Soil Foodweb Articles

Scientific Literature supporting the SFI Approach


October 21 2018

Title: Overview of Engineering Problems of Soil Compaction and Their Effects on Growth and Yields of Crops

Soil compaction constitutes serious engineering problems in agriculture that researchers have been contending with to proffer sustainable solution. This review work was carried out to contribute to the fixing of the problems. Effects of soilcompaction have eaten deep and are adversely affecting the production of food and fibre throughout the world. Soilcompaction occurs when soil particles are pressed together, leading to increased density and reduction in soil porespace. Thus, physical structure of the soil finds it difficult to support and applied mechanical stress leading to loss of soilstructural units, decrease in soil volume, increase in bulk density, decrease in porosity and reduction in hydraulicconductivity of the soil. Compacted soils have reduced available water capacity. The change in pore space restricts rootgrowth, and the gas exchange necessary for plant growth. Compaction restricts infiltration of water, increasing runoffand erosion, leading to the loss of valuable nutrients. Soil strength, cone index, bulk density, porosity, moisture content,erosion and runoff, poor plant growth and yields are the major parameters used as indicators of soil compaction. The problems of soil compaction are a global concern. As farmers continue to till the soil for the purpose of food and fibre production to meet the need of growing world population; prevention and alleviation practices should be taken intoconsideration to avoid the negative effects of soil compaction. Farmers are advised to carry out precision trafficagricultural practice; planting of crops on soils with cone index more than 1.5 kPa should be avoided; deep tillage practices, normally called subsoiling should be carried out on soils confirmed to be compacted. Farmers are advised tocultivate cover crops; incorporation of organic matter into the soil; and practicing of mixed farming in order to alleviatesoil compaction menace.

October 21 2018

Title: Study finds fungi, not plant matter, responsible for most carbon sequestration in northern forests


 OCTOBER 15 2018

Title: Compost could be worth double or triple if only...

TITLE: Carbon Sequestration—The Climate Change Solution That Virtually All Climate Activists Ignore

By Dr. Mercola

2015 has been declared the International Year of Soils,1 and few topics could be more important at this time. One of the objectives of the International Year of Soils is to “create full awareness of civil society and decision makers about the fundamental roles of soils for human’s life.”

Another is to “achieve full recognition of the prominent contributions of soils to food security [and] climate change adaptation.” Rarely do you hear climate activists2 address the issue of soil and land regeneration, yet it is perhaps the most comprehensive solution to everyone’s concerns.

Fighting over whether or not climate change is real; or whether climate change is manmade or not is completely irrelevant. Arguing over whether the temperature is actually rising or falling, or whether arctic ice sheets are shrinking or growing is a waste of time.


May 10, 2010:

Soil life in reconstructed ecosystems: Initial soil food web responses after rebuilding a forest soil profile for a climate change experiment

Summary: How Ecosystem disturbance effects the carbon-uptake cycle with a focus on how the soil foodweb reacts.

SUMMARY: Invitro Studies on Control of Soil-Borne Plant Pathogens by Earthworm Eudriluseugeniae Exudates
By S.V. Shobha and Radha D. Kale, January 2008    

A preliminary study was carried out using simple laboratory techniques to examine the influence of different preparations from the body of earthworm Eudrilus eugeniae on selected soil borne bacterial and fungal pathogens. Since this test was the first of its kind, testing procedures were standardized using different concentrations of extracts following different methods. The experiments were based on the principle of agar diffusion, turbidity development and rate of germination. The experiment involved the recording of inhibition zones formed by various extracts, amount of turbidity and suppression of rate of germination by different extracts. The results showed that the gut and body wall extracts had both antibacterial and antifungal activities by forming total inhibition zones, whereas coelomic fluid was found to be only antibacterial at the used concentrations. Body wall and gut extracts were found to be inhibitory to Xanthomonas campestris, Ralstonia solanacearum, Erwinia carotovora, Fusarium oxysporum and Botryodiplodia theobromae. Colemic fluid was inhibitory to X.campestris and E.carotovora. There was no inhibitory effect recorded by any of the extracts at the used concentrations during this study on Rhizactonia solani, Alternaria solani and Sclerotium rolfsii. Only delayed sporulation was observed in all the cases, but this was only a visual observation. The mixed extract when tested on F.oxysporum has shown a strong clear inhibition zone.
The study has proved that earthworm extracts can be effectively used for suppression of soil borne pathogens and that it can evolve as potential biopesticide.


SUMMARY: The positive influence on plant growth was largely associated with mineral N and gibberellin (GA4) present in the teas.

Archana P. Pant, Theodore J.K. Radovich, Nguyen V. Hue, and Robert E. Paull (2012), Biochemical properties of compost tea associated with compost quality and effects on pak choi growth, Scientia Horticulturae, Volume 148: , 138-146

This study investigated the links between variability in compost quality, the biochemical characteristics of their extracts (compost tea) and plant growth indicator through a series of experiments. Five different commercially produced composts were selected for quality evaluation. They were: (i) chicken manure-based thermophilic compost (ii) green waste thermophilic compost (iii) food waste vermicompost; (iv) chicken manure-based vermicompost (aged); and (v) chicken manure-based vermicompost (fresh). Compost teas were prepared from each compost using aerated extraction method with compost to water ratio of 1:10 (v:v), and were applied weekly for four weeks to pak choi (Brassica rapa cv Bonsai, Chinensis group) grown in a peat-perlite medium. The results demonstrated that compost quality generally impacted: (i) nutrient extraction efficiency (ii) microbial activity (iii) phytohormones and (iv) total nutrient content of the extracts. These differences in extract quality similarly impacted growth and mineral nutrient status of pak choi. Applications of compost tea increased growth and mineral nutrient content of pak choi. The responses were greater with aged chicken manure-based vermicompost tea, chicken manure-based thermophilic compost tea, and food waste vermicompost tea. The positive influence on plant growth was largely associated with mineral N and gibberellin (GA4) present in the teas. In vitro cultivation of pak choi with GA4 concentrations similar to those measured in the teas confirmed a direct positive effect of GA4 on growth. These findings suggest that either vermicompost or thermophilic compost can be used for the production of compost tea but the tea quality and its effect on plant may be predicted based on compost quality.


SUMMARY: Reduced severity of common scab tuber disease in potatoes. Ineffective against fusarium dry rot, black scurg, and silver scurf. Produced higher yields.

Al-Mughrabi, K. I., Berthélémé, C., Livingston, T., Burgoyne, A., Poirier, R., & Vikram, A. (2008). Aerobic compost tea, compost and a combination of both reduce the severity of common scab (Streptomyces scabiei) on potato tubers. Journal of Plant Sciences, 3, 168–175. 

A field experiment was conducted in Woodstock, New Brunswick, Canada to study the efficacy of compost tea and compost on reduction of tuber diseases in potato. A randomized complete block design replicated four times was established in a commercial field setting with four treatments (control, compost, compost tea and compost + compost tea). Tubers were assessed for disease severity, tuber number, tuber weight, defects and total yield. Treatment of potato plants with compost, compost tea or a combination of compost + compost tea significantly reduced the severity of common scab tuber disease by 81, 42 and 81%, respectively, compared to the untreated control. Treatments were ineffective against the potato tuber diseases fusarium dry rot, black scurf and silver scurf. Potato plants treated with compost tea and a combination of compost + compost tea produced higher yield compared to all other treatments. However, the number and weight of knobby tubers were significantly higher in compost tea treatment and significantly lower in the combined treatment of both compost + compost tea compared to other treatments. This is the first study to report on the effect of compost and compost tea against common scab of potatoes.


