Evaluating the survival and environmental fate of the biocontrol agent Trichoderma atroviride SC1 in vineyards in northern Italy

Aims:  To study the survival in the soil and the dispersion in the environment of Trichoderma atroviride SC1 after soil applications in a vineyard.
Methods and Results:  Trichoderma atroviride SC1 was introduced into soil in two consecutive years. The levels of T. atroviride populations at different spatial and temporal points following inoculation were assessed by counting the colony-forming units and by a specific quantitative real-time PCR. A high concentration of T. atroviride SC1 was still observed at the 18th week after inoculation. The vertical migration of the fungus to a soil depth of 0·4 m was already noticeable during the first week after inoculation. The fungus spread up to 4 m (horizontally) from the point of inoculation and its concentration decreased with the increasing distance (horizontal and vertical). It was able to colonize the rhizosphere and was also found on grapevine leaves. One year after soil inoculation, T. atroviride SC1 could still be recovered in the treated areas.
Conclusions:  Trichoderma atroviride SC1 survived and dispersed becoming an integrant part of the local microbial community under the tested conditions.
Significance and Impact of the Study:  The persistence and rapid spread of T. atroviride SC1 represent good qualities for its future use as biocontrol agent against soilborne pathogens.     

Real-time PCR for detection and quantification of the biocontrol agent Trichoderma atroviride strain SC1 in soil

Trichoderma (Hypocreales, Ascomycota) is a widespread genus in nature and several Trichoderma species are used in industrial processes and as biocontrol agents against crop diseases. It is very important that the persistence and spread of microorganisms released on purpose into the environment are accurately monitored. Real-time PCR methods for genus/species/strain identification of microorganisms are currently being developed to overcome the difficulties of classical microbiological and enzymatic methods for monitoring these populations. The aim of the present study was to develop and validate a specific real-time PCR-based method for detecting Trichoderma atroviride SC1 in soil. We developed a primer and TaqMan probe set constructed on base mutations in an endochitinase gene. This tool is highly specific for the detection and quantification of the SC1 strain. The limits of detection and quantification calculated from the relative standard deviation were 6000 and 20,000 haploid genome copies per gram of soil. Together with the low throughput time associated with this procedure, which allows the evaluation of many soil samples within a short time period, these results suggest that this method could be successfully used to trace the fate of T. atroviride SC1 applied as an open-field biocontrol agent.     

Field calibration of soil-core microcosms: Ecosystem structural and functional comparisons

Microcosms containing intact soil-cores are a potential biotechnology risk assessment tool for assessing the ecological effects of genetically engineered microorganisms before they are released to the field; however, microcosms must first be calibrated to ensure that they adequately simulate key field parameters. Soil-core microcosms were compared with the field in terms of ecological response to the introduction of a large inoculum of a rifampicin-resistant rhizobacterium,Pseudomonas sp. RC1. RC1 was inoculated into intact soil-core microcosms incubated in the laboratory at ambient temperature (22°C) and in a growth chamber with temperature fluctuations that mimicked a verage field values, as well as into field lysimeters and plots. The effect of the introduced bacterium on ecosystem structure, including wheat rhizoplane populations of total and fluorescent pseudomonads, total heterotrophic bacteria, and the diversity of total heterotrophic bacteria, was determined. Fluorescent pseudomonads were present on the rhizoplane in significantly lower numbers in soil inoculated with RC1, in both microcosms and the field. Conditions for microbial growth appeared to be most favorable in the growth chamber microcosm, as evidenced by higher populations of heterotrophs and a greater species diversity on the rhizoplane at the three-leaf stage of wheat growth. Ecosystem functional parameters, as determined by soil dehydrogenase activity, plant biomass production, and¹⁵N-fertilizer uptake by wheat, were different in the four systems. The stimulation of soil dehydrogenase activity by the addition of alfalfa was greater in the microcosms than in the field. In general, growth chamber microcosms, which simulated average field temperatures, were better predictors of field behavior than microcosms incubated continuously at 22°C.     

