scholarly journals Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation

2019 ◽  
Vol 80 (1) ◽  
pp. 191-201 ◽  
Author(s):  
Amisha T. Poret-Peterson ◽  
Nada Sayed ◽  
Nathaniel Glyzewski ◽  
Holly Forbes ◽  
Enid T. González-Orta ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Rice Bran ◽  
Grape Pomace ◽  
Soil Microbiome ◽  
Tomato Pomace ◽  
Soil Redox ◽  
Soil Disinfestation ◽  
Anaerobic Soil Disinfestation ◽  
Red Grape ◽  
Over Time

AbstractAnaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.

scholarly journals Plant-Derived Carbon Sources for Anaerobic Soil Disinfestation in Southern California

2021 ◽  
Vol 8 ◽  
pp. 169-175
Author(s):  
Oleg Daugovish ◽  
Joji Muramoto ◽  
Carol Shennan ◽  
Margherita Zavatta
Keyword(s):  
Rice Bran ◽  
Carbon Sources ◽  
Cost Effective ◽  
Fruit Production ◽  
Grape Pomace ◽  
Management Tools ◽  
Soil Disinfestation ◽  
Anaerobic Soil Disinfestation ◽  
Coffee Grounds ◽  
Spent Grain

Anaerobic soil disinfestation (ASD) has been optimized and adopted as an organic alternative to chemical fumigation by strawberry growers in California. The ASD process relies on mixing labile carbon sources into the soil to generate chemical, physical, and microbiological changes aiding suppression of the soil-borne pathogens and enhancing fruit production. Continued ASD adoption is hindered by the increasing cost of rice bran, currently the most widely used carbon source. To address this need and to find suitable and economical alternative carbon sources, we conducted field evaluations of locally produced or sourced plant-based products. ASD with incorporated grass-sod clippings spent grain and coffee grounds from one supplier provided a 47% to 83% increase in fruit yields compared to untreated soil, but coffee grounds from a different supplier decreased strawberry yields. Carbon, nitrogen, and their ratios had important impacts on the efficacy of ASD with coffee grounds and grape pomace. ASD with wheat midds at 20 t/ha provided strawberry yields similar to chloropicrin-fumigated soil while substituting 30% of rice bran carbon rate with on-site grown cereal cover crop biomass resulted in yields similar to the full rate of rice bran but at a reduced cost. As we continue exploring cost-effective methods of soil disinfestation, we utilize ASD integrated with other pest management tools, such as the use of resistant cultivars and crop rotation for sustainable production.

scholarly journals Analysis of Environmental Variables and Carbon Input on Soil Microbiome, Metabolome and Disease Control Efficacy in Strawberry Attributable to Anaerobic Soil Disinfestation

2021 ◽  
Vol 9 (8) ◽  
pp. 1638
Author(s):  
Shashika S. Hewavitharana ◽  
Emmi Klarer ◽  
Joji Muramoto ◽  
Carol Shennan ◽  
Mark Mazzola
Keyword(s):  
Disease Control ◽  
Fusarium Wilt ◽  
Environmental Variables ◽  
Incubation Temperature ◽  
Soil Microbiome ◽  
Charcoal Rot ◽  
Soil Disinfestation ◽  
Anaerobic Soil Disinfestation ◽  
Input Type ◽  
Incubation Duration

Charcoal rot and Fusarium wilt, caused by Macrophomina phaseolina and Fusarium oxysporum f. sp. fragariae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation has been studied as an industry-level option to replace soil fumigants to manage these serious diseases. Studies were conducted to discern whether Gramineae carbon input type, incubation temperature, or incubation duration influences the efficacy of this disease control tactic. In experiments conducted using ‘low rate’ amendment applications at moderate day/night temperatures (24/18 °C), and carbon inputs (orchard grass, wheat, and rice bran) induced an initial proliferation and subsequent decline in soil density of the Fusarium wilt pathogen. This trend coincided with the onset of anaerobic conditions and a corresponding generation of various anti-fungal compounds, including volatile organic acids, hydrocarbons, and sulfur compounds. Generation of these metabolites was associated with increases in populations of Clostridium spp. Overall, carbon input and incubation temperature, but not incubation duration, significantly influenced disease suppression. All Gramineae carbon inputs altered the soil microbiome and metabolome in a similar fashion, though the timing and maximum yield of specific metabolites varied with input type. Fusarium wilt and charcoal rot suppression were superior when anaerobic soil disinfestation was conducted using standard amendment rates of 20 t ha−1 at elevated temperatures combined with a 3-week incubation period. Findings indicate that anaerobic soil disinfestation can be further optimized by modulating carbon source and incubation temperature, allowing the maximum generation of antifungal toxic volatile compounds. Outcomes also indicate that carbon input and environmental variables may influence treatment efficacy in a target pathogen-dependent manner which will require pathogen-specific optimization of treatment protocols.

scholarly journals Efficacy of Anaerobic Soil Disinfestation for Control of Prunus Replant Disease