SUMMARY: Indicates a possible role in fungal degradation. Produced clear inhibition zones against all tested fungi.  

El-Masry, M. H., Khalil, A. I., Hassouna, M. S., & Ibrahim, H. A. H. (2002). In situ and in vitro suppressive effect of agricultural composts and their water extracts on some phytopathogenic fungi. World Journal of Microbiology and Biotechnology, 18, 551–558

In situ and in vitro experiments were carried out to determine the effect of various composts (leafy fruit compost (LFC), garden compost (GC), and crops compost (CC)) and their water extract on Pythium debaryanum, Fusarium oxysporum f.sp. lycopersici,Sclerotium bataticola. Compost water extract (CWE) of LFC, GC, and CC were found to contain Bacillus spp., Micrococcus spp.,Staphylococcus spp. and Corynebacterium spp., and the fungi Aspergillus spp., Rhizopus spp., and Drechslera spp., and various Actinomycetes. In situ results indicated considerable decrease in fungal growth around the unautoclaved compost especially in the case of S. bataticola and F. oxysporum f.sp. lycopersici, compared to the autoclaved compost. In vitro tests showed that concentration of CWE at 5, 10 and 15% (v/v) suppressed the hyphal growth of S. bataticola by 83% using 5% CC and by 94.4% using 5% LFC or 10% GC, and F. oxysporum f.sp. lycopersici by 94.4% using either composts. CWE of GC decreased fungal dry weight of F. oxysporum f.sp. lycopersici by 97.7%, P. debaryanum by 92.8%, and S. bataticola by 84.4%; CC decreased F. oxysporum f.sp. lycopersici by 94%, P. debaryanum by 86.2%, and S. bataticola by 63.3%, while CWE of LFC was the least effective against the tested fungi. CWE produced clear inhibition zones against all the tested fungi. Microflora found in CWE have an important role in suppressing the growth of tested fungi. CWE contained neither antibiotics nor siderophores. The presence of protease, chitinase, lipase and β-1,3 glucanase (lysogenic enzymes) in CWE indicates a possible role in fungal degradation.


SUMMARY: Teas had no effect on plant yield, but improvement in crop quality. 

Fritz, J.I. , I.H. Franke-Whittle, S. Haindl, H. Insam, and R. Braun (2012), Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals, Canadian Journal of Microbiology, Volume 58, Number 7: , 836-847

Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables (Raphanus sativus, Rucola selvatica, and Pisum sativum) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments.



Gea, F. J., Navarro, M. J., & Tello, J. C. (2009). Potential application of compost teas of agricultural wastes in the control of the mushroom pathogen Verticillium fungicola. Journal of Plant Diseases and Protection, 116, 271–273


SUMMARY: Biological amendments reduced soilborne disease and improved yield in some rotations, but not others. Crop rotation more effective than amendments. 

Larkin, Robert P. (2008) Relative effects of biological amendments and crop rotations on soil microbial communities and soilborne diseases of potato, Soil Biology and Biochemistry, Volume 40, Number 6: , 1341-1351

Various biological amendments, including commercial biocontrol agents, microbial inoculants, mycorrhizae, and an aerobic compost tea (ACT), were evaluated, alone and in conjunction with different crop rotations, for their efficacy in introducing beneficial microorganisms, affecting soil microbial community characteristics (SMCC), and reducing soilborne diseases of potato in greenhouse and field trials in Maine. Most amendments successfully delivered microorganisms into the soil, altering microbial populations and activity in accordance with the particular organisms added, and significantly altering SMCC (as determined by FAME analysis) to various degrees from 2 to 24 weeks. Amendment effects were greatest early on (2 weeks after amendment), but effects associated with crop treatment became more dominant at subsequent assessments (10 and 24 weeks after amendment). In field trials, effects on microbial characteristics, soilborne diseases and tuber yield were variable, with some microbial inoculants and a biostimulant producing no significant effects, whereas arbuscular mycorrhizae, reduced stem canker and black scurf by 17–28%. When used in three different 2 yr crop rotations (barley/ryegrass, barley/clover, and potato, all followed by potato), biological amendments reduced soilborne disease and improved yield in some rotations, but not others. Soil-applied ACT and the combination of ACT with a mixture of beneficial microorganisms (Mix) reduced stem canker, black scurf, and common scab on tubers by 18–33% and increased yield 20–23% in the barley/ryegrass rotation, but not in the other rotations. Mix also reduced disease (20–32%) in the barley/clover rotation only. None of the amendments significantly reduced disease in continuous potato plots. Both crop rotation and amendment treatments significantly affected SMCC, but rotation effects were more dominant. These results indicate that certain rotations were better able to support the added beneficial organisms from amendments and enable more effective biological control, and also that favorable crop rotations may be more effective than amendments in manipulating or altering SMCC. Establishment and persistence of amendment effects may depend on many factors, but an effective and supportive crop rotation is apparently important.


SUMMARY: Efficacy of ACT (Aerated Compost Tea) and NCT (Non-Aerated Compost Tea) firstly depend on the microbiota present in them. Teas are a viable way to manage plant diseases and crop fertilization. 

Marín, Francisco, Mila Santos, Fernando Diánez, Francisco Carretero,Francisco J. Gea, José A. Yau, and María J. Navarro (2013), Characters of compost teas from different sources and their suppressive effect on fungal phytopathogens, World Journal of Microbiology and Biotechnology, Volume 29, Number 8: , 1371-1382

Compost teas (CT) are fermented watery extracts of composted materials that are used to control plant diseases and on crop fertilization. In this work, aerated (ACT) and non-aerated compost teas (NCT) were obtained from four different composts: spent mushroom substrate compost, grape marc compost, greenhouse horticultural crop residues compost, and vermicompost. Physico-chemical and microbiological analysis were carried out to determine their properties. In vitro assays were performed to assess their suppressive effect on the mycelial growth of eight fungal phytopathogens. In vivo trials aimed to assess their effect on gummy stem blight (Didymella bryonae) and powdery mildew (Podosphaera fusca) in melon plants. Results showed that ACT and NCT filtrates inhibited the in vitro growth of all tested pathogens while autoclaved CT did not completely lose their inhibitory effect, and CT sterilized by microfiltration had no effect on the pathogen growth. The severity of powdery mildew was highly reduced by ACT and NCT from all sources, though in gummy stem blight assay only a delay in disease development was observed. In general, all compost teas showed a high level of microbial populations and nutrients. Results suggest that the efficacy of ACT and NCT firstly depend on the microbiota present in them. We consider compost teas from the four tested sources as a viable way to manage plant diseases and crop fertilization, throughout its integration in pest management programs and fertigation systems under different dilution rates.