Validation of Microcosms for Examining the Survival of Pseudomonas aureofaciens (lacZY) in Soil

Evaluating the safety and efficacy of a recombinant bacterium prior to its release into the terrestrial environment requires that risk assessment data be collected in the laboratory. Much of this information is obtained with the use of microcosms. The design of the microcosm significantly affects the ability of the recombinant microorganism to survive in soil and, thus, complicates the risk assessment process. To standardize microcosms for future use, we evaluated the survival of Pseudomonas aureofaciens 3732 RN-L11 (lacZY Rif(supr) Nal(supr)) in intact soil cores (5.0 by 15 cm; polyvinyl chloride core) and disturbed soil microcosms (50 g of fresh, sieved soil). Survival data were compared with those obtained during a field release. The intact soil core microcosm was shown to closely simulate results obtained in the field. The intact soil core microcosm closely predicts survival in bulk soil and in the rhizosphere of wheat. Data obtained with the microcosm were also similar when evaluated in separate studies in two different years. In 1993, P. aureofaciens survived for approximately 63 days in bulk soil and 96 days in the rhizosphere. The disturbed soil microcosm exhibited a much more rapid decline in population size (34 days to zero) than the intact core microcosm. We speculate that drying and sieving of soil for the disturbed soil microcosm affected the ability of the soil to support the survival of P. aureofaciens. These results demonstrate that a small, inexpensive, and simple intact soil core microcosm may be appropriate for risk assessment.     

Determining the environmental fate of a filamentous fungus, Trichoderma reesei, in laboratory-contained intact soil-core microcosms using competitive PCR and viability plating

Trichoderma spp. are used extensively in industry and are routinely disposed of in landfill sites as spent biomass from fermentation plants. However, little is known regarding the environmental fate of this biomass. We tracked the survival of T. reesei strain QM6A#4 (a derivative of strain QM6A marked with a recombinant construct) over a 6-month period in laboratory-contained, intact soil-core microcosms incubated in a growth chamber. Survival was tested in 3 different soils and the effect of a plant rhizosphere (bush lima beans, Phaseolus limensis) was investigated. Levels and viability of the fungus were determined, respectively, by quantitative competitive polymerase chain reaction analysis of total soil DNA extracts and dilution-plating of soil on a semiselective growth medium. Whereas chemically killed QM6A#4 became undetectable within 3 d, QM6A#4 added as a live inoculum decreased approximately 4- to approximately 160-fold over the first 1-3 months and then reached a steady state. After 4 months, soil cores were subjected to a 1.5-month simulated winter period, which did not significantly affect QM6A#4 levels. Throughout the experiment, QM6A#4 remained viable. These results indicate that, following release into the environment, live T. reesei will persist in soil for at least 2 seasons.     

Intact soil-core microcosms compared with multi-site field releases for pre-release testing of microbes in diverse soils and climates

Intact soil-core microcosms were used to compare persistence of Pseudomonas chlororaphis 3732RN-L11 in fallow soil and on wheat roots with field releases at diverse sites. Parallel field and microcosm releases at four sites in 1996 were repeated with addition of one site in 1997. Microcosms were obtained fresh and maintained at 60% soil water holding capacity in a growth chamber at 70% relative humidity, a 12-hour photoperiod, and constant temperature. Persistence of 3732RN-L11 was measured at each site in field plots and microcosms at 7-21 day intervals, and in duplicate microcosms sampled at an independent laboratory. Linear regression slopes of field plot and microcosm persistence were compared for each site, and between identical microcosms sampled at different sites, using log10 transformed plate counts. Microcosm persistence closely matched field plots for wheat roots, but persistence in fallow soil differed significantly in several instances where persistence in field plots was lower than in microcosms. Analysis of weather variations at each site indicated that rainfall events of 30-40 mm caused decreased persistence in fallow soil. Cooler temperatures enhanced persistence in field plots at later time points. Inter-laboratory comparison of regression slopes showed good agreement for data generated at different sites, though in two instances, longer sampling periods at one site caused significant differences between the sites. Soil characteristics were compared and it was found that fertility, namely the carbon to nitrogen ratio, and the presence of expanding clays, were related to persistence. These microcosm protocols produced reliable data at low cost, and were useable for pre-release risk analyses for microorganisms.     

Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater

Aims:  To investigate the factors affecting benzene biodegradation and microbial community composition in a contaminated aquifer.
Methods and Results:  We identified the microbial community in groundwater samples from a benzene-contaminated aquifer situated below a petrochemical plant. Eleven out of twelve groundwater samples with in situ dissolved oxygen concentrations between 0 and 2·57 mg l⁻¹ showed benzene degradation in aerobic microcosm experiments, whereas no degradation in anaerobic microcosms was observed. The lack of aerobic degradation in the remaining microcosm could be attributed to a pH of 12·1. Three groundwaters, examined by 16S rRNA gene clone libraries, with low in situ oxygen concentrations and high benzene levels, each had a different dominant aerobic (or denitrifying) population, either Pseudomonas , Polaromonas or Acidovorax species. These groundwaters also had syntrophic organisms, and aceticlastic methanogens were detected in two samples. The alkaline groundwater was dominated by organisms closely related to Hydrogenophaga .
Conclusions:  Results show that pH 12·1 is inimical to benzene biodegradation, and that oxygen concentrations below 0·03 mg l⁻¹ can support aerobic benzene-degrading communities.
Significance and Impact of the Study:  These findings will help to guide the treatment of contaminated groundwaters, and raise questions about the extent to which aerobes and anaerobes may interact to effect benzene degradation.     

