhizobium sp. IRBG74 develops a classical nitrogen-fixing symbiosis with the aquatic legume Sesbania cannabina (Retz.). It also promotes the growth of wetland rice (Oryza sativa L.), but little is known about the rhizobial determinants important for these interactions. In this study, we analyzed the colonization of S. cannabina and rice using a strain of Rhizobium sp. IRBG74 dually marked with β-glucuronidase and the green fluorescent protein. This bacterium colonized S. cannabina by crack entry and through root hair infection under flooded and non-flooded conditions, respectively. Rhizobium sp. IRBG74 colonized the surfaces of wetland rice roots, but also entered them at the base of lateral roots. It became endophytically established within intercellular spaces in the rice cortex, and intracellularly within epidermal and hypodermal cells. A mutant of Rhizobium sp. IRBG74 altered in the synthesis of the rhamnose-containing O-antigen exhibited significant defects, not only in nodulation and symbiotic nitrogen fixation with S. cannabina, but also in rice colonization and plant growth promotion. Supplementation with purified lipopolysaccharides from the wild-type strain, but not from the mutant, restored the beneficial colonization of rice roots, but not fully effective nodulation of S. cannabina Commonalities and differences in the rhizobial colonization of the roots of wetland legume and rice hosts are discussed.

Efficacies of wettable pellet and fresh culture of Trichoderma asperellum biocontrol products in growth promoting and reducing dirty panicles of rice

Wettable pellets and fresh culture (fungus-colonized rice seeds) bioproducts of Trichoderma asperellum isolates 01-52 and CB-Pin-01, respectively, were evaluated for their efficacy in reducing dirty panicle or seed discoloration, and to increase the growth and yield of rice var. Chai Nat 1. Rice seeds were soaked (Sk) in a spore suspension of wettable pellets (20 g/20 L) or a fresh culture of bioproducts (100 g/20 L) of the fungus for 24 h. Soaked seeds were incubated for another 24 h before sowing. The 21-day-old seedlings were transplanted into small plots (1 m2 × 3 m2). Rice plants were sprayed (Sp) three times during the growing period with a spore suspension from the two bioproducts. The results indicated that both wettable pellet 01-52 (Sk + Sp) and fresh culture CB-Pin-01 (Sk + Sp) formulations significantly increased the plant height, number of tillers per hill, 1000-seed weight and total yield of rice compared to the untreated control. The incidence of dirty whole rice panicles, dirty panicle infected seed and empty seed were significantly reduced, while healthy seed were increased compared to the untreated control. Rice root colonization by T. asperellum isolates 01-52 and CB-Pin-01 were detected from the seedling through to the harvesting stage. The seedling vigor index and seedling health index of seedlings grown from 5 month-stored healthy and dirty panicle infected seeds treated by both wettable pellet 01-52 (Sk + Sp) and fresh culture CB-Pin-01 (Sk + Sp) bioproducts were significantly higher than the untreated control. All Trichoderma treatments increased whole kernels plus head rice and reduced broken rice in milled brown rice.

Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission.

The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls methane (CH4 ) emission, we pulse-labeled rice microcosms with (13) CO2 to determine the rates of (13) CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 ((12+13) CH4 ), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analysed by quantitative polymerase chain reaction of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of (13) CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of (13) CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.