SUMMARY: Effect of tea on crop growth largely due to mineral nutrient, particularly N uptake by plants. Aeration and additives not necessary for growth promotion and nutrient quality.  

Pant AP, Radovich TJK, Hue NV, Talcott ST, Krenek KA. 2009. "Vermicompost extracts influence growth, mineral nutrients, phytonutrients and antioxidant activity in pak choi (Brassica rapa cv. Bonsai, Chinensis group) grown under vermicompost and chemical fertiliser." Journal of the Science of Food and Agriculture, 89.14 (2009): 2383-2392. 

BACKGROUND: Multiple studies have been reported on the effect of compost tea on suppression of certain plant diseases. However, relatively little work has been done to investigate the effect of vermicompost tea on yield and nutritional quality of vegetable crops. In this study, experiments were conducted to determine the effect of extraction method on vermicompost tea quality and subsequent effects on growth, mineral nutrients, phytonutrients and antioxidant activity of pak choi plants grown under organic (vermicompost) and synthetic (Osmocote) fertilisation. Three vermicompost teas obtained by different extraction methods, namely non-aerated vermicompost tea (NCT), aerated vermicompost tea (ACT) and aerated vermicompost tea augmented with microbial enhancer (ACTME), were applied to the plants. Aerated water served as control.

RESULTS: Mineral nutrients were significantly higher in ACTME compared with other teas, but total microbial population and activity did not differ with extraction method. All vermicompost teas similarly enhanced plant production, mineral nutrients and total carotenoids, and this effect was most prominent under organic fertilisation. Antioxidant activity and total phenolics were higher under organic compared with synthetic fertilisation. Vermicompost teas generally decreased phenolics under organic fertilisation and increased them under synthetic fertilisation compared with the control.

CONCLUSION: The effect of vermicompost tea on crop growth is largely attributable to mineral nutrient, particularly N, uptake by plants. Non-significant differences among extraction methods on plant response within fertiliser regimes suggest that aeration and additives are not necessary for growth promotion and nutrient quality under the conditions reported here. Copyright © 2009 Society of Chemical Industry


SUMMARY: Compost tea helps to restore and increase the populations of beneficial micro-organisms. Control percentage of compost tea treatment was the most.  

Samin Seddigh, Leila Kiani, Bahram Tafaghodinia, and Bahareh Hashemi (2014), Using aerated compost tea in comparison with a chemical pesticide for controlling rose powdery mildew, Archives Of Phytopathology And Plant Protection, Volume 47, Number 6: , 658-664

Rose powdery mildew (Sphaerotheca pannosa var. rosae) is one of the most common foliar diseases of roses worldwide. Application of chemical products on the plant or in the soil kills a range of the beneficial micro-organisms thereby disturbing ecosystem. Compost tea helps to restore and increase the populations of those beneficial micro-organisms. The objective of the present study was to evaluate the comparison of biopesticide (compost tea) and a chemical pesticide. The experiment was performed in three treatments, which were compost tea, fungicide (Topaz) and no treatment in three replications. After foliar applications of biopesticide and fungicide, the control percentage was estimated based on the number of infected flowers with powdery mildew. The results indicated that there was a significant difference between these treatments on rose in controlling powdery mildew (F = 23.25, p = 0.0015, df = 2), at a probability level of 1% (p ⩽ 0.01). So, that control percentage of compost tea treatment was the most.



SUMMARY: All selected CWE (water extracts of composts) significantly (P<0.05) reduced the disease incidence and severity in the seedling and plant assays. Summary: Heat stable chemicals in CWE can suppress root and foliar infection by P. Capsici in pepper plants.   

Sang, M. K., Kim, J. G., & Kim, K. D. (2010). Biocontrol activity and induction of systemic resistance in pepper by compost water extracts against Phytophthora capsici. , 100, 774–783

We investigated the effects of water extracts of composts (CWE) from commercial compost facilities for controlling root and foliar infection of pepper plants by Phytophthora capsici. Among 47 CWE tested, CWE from composts Iljuk-3, Iljuk-7, Shinong-8, and Shinong-9 significantly (P < 0.05) inhibited zoospore germination, germ tube elongation, mycelial growth, and population of P. capsici. All selected CWE significantly (P < 0.05) reduced the disease incidence and severity in the seedling and plant assays compared with the controls. However, there were no significant differences in zoospore germination, disease incidence, and disease severity between treatments of untreated, autoclaved, and filtered CWE. In addition, CWE significantly (P < 0.05) suppressed leaf infection of P. capsici through induced systemic resistance (ISR) in plants root-drenched with CWE. The tested CWE enhanced the expression of the pathogenesis-related genes, CABPR1, CABGLU, CAChi2, CaPR-4, CAPO1, or CaPR-10 as well as β-1,3-glucanase, chitinase, and peroxidase activities, which resulted in enhanced plant defense against P. capsici in pepper plants. Moreover, the CWE enhanced the chemical and structural defenses of the plants, including H2O2 generation in the leaves and lignin accumulation in the stems. The CWE could also suppress other fungal pathogens (Colletotrichum coccodes in pepper leaves and C. orbiculare in cucumber leaves) through ISR; however, it failed to inhibit other bacterial pathogens (Xanthomonas campestris pv. vesicatoria in pepper leaves and Pseudomonas syringae pv. lachrymans in cucumber leaves). These results suggest that a heat-stable chemical(s) in the CWE can suppress root and foliar infection by P. capsici in pepper plants. In addition, these suppressions might result from direct inhibition of development and population of P. capsici for root infection, as well as indirect inhibition of foliar infection through ISR with broad-spectrum protection.


SUMMARY: The most consistent formulation for damping-off suppression was ACT (Aerated Compost Tea) produced with kelp and humic acid additives. 

Scheuerell, Steven J. and Walter F. Mahaffee (2004) Compost Tea as a Container Medium Drench for Suppressing Seedling Damping-Off Caused by Pythium ultimum, Biological Control, Volume 94, Number 11, Pages 1156-1163

Compost tea is being used increasingly in agricultural production to control plant diseases. However, there has been limited investigation relating disease control efficacy to various compost tea production methods, particularly compost tea produced with active aeration and additives to increase microbial population densities in compost tea. Aerated compost tea (ACT) and nonaerated compost tea (NCT), produced with or without additives, was investigated for the suppression of damping-off of cucumber caused by Pythium ultimum. Compost tea was used to drench soilless container medium inoculated with P. ultimum; effect on damping-off ranged from not suppressive to consistently suppressive depending on the method used to produce the tea. The most consistent formulation for damping-off suppression was ACT produced with kelp and humic acid additives. Producing ACT with a molasses-based additive inconsistently suppressed damping-off; evidence suggests that residual nutrients can interfere with disease suppression. Heating or diluting compost tea negated suppression. Across all compost tea samples, there was no significant relationship of bacterial populations, measured as active cells, total cells, or CFU, to disease suppression. However, for all ACT produced without the molasses-based additive, there was a threshold of bacterial population density (6 log10 active cells per ml, 7.48 log10 total cells per ml, or 7 log10 CFU per ml) above which compost teas were suppressive.



Segarra, G., Reis, M., Casanova, E., & Trillas, M. I. (2009). Control of powdery mildew (Erysiphe polygoni) in tomato by foliar applications of compost tea. Journal of Plant Pathology, 91, 683–689.