Does Tetranychus urticae (Acari: Tetranychidae) use flying insects as vectors for phoretic dispersal?

Whether the spider mite Tetranychus urticae uses flying insects as vectors for phoretic dispersal was experimentally tested. Two bean plants were placed in a microcosm, and a mite population was introduced onto one of the plants. Either Phaenicia cuprina Wiedemann (Diptera: Calliphoridae) or Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) was then introduced into the microcosms as a hypothetical vector insect. T. urticae populations on the second bean plant were monitored to detect any evidence of phoretic dispersal. Instances of dispersal were detected at extremely low frequency, suggesting that phoretic dispersal of T. urticae mediated by winged insects is probably rare in the wild.     

SCAR-based real time PCR to identify a biocontrol strain (T1) of Trichoderma atroviride and study its population dynamics in soils

Strains of Trichoderma spp. are known for their antagonistic properties against plant pathogens, some are already on the market, others are under development. In order to launch a strain on the market its perfect identification at the species and strain levels is needed. The aim of this study is to (i) design a SCAR marker for specific identification of strain T1 of Trichoderma atroviride and (ii) monitor population dynamics of this strain in soil by real time PCR. A primer pair targeting a 141-bp fragment enabled specific detection of this strain without cross detection of autochthonous populations of Trichoderma in several field soils. In two soils, population dynamics assessed by real time PCR and the soil plate technique gave similar results. The molecular tools developed in this study satisfy the requirement for specific identification of the biocontrol strain and for detection and quantification of T. atroviride T1 population in complex environments.     

Hypocrea atroviridis sp. nov., the teleomorph of Trichoderma atroviride

A new species, Hypocrea atroviridis, is described for the teleomorph of Trichoderma atroviride. Based on sequences of ITS-1, 5.8S, and ITS-2 regions of the rDNA complex and translation-elongation factor (EF-1α), T. atroviride and H. atroviridis form a well-supported clade within Trichoderma sect. Trichoderma. The conserved anamorphic phenotype of T. atroviride, observed for both conidial and ascospore derived cultures, was only found within that clade. In contrast, the teleomorph phenotype of H. atroviridis was morphologically indistinguishable from H. rufa, the teleomorph of T. viride. This Hypocrea phenotype may, therefore, be considered to be plesiomorphic within Trichoderma sect. Trichoderma, suggesting that genes controlling the expression of the teleomorph and anamorph evolve at different rates and that the genes controlling expression of the teleomorph are more conserved than are those controlling the expression of the anamorph.     

In vivo study of trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems

Plant tissue colonization by Trichoderma atroviride plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in situ interactions between gfp-tagged biocontrol strains of T. atroviride and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of T. atroviride adhered to Pythium ultimum mycelia in coculture experiments. In mycoparasitic interactions of T. atroviride with P. ultimum or Rhizoctonia solani, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of T. atroviride mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of P. ultimum by T. atroviride occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific Trichoderma genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or Rhizoctonia by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.     

Histopathological studies of sclerotia of Rhizoctonia solani parasitized by the EGFP transformant of Trichoderma virens

Aims:  The aim of the study was to investigate the antagonistic interactions of Trichoderma species against Rhizoctonia solani sclerotia by enhanced green fluorescence protein (EGFP)-tagged transformant of Trichoderma virens TY009.
Methods and Results:  An EGFP was used as a report gene for transforming T. virens strain, and a stable EGFP transformant GF5 was obtained with the mycoparasitic activity against sclerotia of R. solani . Observation of parasitized sclerotia by fluorescence microscopy showed hyphae of transformant GF5 was able to invade into sclerotia and its colonization was mainly intercellar with uniformly distributed mycelium in sclerotia. The host cells were colonized, penetrated, and then the whole cells were replaced by transformant GF5 hyphae. Chlamydospores were seen after 10 days but mature ones after 20 days. Sclerotia became soft and decayed after 40 days but a few cells seemed not to be colonized completely.
Conclusions:  Trichoderma virens was able to parasitize sclerotia to make sclerotia soft and decayed, and its colonization was mainly intercellar in sclerotial tissues.
Significance and Impact of the Study:  This is first report of parasitism of sclerotia of R. solani by EGFP-tagged transformant, providing useful information for using T. virens as effective biocontrol agent.     

