Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings

Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.

Induction of Soil Suppressiveness Against Rhizoctonia solani by Incorporation of Dried Plant Residues into Soil

ABSTRACT Suppressive effects of soil amendment with residues of 12 cultivars of Brassica rapa on damping-off of sugar beet were evaluated in soils infested with Rhizoctonia solani. Residues of clover and peanut were tested as noncruciferous controls. The incidence of damping-off was significantly and consistently suppressed in the soils amended with residues of clover, peanut, and B. rapa subsp. rapifera 'Saori', but only the volatile substance produced from water-imbibed residue of cv. Saori exhibited a distinct inhibitory effect on mycelial growth of R. solani. Nonetheless, disease suppression in such residue-amended soils was diminished or nullified when antibacterial antibiotics were applied to the soils, suggesting that proliferation of antagonistic bacteria resident to the soils were responsible for disease suppression. When the seed (pericarps) colonized by R. solani in the infested soil without residues were replanted into the soils amended with such residues, damping-off was suppressed in all cases. In contrast, when seed that had been colonized by microorganisms in the soils containing the residues were replanted into the infested soil, damping-off was not suppressed. The evidence indicates that the laimosphere, but not the spermosphere, is the site for the antagonistic microbial interaction, which is the chief principle of soil suppressiveness against Rhizoctonia damping-off.

Survival and Inoculum Production of Gibberella zeae in Wheat Residue

Survival and inoculum production of Gibberella zeae (Schwein.) Petch (anamorph Fusarium graminearum (Schwabe)), the causal agent of Fusarium head blight of wheat and barley, was related to the rate of wheat (Triticum aestivum L.) residue decomposition. Infested wheat residue, comprising intact nodes, internodes, and leaf sheaths, was placed in fiberglass mesh bags on the soil surface and at 7.5- to 10-cm and 15- to 20-cm depths in chisel-plowed plots and 15 to 20 cm deep in moldboard-plowed plots in October 1997. Residue was sampled monthly from April through November during 1998 and every 2 months through April to October 1999. Buried residue decomposed faster than residue placed on the soil surface. Less than 2% of the dry-matter residue remained in buried treatments after 24 months in the field, while 25% of the residue remained in the soil-surface treatment. Survival of G. zeae on node tissues was inversely related to the residue decomposition rate. Surface residue provided a substrate for G. zeae for a longer period of time than buried residue. Twenty-four months after the initiation of the trial, the level of colonization of nodes in buried residue was half the level of colonization of residue on the soil surface. Colonization of node tissues by G. zeae decreased over time, but increased for other Fusarium spp. Ascospores of G. zeae were still produced on residue pieces after 23 months, and these spores were capable of inducing disease. Data from this research may assist in developing effective management strategies for residues infested with G. zeae.

Diversity and Longevity of the Soybean Debris Mycobiota in a No-Tillage System

The survival of the mycobiota on pod and stem debris of soybean produced in a no-tillage system with cover crops of alfalfa, canola, rye, or wheat or with no cover was studied during 1994 and 1995. Fiberglass mesh bags containing pods and stems were assayed every 28 to 31 days to determine the isolation frequency of fungi. Over 90% of the 11,906 isolates obtained were members of the Deuteromycotina. The most common genera isolated were Alternaria, Cercos-pora, Colletotrichum, Epicoccum, Fusarium, and Phoma. Alternaria spp. had the greatest isolation frequencies and constituted 40% of the total cultures. Numbers of total fungi (all fungi isolated) on sampling dates in 1994 were similar to the totals in 1995. In May 1994, the mean isolation rates for many of the fungal species were significantly lower (P = 0.05) in several of the cover crops, but no consistent pattern could be determined. Common soybean pathogens isolated included Colletotrichum spp., Diaporthe spp., and Cercospora kikuchii. Fusarium graminearum, which is responsible for several diseases of maize and wheat, was commonly isolated during this study. Of the Diaporthe spp. (anamorph Phomopsis spp.), 87% were identified as D. phaseolorum var. sojae. Colletotrichum spp. were identified as C. truncatum in 85% of the isolates, C. destructivum (teleomorph Glomerella glycines) in 12%, and both species in 3%. Cercospora kikuchii was more commonly isolated from pods than from stem tissue, and Colletotrichum spp. occurred more frequently on stems. Isolation frequencies of Diaporthe spp. were greater in May of both years than in the preceding months. These results show that no-tillage soybean debris harbors numerous fungi pathogenic to soybean, and producers who grow soybeans continuously may find more disease in this crop and lower yields. Fungi that attack crops such as maize and wheat were commonly isolated from soybean debris in both years, and a no-tillage rotation which includes maize or wheat could result in increased disease in these crops. Isolation frequencies of the fungi from cover crops varied with the sampling date, but no consistent patterns could be determined for a particular cover crop or fungal species. This is the first detailed study of survival rates of soybean, maize, and wheat pathogens that overwinter on soybean debris in a no-tillage system.

Population Dynamics of Phialophora gregata in Soybean Residue

Brown stem rot frequently is more severe in no-till cropping systems. Population density of Phialophora gregata was monitored in soybean residue positioned below and on the soil surface. Current season residue was confined in nylon mesh bags that were placed in the field in the fall. Population density of the pathogen was measured monthly through the winter, or seasonally for 30 months, and expressed as CFU per gram of soybean residue. Population dynamics of P. gregata differed in surface residue, compared with buried residue. Population density of P. gregata was not significantly different in buried and surface residue from November/December to April. Beginning in late April or May, population density of P. gregata was significantly greater in surface residue than in buried residue. The population density of P. gregata in surface residue remained above 10⁵ CFU per gram of residue after 30 months in the field. In contrast, the fungus was not detected in buried residue after 11 to 17 months. From November to May, the population destiny of P. gregata in surface residue increased more than 14 times the initial density. In contrast, the density of P. gregata in buried residue increased sixfold by April, then decreased to densities not significantly different from the initial population by May and June. Mass of buried residue decreased more rapidly than that of surface residue during April, May, and June. There was a positive correlation between residue weight and the population density of P. gregata in residue. P. gregata survived longer and at higher population densities in residue positioned on the soil surface (simulated no-till) than in buried residue (simulated conventional tillage). Although inoculum density of P. gregata remained high in surface residue, total inoculum declined because of loss of residue biomass.