SUMMARY: Plants should be sprayed at short intervals with the compost tea to sustain the suppressive effect.  

Siddiqui, Y., Meon, S., Ismail, R., & Rahmani, M. (2009). Bio-potential of compost tea from agro-waste to suppress Choanephora cucurbitarum L. the causal pathogen of wet rot of okra. Biological Control, 49, 38–44. 

In vitro and in vivo experiments were carried out to determine the mechanisms involved in suppression ofChoanephora cucurbitarum the causal pathogen of wet rot disease of okra by using the tea produced from agro-waste such as rice straw (RST) and empty fruit bunch (EFB) of oil palm composts. Non-sterilized, filter-sterilized and heat-sterilized compost teas were tested on the growth of C.cucurbitarum. The highest percentage of inhibition in conidial germination was obtained by both the non-sterilized RST and EFB compost tea with values of 84% and 79%, respectively. The inhibitory efficacy was reduced significantly (P ⩽ 0.05) when the teas were subjected to millipore membrane filters or heat-sterilization. The mycelial growth of C. cucurbitarum was reduced by 100% in plates amended with both the non-sterilized compost tea. Light microscopy micrographs of mycelial samples of C. cucurbitarum exposed to non-sterilized RST and EFB compost tea showed alterations in mycelial morphology and lysis, resulting in inhibition in mycelial growth. Glass house trials indicated that induced host resistance was stimulated in okra plants treated with non-sterilized and filter-sterilized compost teas based on the detection of inducible resistance-related compounds. The mean values for inducible enzymes which have a role in disease resistance [peroxidase (PO), polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL)] increased until day 8, which were significantly higher in okra plants pre-treated with non-sterilized tea in view of the high nutritive and microbiological properties. There was a further increase in inducible compounds when the pre-treated okra plants were challenged with C. cucurbitarum. Following the increase in total PO, PPO and PAL activities, development of Choanephora wet rot was delayed, confirming the possible involvement of induced resistance. However, resistance was not maintained since it decreased over time. This could be due to the highly stressed environment of the leaf surfaces which had a detrimental effect on the survival of the antagonists and subsequently affected the efficacy of compost tea. It was therefore suggested that plants should be sprayed at short intervals with the compost tea to sustain the suppressive effect.





St. Martin, C.C.G., W. Dorinvil, R. A.I. Brathwaite, and A. Ramsubhag (2012), Effects and relationships of compost type, aeration and brewing time on compost tea properties, efficacy against Pythium ultimum , phytotoxicity and potential as a nutrient amendment for seedling production, Biological Agriculture & Horticulture, Volume 28, Number 3: , 185-205

Studies were undertaken to determine the effects and relationships of compost type, aeration, and brewing time on compost tea properties, phytotoxicity, and efficacy in inhibiting growth of Pythium ultimum in vitro. The effect of compost tea on dry matter of tomato and sweet pepper seedlings cultivated on compost-amended substrate was also investigated. Compost type, aeration, and brewing time significantly affected the microbial and chemical properties of compost teas made from banana leaf (BLC) and lawn clipping (LCC) composts. Both aerated and nonaerated compost teas made from BL and LC composts significantly inhibited mycelial growth of P. ultimum. However, growth inhibition (GI) levels were significantly higher in compost teas produced from LCC. Aerating compost tea (ACT) did not consistently result in higher GI levels across compost types. Neither did increasing brewing time beyond 18 h for ACT and 56 h for nonaerated compost tea (NCT). Across all ACTs, yeast population was positively related to GI whereas bacterial population had a positive relationship with GI across all NCTs. Evidence suggests that multiple groups of microorganisms contributed to GI through antibiosis and competition for resources. All compost teas stimulated seed germination of tomato and root growth in sweet pepper. However, NCTs brewed for 56 h using LCC or BLC, and ACT produced from BLC brewed for 18 h, significantly reduced seed germination of sweet pepper. Application of NCT brewed for 168 h made from BLC significantly increased total dry matter of tomato seedlings by 122% compared with the control.


SUMMARY: The inoculation of composts with biological control agents, manipulation of composttea production process, and the use of new techniques for organic matter characterization and microbial community profiling may improve the efficacy and reliability of disease control obtained.  

St. Martin, C. C. G. and R. A.I. Brathwaite, "Compost adn compost tea: Principles and prospects as substrates and soil-borne disease management strategies in soil-less vegetable production." Biological Agriculture & Horticulture 28:1(2012): 1-33.  

Numerous studies have demonstrated the potential of composted organic wastes not only as substitutes for peat as a growth substrate but also to stimulate plant growth and suppress soil-borne diseases. The major impediment to the use of compost as substrates or biocontrol agents has been variation in physical and chemical characteristics and disease suppression levels across and within compost types, sources, and batches. Compost tea, a product of compost, has also been shown to suppress soil-borne diseases including damping-off and root rots (Pythium ultimum, Rhizoctonia solani,Phytophthora spp.) and wilts (Fusarium oxysporum and Verticillium dahliae). Although the mechanisms involved in disease suppression are not fully understood, sterilization of composts and compost teas has generally resulted in a loss in disease suppressiveness. This indicates that the mechanism of suppression is often, or predominantly, biological, although chemical and physical factors have also been implicated. The inoculation of composts with biological control agents, manipulation of compost tea production process, and the use of new techniques for organic matter characterization and microbial community profiling may improve the efficacy and reliability of disease control obtained.



SUMMARY: The microbial population in compost extracts was considered to be the most significant factor of inhibition pathogenic fungal growth. No markedly correlations among bacterial community diversity, the inhibition of pathogenic fungal growth adn the reduction of root-knot nematodes were observed.  

Xu, Dabing, Waseem Raza, Guanghui Yu, Qingyun Zhao, Qirong Shen, and Qiwei Huang (2011) Phytotoxicity analysis of extracts from compost and their ability to inhibit soil-borne pathogenic fungi and reduce root-knot nematodes, World Journal of Microbiology and Biotechnology 28.3 (2012): 1193-1201. 

Compost extracts are novel organic amendments, typically applied to suppress soil-borne diseases. This research evaluated the phytotoxicity of compost extracts and analyzed their ability to inhibit pathogenic fungal growth and reduce root-knot nematodes. The physical, chemical and biological characteristics of extracts from a pig manure and straw compost were analyzed. Three types of extracts were tested: direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC). All compost extracts showed low phytotoxicity against lettuce and cress, but AFEC and NAFEC were more phytotoxic than DEC. All compost extracts significantly inhibited pathogenic fungal growth except for the fungus Rhizoctonia solania AG4. For two seasons, tomato root biomass of three compost extracts was 1.25–5.67 times greater than CK (water control), and AFEC and NAFEC showed the best tomato root growth promotion. The reduction ratio of root egg mass and density of soil nematodes were 34.51–87.77% and 30.92–51.37%, when applied with three compost extracts. The microbial population in compost extracts was considered to be the most significant factor of inhibition pathogenic fungal growth. No markedly correlations among bacterial community diversity, the inhibition of pathogenic fungal growth and the reduction of root-knot nematodes were observed. This information adds to the understanding of the growth-promoting and suppression effects of compost extracts and will help to enhance crop production.