A unique laboratory method for evaluating agro-ecosystem effects of an industrial waste product

Summary This paper describes the design, extraction, and maintenance of intact soil-core microcosms which accurately predicted biomass reduction, nutrient loss and trace element enrichment in field-grown crops amended with acidic precipitator fly ash. These agricultural microcosms sustain ecosystem-level interactions while offering a cost-effective, manageable, experimental unit which can be subjected to laboratory controls.     

中国西南地区木霉属分类研究

从西南四省区(云、贵、川、藏)的土壤和其它样品中分离木霉301株,鉴定出9个木霉集合种(species aggregates) :哈茨木霉(Trichoderma harzianum Rifai),拟康氏木霉(T.pseudokoningii Rifai),长枝木霉(T.longibrachiatum Rifai),深绿木霉(T.atrovirideBissett),桔绿木霉(T.citrinoviride Bissett),绿色木霉(T.viride Pers.ex S.F.Gray),钩状木霉(T.hamatum(Bon)Bain),康氏木霉(T.koningii Oud.)以及黄绿木霉(T.aureoviride Rifai)。从各个样点收集的42种不同作物和其它植被土样中都分离到木霉;土样pH值为4—8.5,海拔300—5400m。以哈茨木霉和拟康氏木霉出现频率最高,分别为28.5%和21.1%,似为西南地区木霉优势种群,而绿色木霉、钩状木霉和深绿木霉很少分离到。这样的种群结构可能与西南地区气候和采样季节有关。     

Effects of artificial ultraviolet-B radiation on experimental aquatic microcosms

1. The effects of prolonged ultraviolet-B (UVB) radiation on freshwater communities were studied in indoor microcosms (600 L) with artificial light sources, simulating a clear, shallow, mesotrophic aquatic ecosystem. A range of six intensities (in duplicate) of UVB radiation, ranging from 0 (control) to 9.56 kJ m⁻² day⁻¹ at the water surface, was applied for 8 weeks. The UVB radiation levels, attenuation, shading and scattering were comparable to those in Dutch shallow freshwater systems. Physical, chemical and biological variables were monitored weekly.
2. The UVB treatment did not affect the abundance, species composition or biovolume of the phytoplankton or zooplankton communities, nor did it affect the periphyton or the macroinvertebrate community. A few species showed a significant response on some of the sampling dates, but there was no negative UVB effect at the community level. Overall, the ecosystems in the microcosms were not affected by the UVB treatment.
3. In a bio-assay, a laboratory clone of Daphnia pulex , not subjected to UVB radiation, was fed with seston from the microcosms. Daphnia pulex feeding on seston from the control microcosms grew faster, had better survival and better reproduction than D. pulex feeding on seston from the UVB treated microcosms. The phytoplankton–zooplankton interaction may have been influenced by the UVB treatment.
4. The dissolved oxygen content (DOC) concentrations in the microcosms were around 5 mg L^−1. The DOC levels in Dutch systems rarely fall below 10 mg L^−1. This might provide sufficient protection against the detrimental effects of increased UVB radiation.     

Field calibration of soil-core microcosms: Fate of a genetically altered rhizobacterium

Microcosms containing intact soil-cores are a potential tool for assessing the risks of the release of genetically engineered microorganisms (GEMs) to the environment. Before microcosms become a standard assessment tool, however, they must first be calibrated to ensure that they adequately simulate key parameters in the field. Four systems were compared: intact soil-core microcosms located in the laboratory at ambient temperature and in a growth chamber with temperature fluctuations that simulated average conditions in the field, field lysimeters, and field plots. These four systems were inoculated with rifampicin-resistantPseudomonas sp. and planted to winter wheat. Populations of thePseudomonas sp. in soil decreased more rapidly at ambient temperature, but population size at the three-leaf stage of wheat growth was the same in all four systems. Populations of thePseudomonas sp. on the rhizoplane of wheat were the same at the three-leaf stage in all four systems, and colonization with depth at the final boot stage-sampling was also similar. In general, microcosms incubated at ambient temperature in the laboratory or in the growth chamber were similar to those in the field with respect to survival of and colonization of the rhizoplane by the introducedPseudomonas sp.     