Plant Disease ◽  
2018 ◽  
Vol 102 (1) ◽  
pp. 209-219 ◽  
Author(s):  
G. Browne ◽  
N. Ott ◽  
A. Poret-Peterson ◽  
H. Gouran ◽  
B. Lampinen
Keyword(s):  
Rice Bran ◽  
Sandy Loam ◽  
Field Capacity ◽  
Pythium Ultimum ◽  
Effective Control ◽  
Cross Sectional ◽  
Soil Disinfestation ◽  
Soilborne Disease ◽  
Anaerobic Soil Disinfestation ◽  
Replant Disease

Prunus replant disease (PRD) is an important soilborne complex that suppresses growth and productivity of replanted stone fruit and nut orchards. It is effectively managed with preplant soil fumigation but, due to regulatory challenges, nonfumigant-based control strategies for PRD and other soilborne disease problems may become increasingly important, especially in California. We examined the potential of preplant anaerobic soil disinfestation (ASD) for control of PRD in four repeated orchard replant trials on sandy loam soil near Parlier, CA. After removal of the old orchard trees, alternative ASD treatments, all using rice bran as the main carbon source, were implemented, starting in late September. The alternative treatments incorporated rice bran at (i) 20 t ha−1, alone, in 3.0-m-wide row strips; (ii) 20 t ha−1, preceded by incorporation of a sudangrass cover crop and followed by drip application of molasses (10 t ha−1), in 3.0-m-wide row strips; (iii) 20 t ha−1, alone, in 1.8-m-wide strips; or (iv) 12 t ha−1, alone, in 1.8-m-wide strips. All ASD-treated areas were covered with clear tarp and drip irrigated with 25 cm of water. Tarps remained for 6 weeks, during which the soil moisture level was kept at or above field capacity by drip irrigation. All trials included nontreated control and fumigated standard treatments. ASD raised temperature and reduced redox potential in soil at 15- and 46-cm depths for 6 weeks. Fumigation and ASD treatments both nearly eradicated bioassay inoculum of Pythium ultimum in the soil before almond trees were replanted and significantly affected almond tree root communities of fungi and oomycetes after planting. Fumigation treatments and ASD treatments with rice bran at 20 t ha−1 in 3.0-m strips increased tree growth significantly and by similar magnitudes. Among repeated experiments, mean increases in trunk cross-sectional area growth due to fumigation ranged from 137 to 264%, while the increases due to ASD at 20 t ha−1 in 3.0-m strips ranged from 148 to 214%, compared with controls. ASD offers effective control of PRD and is worthy of further optimization and testing for management of PRD and additional orchard replant problems.

scholarly journals Carbon Source-Dependent Effects of Anaerobic Soil Disinfestation on Soil Microbiome and Suppression of Rhizoctonia solani AG-5 and Pratylenchus penetrans

2016 ◽  
Vol 106 (9) ◽  
pp. 1015-1028 ◽  
Author(s):  
Shashika S. Hewavitharana ◽  
Mark Mazzola
Keyword(s):  
Carbon Source ◽  
Rhizoctonia Solani ◽  
Application Rate ◽  
Disease Suppression ◽  
Soil Microbiome ◽  
Pratylenchus Penetrans ◽  
Root Infection ◽  
Soil Suppressiveness ◽  
Soil Disinfestation ◽  
Anaerobic Soil Disinfestation

The effect of carbon source on efficacy of anaerobic soil disinfestation (ASD) toward suppression of apple root infection by Rhizoctonia solani AG-5 and Pratylenchus penetrans was examined. Orchard grass (GR), rice bran (RB), ethanol (ET), composted steer manure (CM), and Brassica juncea seed meal (SM) were used as ASD carbon inputs, with plant assays conducted in natural and pasteurized orchard soils. Subsequent studies investigated the effect of GR application rate used in ASD on control of these pathogens. In general, apple root infection by R. solani AG-5 was significantly lower in ET, GR, RB, and SM ASD treatments compared with the control. Among different ASD treatments, apple seedling growth was significantly greater when GR or SM was used as the carbon input relative to all other ASD treatments. R. solani AG-5 DNA abundance was significantly reduced in all ASD treatments, regardless of amendment type, compared with the control. In independent experiments, ASD-GR was consistently superior to ASD-CM for limiting pathogen activity in soils. ASD treatment with a grass input rate of 20 t ha−1 provided superior suppression of P. penetrans but grass application rate did not affect ASD efficacy in control of R. solani AG-5. The soil microbiome from ASD-GR-treated soils was clearly distinct from the control and ASD-CM-treated soils. In contrast, composition of the microbiome from control and ASD-CM-treated soils could not be differentiated. Comparative results from pasteurized and nonpasteurized soils suggest that there is potential for GR based ASD treatment to recruit microbial elements that persist over the anaerobic phase of soil incubation, which may functionally contribute to disease suppression. When ASD was conducted with GR, microbial diversity was markedly reduced relative to the control or ASD-CM soil suggesting that this parameter, typically associated with system resilience, was not instrumental to the function of ASD-induced soil suppressiveness.

scholarly journals Effect on the Antioxidant, Lipoperoxyl Radical Scavenger Capacity, Nutritional, Sensory and Microbiological Traits of an Ovine Stretched Cheese Produced with Grape Pomace Powder Addition