SUMMARY: The best growth promotion by application of AFEC (Aerated fermentation extracts of compost) was mainly attributed to the humic-like substances in the AFEC.  

XU, Da-Bing, Qiu-Jun WANG, Yun-Cheng WU, Guang-Hui YU, Qi-RongSHEN, and Qi-Wei HUANG (2012), Humic-Like Substances from Different Compost Extracts Could Significantly Promote Cucumber Growth, Pedosphere, Volume 22, Number 6: , 815-824

The effects of direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC) on cucumber growth and the action mechanisms were evaluated based on the structure and activity analysis of humic-like substances. AFEC increased cucumber growth most significantly, followed by DEC and NAFEC, which was insignificant compared to the control treatment. Humic-like substances from compost extracts played an important role in promoting cucumber growth. Application of humic-like substances stimulated auxin-like activity and increased chlorophyll content and nitrogen accumulation in plants. The positive auxin-like activity of humic-like substances could be attributed to the relative distribution of special carbon groups, such as those with a large amount of peptidic and carbohydratic groups or with a low content of phenolic groups. In conclusion, the best growth promotion by application of AFEC was mainly attributed to the humic-like substances in the AFEC.



SUMMARY: Microbial-enriched Compost tea (CT) may be used to inhibit the development of powdery mildew on melons, thus reducing the dependency on chemical fertilizers.  

Yuvarani Naidu, Sariah Meon, and Yasmeen Siddiqui (2012), In vitro and in vivo evaluation of microbial-enriched compost tea on the development of powdery mildew on melon, BioControl 57.6 (2012): 827-836.  

This study evaluated the effects of microbial-enriched compost tea (CT) on the conidial germination of Golovinomyces cichoracearum DC. and development of powdery mildew on melons in a time-dependent manner. In vitro conidial germination was significantly reduced by 94 % and 85 % upon treatment with Daconil® (fungicide) or microbial-enriched CT, respectively, 96 h after incubation (hai). Morphological analysis under light microscopy demonstrated that conidia co-incubated with microbial-enriched CT at 48 hai appeared ruptured, which contributed to higher inhibition of conidial germination, increased cell permeability and leakage of cellular contents. These observations may be explained by antibiosis. Moreover, different application time of microbial-enriched CT on melons significantly affected disease development. There was a delay in disease development by 12 days in plants treated with Daconil®, microbial-enriched CT applied 24 h after inoculation and microbial-enriched CT applied simultaneously with inoculation when compared to the control treatment. Curative application of microbial-enriched CT (24 h after inoculation) delayed the onset of disease, and the efficiency of inhibition was comparable to a fungicidal spray (Daconil®). Hence, microbial-enriched CT may be used to inhibit the development of powdery mildew on melons, thus reducing the dependency on chemical fertilisers.


SUMMARY: The use of vermicompost might be considered more in organic farming not only a substitute for peat in potting media but also as foliar sprarys for fertilization and biological disease prevention.  

Zaller JG. 2006. Foliar spraying of vermicompost extracts: effects on fruit quality and indications of late-blight suppression of field-grown tomatoes.  Biological Agriculture & Horticulture, 24(2): 165-180 

The effect of foliar sprays with aqueous vermicompost extracts on growth, yields, morphological and chemical fruit quality and natural infection with late blight disease (Phytophthora infestons (Mont.) de Bary)) on three tomato varieties (Lycopersicon esculentnm Mill., cv. Diplom Fl, cv. Malina, cv. Rheinlands Ruhm) was investigated in a field experiment. Extracts were prepared of vermicompost produced from fruit, vegetable and cotton waste by redworms (Eisenia fetidaSav., Lumbricidae); tap water served as control treatment. Foliar application (spraying) of vermicompost extracts did not affect plant growth, biomass or nutrient allocation, or yields and number of fruits of the three tomato varieties; however, for several dates it significantly reduced the number of flowers produced. Foliar vermicompost spraying cither increased or decreased peel firmness dependent on tomato variety and increased fruit circumference consistently as well as contents of nitrogen but decreased L-ascorbic acid compared with water sprayed fruits. All other measured parameters of fruit quality (dry matter, C, N, P, K, Ca, Mg, glucose and fructose content) were similar for vermicompost and water sprayed plants. Natural infection of leaves, stems and fruits by P. infestans was generally very low under the experimental conditions; however, across varieties, only half as many vermicompost sprayed plants showed clear signs ofP. infestans infection as water sprayed plants; the severity of the infection was unaffected by the two spraying treatments. In conclusion, these results suggest that the use of vermicompost might be considered more in organic farming not only as a substitute for peat in potting media but also as foliar sprays for fertilization and biological disease prevention.

SUMMARY: Use of good compost in various forms of liquid biological amendments (brewed and not brewed) knocks out a pathogen 

S.J. Tollefson, G. Curlango-Rivera, D.A. Huskey, T. Pew, G. Giacomelli, M.C. Hawes.  (2014).  Altered carbon delivery from roots: rapid, sustained inhibition of border cell dispersal in response to compost water extracts.  Plant Soil DOI 10.1007/s11104-014-2350-z

Background and aims In a previous study, a compost water extract (CWE) applied to pea seedlings resulted in >95 % protection against root infection. The protection was correlated with retention of a sheath of root border cells surrounding each root tip. A transient exposure to CWE was correlated with 80 % reduction in infection, and with retention of border cell sheaths. Early effects of CWE on border cell dispersal therefore were examined. Materials and methods Temporal and spatial dynamics of pea, maize, cotton, and cucumber border cell dispersal
into water or CWE were measured. Results Border cells formed a mass surrounding root tips within seconds after exposure to water, and most cells dispersed into suspension spontaneously. In CWE, >90 % of the border cell population instead remained appressed to the root surface, even after vigorous agitation. In cotton, for example, >25,000 border cells dispersed within seconds of immersion in water, but <100
border cells dispersed after >24 h in CWE. Conclusions Border cells can contribute >90 % of carbon released from young roots, and a single border cell can trap hundreds of bacteria within minutes. The impact of altered border cell dispersal on soil properties, plant nutrition, and root disease development warrants further study
New research involving a scientist at the University of York has revealed a potential natural defense against invasive pathogens which damage food crops across the world.

Dr Ville Friman, of the Department of Biology at York, worked with colleagues in China and the Netherlands in the search for new ways to suppress the pathogen Ralstonia solanacearum which causes bacterial wilt of tomato and potato. Global damage estimates of bacterial wilt of potato currently exceed $950 million per year.
Traditionally, farmers have employed integrated management -- potentially involving the use of chemicals -- to protect crops against pathogen invasion and increase yields. But some chemicals are banned within the EU because of their detrimental effects on the environment.
The researchers studied if the soil microbial community that interacts with the plant could be harnessed to act as an ecological defence against pathogen invasion. They specifically concentrated on bacterial resource competition networks and studied pathogen invasion success in simplified laboratory experiments and tomato plant roots.
These tests showed that the greater niche overlap between the resident microbial community and the invading pathogen led to intensified resource competition constraining the spread of bacterial wilt. Moreover, pathogen invasion success was further reduced when competition between the members of resident bacterial community was minimized.Dr Friman said: "Soil-borne plant pathogens are difficult to control because of their variable populations and their ability to evolve to overcome plant resistance. A significant proportion of global food production is lost to soil-borne plant diseases. Thus, improving rhizosphere community invasion resistance could significantly improve crop yields across different agricultural systems."
The researchers suggest adopting an ecological approach to improve planthealth by engineering the resource competition interaction networks of plant-associated bacterial communities. The research is published in Nature Communications.