Intact Soil-Core Microcosms for Evaluating the Fate and Ecological Impact of the Release of Genetically Engineered Microorganisms

Intact soil-core microcosms were studied to determine their applicability for evaluating the transport, survival, and potential ecosystem effects of genetically engineered microorganisms before they are released into the environment. Soil-core microcosms were planted with wheat and maize seeds and inoculated with Azospirillum lipoferum SpBr17 and SpRG20a Tn5 mutants, respectively. Microcosm leachate, rhizosphere soil, plant endorhizosphere, insects, and xylem exudate were sampled for A. lipoferum Tn5 mutant populations. A. lipoferum Tn5 populations, determined by most-probable-number technique-DNA hybridization, varied from below detection to 10⁶ g of dry root⁻¹ in the rhizosphere, with smaller populations detected in the endorhizosphere. Intact soil-core microcosms were found to maintain some of the complexities of the natural ecosystem and should be particularly useful for initial evaluations of the fate of plant-associated genetically engineered bacteria.     

Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates

We have used isolates of Trichoderma spp. collected in South-East Asia, including Taiwan and Western Indonesia, to assess the genetic and metabolic diversity of endemic species of Trichoderma. Ninety-six strains were isolated in total, and identified at the species level by analysis of morphological and biochemical characters (Biolog system), and by sequence analysis of their internal transcribed spacer regions 1 and 2 (ITS1 and 2) of the rDNA cluster, using ex-type strains and taxonomically established isolates of Trichoderma as reference. Seventy-eight isolates were positively identified as Trichoderma harzianum/Trichoderma inhamatum (37 strains) Trichoderma virens (16 strains), Trichoderma spirale (8 strains), Trichoderma koningii (3 strains), Trichoderma atroviride (3 strains), Trichoderma asperellum (4 strains), Hypocrea jecorina (anamorph: Trichoderma reesei; 2 strains), Trichoderma viride (2 strains), Trichoderma hamatum (1 strain), and Trichoderma ghanense (1 strain). Analysis of biochemical characters revealed that T. virens, T. spirale, T. asperellum, T. koningii, H. jecorina, and T. ghanense formed clearly defined clusters, thus exhibiting species-specific metabolic properties. In biochemical character analysis T. atroviride and T. viride formed partially overlapping clusters, indicating that these two species may share overlapping metabolic characteristics. This behavior was even more striking with T. harzianum/T. inhamatum where genotypes defined on the basis of ITS1 and 2 sequences overlapped significantly with adjacent genotypes in the biochemical character analysis, and four strains from the same location (Bali, Indonesia) even clustered with species from section Longibrachiatum. The data indicate that the T. harzianum/T. inhamatum group represents species with high metabolic diversity and partially unique metabolic characteristics. Nineteen strains yielded three different ITS1/2 sequence types which were not alignable with any known species. They were also uniquely characterized by morphological and biochemical characters and therefore represent three new taxa of Trichoderma.     

Acorn removal and dispersal by the dung beetle Thorectes lusitanicus: ecological implications

Abstract.  1. Plant–animal interactions, and in particular the processes of seed predation and dispersal, are crucial for tree regeneration and forest dynamics. A novel and striking case of interaction between a dung beetle ( Thorectes lusitanicus ) and two Quercus species ( Q. suber and Q. canariensis ) in forests of southern Spain is presented here.
2. During the autumn, T. lusitanicus beetles (endemic to the southern Iberian Peninsula) bury and feed on single-seeded fruits (acorns) of Quercus , with important ecological implications.
3. Field experiments found differences in the removal rate of acorns by T. lusitanicus , depending on the type of microsite within the forest, the species of oak, the exclosure of large herbivores, and the forest site.
4. Acorn consumption by T. lusitanicus was studied under laboratory conditions, confirming for the first time that this dung beetle is a legitimate seed predator.
5. In addition, some buried acorns can be abandoned partially predated or even intact, and emerge as seedlings; thus, T. lusitanicus also has a potential role as secondary seed disperser.     

木霉属Trichoderma组和Pachybasium组的分子系统学研究

对来源不同的木霉及其有性型Longibrachiatum组、Trichoderma 组和Pachybasium组的81个菌株进行了ITS序列测定,并对ITS1序列用PHYLIP程序包中的DNAPARS程序进行系统发育分析。结果表明Trichoderma 组和Pachybasium组的所有菌株可分成两个群(A,B),B群进一步分为4个分支(B1,B2,B3,B4);A群由Trichoderma 组的H. aureoviridis和未鉴定到种的3个Hypocrea菌株构成;B1,B2,B4群均由Pachybasium组菌株构成;B3群由Pachybasium组的T. hamatum、T. strigosum和Trichoderma 组的T. asperellum、T. atroviride、T. koningii、T. viride和Hypocrea菌株T261构成。2个组相互交叉,组间没有明确的区分,进一步证明Pachybasium组是多系的。建议将Trichoderma 组中的T. viride aggr.、T. atroviride、T. koningii归并入Pachybasium组,对Trichoderma 组重新定义。