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 306 ◽  
Author(s):  
Raimondo Gaglio ◽  
Ignazio Restivo ◽  
Marcella Barbera ◽  
Pietro Barbaccia ◽  
Marialetizia Ponte ◽  
...  
Keyword(s):  
Grape Pomace ◽  
Pcr Analysis ◽  
Radical Scavenger ◽  
Acid Generation ◽  
Functional Aspects ◽  
Ovine Cheese ◽  
Plate Counts ◽  
Ewe's Milk ◽  
Red Grape ◽  
Experimental Trials

An innovative ovine cheese enriched with red grape pomace powder (GPP) was produced to improve the functional properties of Vastedda cheese typology. Vastedda cheese making was performed adding GPP and four selected Lactococcus lactis strains (Mise36, Mise94, Mise169 and Mise190). For each strain, 40 L of pasteurized ewe’s milk was divided into two aliquots representing control and experimental trials. Control cheese (CC) production did not contain GPP, while the experimental cheese (EC) production was enriched with 1% (w/w) GPP. GPP did not slow down starter development and acid generation. Plate counts and randomly amplified polymorphic DNA (RAPD)-PCR analysis confirmed the dominance of the starters in all trials. The evolution of the physicochemical parameters showed that EC productions were characterized by lower fat content, higher protein content, and higher values of secondary lipid oxidation. Sensory evaluation indicated that the cheeses produced with the strain Mise94 were those more appreciated by the judges. Thus, the last cheeses were investigated for some functional aspects: GPP enrichment significantly increased antioxidant activity and lipoperoxyl radical scavenger capacity, confirming that grape polyphenol inclusion in cheese represents an optimal strategy for the valorization of ovine cheeses as well as winemaking industry by-products.

scholarly journals Surface functionalization of Ti6Al4V with an extract of polyphenols from red grape pomace

2021 ◽  
pp. 109776
Author(s):  
G. Riccucci ◽  
M. Cazzola ◽  
S. Ferraris ◽  
V.A. Gobbo ◽  
M. Guaita ◽  
...  
Keyword(s):  
Surface Functionalization ◽  
Grape Pomace ◽  
Red Grape

scholarly journals A Lyophilized Red Grape Pomace Containing Proanthocyanidin-Rich Dietary Fiber Induces Genetic and Metabolic Alterations in Colon Mucosa of Female C57BL/6J Mice

2011 ◽  
Vol 141 (9) ◽  
pp. 1597-1604 ◽  
Author(s):  
Daneida Lizarraga ◽  
M. Pilar Vinardell ◽  
Véronique Noé ◽  
Joost H. van Delft ◽  
Gema Alcarraz-Vizán ◽  
...  
Keyword(s):  
Dietary Fiber ◽  
Grape Pomace ◽  
Colon Mucosa ◽  
Metabolic Alterations ◽  
Red Grape

scholarly journals Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
J. C. Madan ◽  
D. C. Koestler ◽  
B. A. Stanton ◽  
L. Davidson ◽  
L. A. Moulton ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Respiratory Tract ◽  
Microbial Communities ◽  
Effective Means ◽  
Significant Proportion ◽  
Gut Colonization ◽  
Pulmonary Damage ◽  
Chronic Colonization ◽  
High Degree ◽  
Over Time

ABSTRACT Pulmonary damage caused by chronic colonization of the cystic fibrosis (CF) lung by microbial communities is the proximal cause of respiratory failure. While there has been an effort to document the microbiome of the CF lung in pediatric and adult patients, little is known regarding the developing microflora in infants. We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Distinct genera dominated in the gut compared to those in the respiratory tract, yet some bacteria overlapped, demonstrating a core microbiota dominated by Veillonella and Streptococcus. Bacterial diversity increased significantly over time, with evidence of more rapidly acquired diversity in the respiratory tract. There was a high degree of concordance between the bacteria that were increasing or decreasing over time in both compartments; in particular, a significant proportion (14/16 genera) increasing in the gut were also increasing in the respiratory tract. For 7 genera, gut colonization presages their appearance in the respiratory tract. Clustering analysis of respiratory samples indicated profiles of bacteria associated with breast-feeding, and for gut samples, introduction of solid foods even after adjustment for the time at which the sample was collected. Furthermore, changes in diet also result in altered respiratory microflora, suggesting a link between nutrition and development of microbial communities in the respiratory tract. Our findings suggest that nutritional factors and gut colonization patterns are determinants of the microbial development of respiratory tract microbiota in infants with CF and present opportunities for early intervention in CF with altered dietary or probiotic strategies. IMPORTANCE While efforts have been focused on assessing the microbiome of pediatric and adult cystic fibrosis (CF) patients to understand how chronic colonization by these microbes contributes to pulmonary damage, little is known regarding the earliest development of respiratory and gut microflora in infants with CF. Our findings suggest that colonization of the respiratory tract by microbes is presaged by colonization of the gut and demonstrated a role of nutrition in development of the respiratory microflora. Thus, targeted dietary or probiotic strategies may be an effective means to change the course of the colonization of the CF lung and thereby improve patient outcomes.

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