Biological Nitrogen Fixation for Sustainable Agriculture: A Perspective


The economic and environmental costs of the heavy use of chemical N fertilizers in agriculture are a global concern. Sustainability considerations mandate that alternatives to N fertilizers must be urgently sought. Biological nitrogen fixation (BNF), a microbiological process which converts atmospheric nitrogen into a plant-usable form, offers this alternative. Nitrogen-fixing systems offer and economically attractive and ecologically sound means of reducing external inputs and improving internal resources. Symbiotic systems such as that of legumes and Rhizobium can be a major source of N in most cropping systems and that of Azolla and Anabaena can be of particular value to flooded rice crop. Nitrogen fixation by associative and free-living microorganisms can also be important. However, scientific and socio-cultural constraints limit in the utilization of BNF systems in agriculture. While several environmental factors that affect BNF have been studied, uncertainties still remain on how organisms respond to a given situation. In the case of legumes, ecological models that predict the likelihood and the magnitude of response to rhizobial inoculation are now becoming available. Molecular biology has made it possible to introduce choice attributes into nitrogen-fixing organisms but limited knowledge on how they interact with the environment makes it difficult to tailor organisms to order. The difficulty in detecting introduced organisms in the field is still a major obstacle to assessing the success or failure of inoculation. Production-level problems and socio-cultural factors also limit the integration of BNF systems into actual farming situations. Maximum benefit can be realized only through analysis and resolution of major constraints to BNF performance in the field and adoption and use of the technology by farmers.

Scientific Literature on Bioremediation


SUMMARY: Heavy Metals Bioremediation of Soil

L. Diels, M. De Smet, L. Hooyberghs, and P. Corbisier (1999). Heavy metals bioremediation of soil. Molecular Biotechnology, Vol.12, Issue 2, pp. 149-158.


Historical emissions of old nonferrous factories lead to large geographical areas of metals-contaminated sites. At Least 50 sites in Europe are contaminated with metals like Zn, Cd, Cu, and Pb. Several methods, based on granular differentiation, were developed to reduce the metals content. However, the obtained cleaned soil is just sand. Methods based on chemical leaching or extraction or on electrochemistry to release a soil without any salts and with an increased bioavailability of the remaining metals content. In this review a method is presented for the treatment of sandy soil contaminated with heavy metals. The system is based on the metal solubilization on biocrystallization capacity of Alcaligenes eutrophus CH34. The bacterium can solubilize the metals (or increase their bioavailability) via the production of siderophores and adsorb the metals in their biomass on metal-induced outer membrane proteins and by bioprecipitation. After the addition of CH34 to a soil slurry, the metals move toward the biomass. As the bacterium tends to float quite easily, the biomass is separated from the water via a flocculation process. The Cd concentration in sandy soils could be reduced from 21 mg Cd/kg to 3.3 mg Cd/kg. At the same time, Zn was reduced from 1070 mg Zn/kg to 172 mg Zn/kg. The lead concentration went down from 459 mg Pb/kg to 74 mg Pb/kg. With the aid of biosensors, a complete decrease in bioavailability of the metals was measured.

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SUMMARY: Bioremediation of Lead

Chen, H. Pan, S. (2005). Bioremediation potential of spirulina: toxicity and biosorption studies of lead. Journal of Zhejiang University SCIENCE, 6B(3):171-174

This study examines the possibility of using live spirulina to biologically remove aqueous lead of low concentration (below 50 mg/L) from wastewater. The spirulina cells were first immersed for seven days in five wastewater samples containing lead of different concentrations, and the growth rate was determined by light at wavelength of 560 mm. The 72 h-EC50 (72 h medium effective concnetration) was estimated to be 111.46 mg/L (lead). Afterwards, the lead adsorption by live spirulina cells was conducted. It was observed that at the initial stage (0-12 min) the adsorption rate was so rapid that 74% of the metal was biologically adsorbed. The maximum biosorption capacity of live spirulina was estimated to be 0.62 mg lead per 10alga cells.

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SUMMARY: Uptake of Lead by a Ciliate

A. Rehman, S. Ashraf, J. I. Qazi, & A. R. Shakoori (2005). Uptake of Lead by a Ciliate, Stylonchia mytilus, isolated from Industrial Effluents: Potential Use in Bioremediation of Wastewater. Bulletin of Environmental Contamination and Toxicology, Vol. 75, Issue 2, pp. 290-296.

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Scientific Literature dealing with Decomposition

Zhang X, Wang W, Chen W, Zhang N, Zeng H (2014) Comparison of Seasonal Soil Microbial Process in Snow-Covered Temperate Ecosystems of Northern China. PloS one 9.3 (2014): e92985. doi: 10.1371/journal.pone.0092985.   

More than half of the earth's terrestrial surface currently experiences seasonal snow cover and soil frost. Winter compositional and functional investigations in soil microbial community are frequently conducted in alpine tundra and boreal forest ecosystems. However, little information on winter microbial biogeochemistry is known from seasonally snow-covered temperate ecosystems. As decomposer microbes may differ in their ability/strategy to efficiently use soil organic carbon (SOC) within different phases of the year, understanding seasonal microbial process will increase our knowledge of biogeochemical cycling from the aspect of decomposition rates and corresponding nutrient dynamics. In this study, we measured soil microbial biomass, community composition and potential SOC mineralization rates in winter and summer, from six temperate ecosystems in northern China. Our results showed a clear pattern of increased microbial biomass C to nitrogen (N) ratio in most winter soils. Concurrently, a shift in soil microbial community composition occurred with higher fungal to bacterial biomass ratio and gram negative (G-) to gram positive (G+) bacterial biomass ratio in winter than in summer. Furthermore, potential SOC mineralization rate was higher in winter than in summer. Our study demonstrated a distinct transition of microbial community structure and function from winter to summer in temperate snow-covered ecosystems. Microbial N immobilization in winter may not be the major contributor for plant growth in the following spring.

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Shen H, Cao J, Zhang W, Zeng X, Wang H. (2014). Winter Soil CO2 Flux from Different Mid-Latitude Sites from Middle Taihang Mountain in North China. PLoS ONE 9(3): e91589. doi: 10.1371/journal.pone.0091589.    


Winter soil respiration is a very important component of the annual soil carbon flux in some ecosystems. We hypothesized that, with all other factors being equal, shorter winter SR result in reduced contribution to annual soil C flux. In this study, the contribution of winter soil respiration to annual soil respiration was measured for three sites (grassland: dominated byArtemisia sacrorum, Bothriochloa ischaemum and Themeda japonica; shrubland: dominated byVitex negundo var. heterophylla; plantation: dominated by Populus tomatosa) in a mountainous area of north China. Diurnal and intra-annual soil CO2 flux patterns were consistent among different sites, with the maximum soil respiration rates at 12:00 or 14:00, and in July or August. The lowest respiration rates were seen in February. Mean soil respiration rates ranged from 0.26 to 0.45 µmol m−2 s−1 in the winter (December to February), and between 2.38 to 3.16 µmol m−2 s−1 during the growing season (May-September). The winter soil carbon flux was 24.6 to 42.8 g C m−2, which contributed 4.8 to 7.1% of the annual soil carbon flux. Based on exponential functions, soil temperature explained 73.8 to 91.8% of the within year variability in soil respiration rates. The Q10 values of SR against ST at 10 cm ranged from 3.60 to 4.90 among different sites. In addition, the equation between soil respiration and soil temperature for the growing season was used to calculate the “modeled” annual soil carbon flux based on the actual measured soil temperature. The “measured” annual value was significantly higher than the “modeled” annual value. Our results suggest that winter soil respiration plays a significant role in annual soil carbon balance, and should not be neglected when soil ecosystems are assessed as either sinks or sources of atmospheric CO2.

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ZongQiang, C., XiaoQing, L., Qi, F. ZongXI, C., HaiYang, X., YongHong, S., JianHua, S. (2013). Non-growing season soil CO2 efflux and its changes in an alpine meadow ecosystem of the Qilian Mountains, Northwest China. Journal of Arid Land, Vol. 5, Issue 4, pp. 488-499.


Most soil respiration measurements are conducted during the growing season. In tundra and boreal forest ecosystems, cumulative, non-growing season soil CO2 fluxes are reported to be a significant component of these systems’ annual carbon budgets. However, little information exists on soil CO2efflux during the non-growing season from alpine ecosystems. Therefore, comparing measurements of soil respiration taken annually versus during the growing season will improve the accuracy of estimating ecosystem carbon budgets, as well as predicting the response of soil CO2efflux to climate changes. In this study, we measured soilCO2 efflux and its spatial and temporal changes for different altitudes during the non-growing season in an alpine meadow located in the Qilian Mountains, Northwest China. Field experiments on the soil CO2 efflux of alpine meadow from the Qilian Mountains were conducted along an elevation gradient from October 2010 to April 2011. We measured the soil CO2 efflux, and analyzed the effects of soil water content and soil temperature on this measure. The results show that soil CO2 efflux gradually decreased along the elevation gradient during the non-growing season. The daily variation of soil CO2 efflux appeared as a single-peak curve. The soil CO2 efflux was low at night, with the lowest value occurring between 02:00–06:00. Then, values started to rise rapidly between 07:00–08:30, and then descend again between 16:00–18:30. The peak soil CO2 efflux appeared from 11:00 to 16:00. The soil CO2 efflux values gradually decreased from October to February of the next year and started to increase in March. Non-growing season Q10 (the multiplier to the respiration rate for a 10°C increase in temperature) was increased with raising altitude and average Q10 of the Qilian Mountains was generally higher than the average growing season Q10 of the Heihe River Basin. Seasonally, non-growing season soil CO2 efflux was relatively high in October and early spring and low in the winter. The soil CO2 efflux was positively correlated with soil temperature and soil water content. Our results indicate that in alpine ecosystems, soil CO2 efflux continues throughout the non-growing season, and soil respiration is an important component of annual soil CO2 efflux.

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Barry R. Taylor, H. Gerald Jones. (1990). Litter decomposition under snow cover in a balsam fir forest. Canadian Journal of Botany, 1990, 68(1): 112-120


In a subalpine balsam fir forest in Quebec, Canada, mass losses, respiration rates, and nitrogen and sulphur dynamics were measured on fir needles, birch leaves, lichens (mixed species), and small twigs decomposing under deep (> 1.5 m) winter snow for 6 months. Mass losses ranged from <6% (twigs) to 70% (lichens) and relative decomposition rates of needles and leaves were reversed from those expected at higher temperatures. Isolation of fir needles from direct contact with the snow did not affect decay rate, nor was decay accelerated by spring snowmelt. In siturespiration rates increased from about 1 mg CO2/(g∙day)) in February to 3–5 mg CO2/(g∙day)) in May, mostly because of rising temperatures. Summer respiration rates were much higher (> 6 mg CO2/(g∙day)). Nitrogen and suphur concentrations increased in all nonwoody litter over winter, but only birch leaves and some fir needles appeared to assimilate nutrients from the environment. Melting snow could easily have provided all of the nitrogen and sulphur taken up by decomposing litter. Decomposing lichens released 40 and 60%, respectively, of their initial nitrogen and sulphur contents. A literature review indicates mass losses from leaf litter decomposing under deep snow vary according to the proportion of labile material in the litter and usually constitute 40–60% of total first-year mass losses. Key words: decomposition, winter, balsam fir, snow.



S.K. Schmidt, D.A. Lipson. (2004). Microbial growth under the snow: Implications for nutrient and allelochemical availability in temperate soils. Plant and Soil, Vol. 259, Issue 1-2, pp. 1-7.


Recent work has shown that plant litter inputs fuel microbial growth in autumn and winter resulting in a large increase of microbial biomass under the snow pack in tundra soils. This winter-adapted microbial community can grow at low temperatures (−5 to 3 °C) and depletes the litter of easily degraded constituents, such as simple phenolic compounds, and immobilizes nitrogen. During snowmelt there is a die-off of this winter microbial community (due to starvation and intolerance to higher soil temperature) resulting in a release of nitrogen that can be utilized by plants and the summer microbial community. The summer microbial community can tolerate higher temperatures (5 to 20 °C) and utilizes mostly plant root exudates for growth. These yearly cycles of microbial growth dynamics have profound implications for both nutrient and alleochemical availability to plants. Firstly, these results show that release (from litter) and degradation of plant phenolic compounds (potential alleochemicals) occurs before plant growth commences in the spring. Secondly, nitrogen (N) immobilized by over-winter microbial growth is released back to the soil during and after snowmelt, thus becoming available to plants. Both of these results need to be incorporated in the design of experiments to explore plant-plant interactions. Many experiments in which chemicals (or fresh litter) are incorporated during plant growth do not reflect the fact that these two events are temporally uncoupled in many natural systems.

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Scientific Literature on Infection Sites on Plant Surfaces


Chitin Signaling in Plants: Insights into the Perception of Fungal Pathogens and Rhizobacterial Symbionts
Eckardt, N.A. (2008).The Plant Cell, Chitin Signaling in Plants: Insights into the Perception of Fungal Pathogens and Rhizobacterial Symbionts, American Society of Plant Biologists, Vol. 20: 241–243

In addition to the R gene–mediated pathways of plant resistance to specific pathogens, plants have the capacity to recognize a number of microbial surface-derived molecules, which elicit a general immune response in both host and nonhost plants. These are known as pathogen-associated or microbe-associated molecular patterns (PAMPs/MAMPs), so named because they are presumed to contain a structure or a pattern that is absent from eukaryotic host molecules and allows the host to recognize a microbial (and potentially pathogenic) invader. Many PAMPs that have been identified are essential for microbial metabolism or for penetration and invasion of a host cell and are therefore broadly conserved among diverse microbial pathogens (Parker, 2003). These include lipopolysaccharides of Gram-negative bacteria, peptidoglycans from Gram-positive bacteria, eubacterial flagellin, and glucans, chitins, and proteins derived from fungal cell walls (Nürnberger and Brunner, 2002).

Chitin is a polymer of N-acetyl-D-glucosamine that is a major component of fungal cell walls and has been recognized as a general elicitor of plant defense responses for many years (Boller, 1995). Fungal infection induces the expression of chitinases in plant cells, and these chitin-degrading enzymes accumulate at the site of invasion. In addition to the direct effect of limiting fungal invasion by degrading the fungal cell wall, the resulting chitin fragments (chitooligosaccharides) also appear to function as elicitors of numerous downstream defense response genes. Interestingly, Nod factors, which are produced by rhizobia (symbiotic N2-fixing bacteria) and are essential for the induction of the nodulation process in legumes, are chitin-related molecules (lipochitooligosaccacharides). The predicted Nod factor receptor proteins NFR1 and NFR5 in legumes are LysM domain–containing receptor-like kinases (LysM RLKs) (Limpens et al., 2003; Radutoiu et al., 2003). The LysM RLKs represent a relatively large plant-specific protein family present in nonlegumes and legumes (Zhang et al., 2007) and have been considered good candidates for playing a role in fungal chitin perception.

In this issue of The Plant Cell, Wan et al. (pages 471–481) show that LysM RLK1 is required for chitin signaling in Arabidopsis. The authors demonstrate that a mutation in RLK1 blocks the induction of chitooligosaccharide-responsive genes and leads to enhanced susceptibility of plants to fungal pathogens. These results are similar to those reported recently by Miya et al. (2007), who also showed that LysM RLK1 (called CERK1 by these authors) is essential for the chitin response in Arabidopsis. Both of these studies provide strong evidence that LysM RLK1 is involved in the perception of chitin and that it plays a role in resistance to fungal diseases. The work of Wan et al. also provides interesting insights into the evolution of Nod factor signaling, suggesting that some elements of Nod factor perception and signaling, which is specific to legumes, may be derived from the more general system of fungal chitin perception.

Arabidopsis encodes five LysM RLKs (RLK1-5) that are similar to the Nod factor receptor proteins NFR1 and NFR5 in legumes, and Wan et al. obtained homozygous T-DNA insertion mutants of all five of these genes to study their potential role in chitin perception and signaling. The authors treated all of these mutants with a purified chitooligosaccharide (chitooctaose) and monitored the expression of several genes previously shown to be induced by such treatment. The LysM RLK1 insertional mutant lacked any chitin induction of all tested genes, whereas the mutations in the other four RLK genes had no effect, suggesting a specific role for LysM RLK1 in chitin signaling. Whole-genome expression analysis using microarrays showed that of hundreds of genes regulated by chitooctaose (nearly 900 genes showing significant induction or repression in wild-type Arabidopsis), only a handful (33) were weakly induced or repressed in the LysM RLK1 mutant, demonstrating that the chitin-responsive pathway in this mutant was almost completely blocked. This shows that LysM RLK1 is critical for chitin perception and signal transduction.

Interestingly, Kaku et al. (2006) previously identified a LysM domain–containing receptor protein, called CEBiP, that is important for chitin perception in rice. However, CEBiP lacks an intracellular kinase domain, so it is unclear how it participates in signal transduction. The characterization of LysM RLK1 raises the possibility that CEBiP interacts, directly or indirectly, with LysM RLK1, although a homolog has not been identified in rice. Arabidopsis contains three CEBiP-like proteins, all of which similarly lack the kinase domain, so it will be of interest to determine if these proteins participate with LysM RLK1 in chitin perception and signaling.

Wan et al. next conducted experiments to determine if the LysM RLK1 mutant was affected in its response to fungal pathogens, as would be expected if the chitin-responsive pathway plays an important role in pathogen defense. Mutant plants were found to be more susceptible to the biotrophic powdery mildew fungal pathogen Erysiphe cichoracearum and to the necrotrophic fungus Alternaria brassicicola. The effect was moderate rather than severe, but no effect was observed in response to a Pseudomonas bacterial pathogen, suggesting that the RLK1-dependent pathway may be induced specifically by fungal invaders but that it is only one of several pathways involved in defense against these pathogens.

To investigate potential overlap of RLK1-dependent signaling with other defense-related signaling pathways, LysM RLK1 mutant and wild-type plants were treated with salicylic acid (SA), methyl jasmonic acid (MeJA), 1-aminocyclopropane-1-carboxylic acid (ACC), and the bacterial PAMP flagellin, and expression of known early-responsive genes to these treatments was monitored. Both the mutant and wild-type plants showed similar induction of PR-1 by SA, PDF1.2 by MeJA or ACC, and four selected early flagellin-responsive genes, suggesting that RLK1 operates independently of these other defense-related signaling pathways, at least in the early stages. However, microarray analysis suggested downstream convergence of signaling pathways induced by chitin and the bacterial PAMPs flagellin and EF-Tu, as the expression of a large number of genes (>400) was found to be upregulated by all three elicitors. In addition, exogenously applied chitooligosaccharides were found to enhance resistance of plants to subsequent challenge with both fungal and bacterial pathogens. These data support previous work suggesting that different PAMPs activate a common downstream pathway to induce pathogen resistance (e.g., Asai et al., 2002).

Since chitooligosaccharides also induce defense-related genes in legumes, the authors next investigated whether NFR1 and NRF5 in Lotus japonicus might be involved in general chitin signaling, in addition to their specialized roles in Nod factor signaling. Expression of selected chitooligosaccharide-responsive genes was similarly induced in response to chitooctaose treatment in L. japonicus wild-type and nfr1 and nfr5 mutant plants, showing that these LysM RLKs do not participate in general chitin signaling. The similarity between these LysM RLKs suggests that they are evolutionarily related, but the NFR proteins appear to have evolved a specific function in Nod factor perception and signaling, as previously suggested (Zhang et al., 2007).

Previous work has identified several Leu-rich repeat RLKs in Arabidopsis as receptors for important bacterial-derived PAMPs, including the flagellin receptor FLS2 (Gomez-Gomez and Boller, 2000) and more recently the bacterial elogation factor EF-Tu receptor EFR (Zipfel et al., 2006). Miya et al. (2007) and Wan et al. (2008) provide important new information on fungal-derived PAMPs with the identification of LysM RLK1 as a component of chitin perception and signaling. In addition, the work suggests a potential evolutionary link between the recognition of pathogenic microbes and symbiotic beneficial microbes. It will be of great interest to determine how the plant can distinguish between a benefical symbiont (rhizobia) and a detrimental pathogen (fungi) when the signals (lipo-chitin Nod factors and chitin elicitors) and initial perception mechanisms (LysM RLKs) are structurally very similar (see figure ). What are the downstream components that allow divergence of these pathways to direct the appropriate responses in each case? Further investigation into the functions of other members of the LysM RLK family may provide additional clues as to how plants distinguish between beneficial versus pathogenic microbes.


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