Assessment of Biological Soil Amendments of Animal Origin Use, Research Needs, and Extension Opportunities in Organic Production

Ramos, Thais Melo; Jay-Russell, Michele; Millner, Patricia D.; Shade, Jessica; Misiewicz, Tracy M.; Sorge, Ulrike S; Hutchinson, Mark; Lilley, Jason; Pires, Alda F. A.

doi:10.3389/fsufs.2019.00073

Cited by 21 publications

(17 citation statements)

References 35 publications

(49 reference statements)

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“…Organic fertilizers are commonly used as nutrient sources in small-scale crop-livestock integrated systems. The use of OFs is an important practice to maintain or improve soil health and fertility in organic production systems where no synthetic nutrient sources are allowed [ 59 ]. Furthermore, in recent years, scientific evidence on the role of soil organic matter in soil health and climate change mitigation, together with an increasing emphasis on the circular economy, has reinvigorated the interest in using OFs in agriculture at large, including conventional and industrial large-scale crop productions.…”

Section: Sources Of Organic Fertilizers and N 2 O Emissionsmentioning

confidence: 99%

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

2021

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The use of organic fertilizers constitutes a sustainable strategy to recycle nutrients, increase soil carbon (C) stocks and mitigate climate change. Yet, this depends largely on balance between soil C sequestration and the emissions of the potent greenhouse gas nitrous oxide (N2O). Organic fertilizers strongly influence the microbial processes leading to the release of N2O. The magnitude and pattern of N2O emissions are different from the emissions observed from inorganic fertilizers and difficult to predict, which hinders developing best management practices specific to organic fertilizers. Currently, we lack a comprehensive evaluation of the effects of OFs on the function and structure of the N cycling microbial communities. Focusing on animal manures, here we provide an overview of the effects of these organic fertilizers on the community structure and function of nitrifying and denitrifying microorganisms in upland soils. Unprocessed manure with high moisture, high available nitrogen (N) and C content can shift the structure of the microbial community, increasing the abundance and activity of nitrifying and denitrifying microorganisms. Processed manure, such as digestate, compost, vermicompost and biochar, can also stimulate nitrifying and denitrifying microorganisms, although the effects on the soil microbial community structure are different, and N2O emissions are comparatively lower than raw manure. We propose a framework of best management practices to minimize the negative environmental impacts of organic fertilizers and maximize their benefits in improving soil health and sustaining food production systems. Long-term application of composted manure and the buildup of soil C stocks may contribute to N retention as microbial or stabilized organic N in the soil while increasing the abundance of denitrifying microorganisms and thus reduce the emissions of N2O by favoring the completion of denitrification to produce dinitrogen gas. Future research using multi-omics approaches can be used to establish key biochemical pathways and microbial taxa responsible for N2O production under organic fertilization.

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Section: Sources Of Organic Fertilizers and N 2 O Emissionsmentioning

confidence: 99%

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

2021

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“…The rationale for NOP application intervals was based on crop production cycles rather than survival and transfer of foodborne pathogens from soil to fresh produce systems (Sharma and Reynnells, 2016;Ramos et al, 2019). These application intervals can be burdensome for organic farmers with complex crop rotations and polycultures, particularly when short-season crops are included in the mix.…”

Section: Introductionmentioning

confidence: 99%

Survival and Persistence of Foodborne Pathogens in Manure-Amended Soils and Prevalence on Fresh Produce in Certified Organic Farms: A Multi-Regional Baseline Analysis

Ramos

Jay-Russell

Millner

et al. 2021

Front. Sustain. Food Syst.

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Biological soil amendments of animal origin (BSAAOs), including untreated (e.g., raw or aged manure, or incompletely composted manure) and treated animal products (e.g., compost), are used for crop production and as part of soil health management. Application of BSAAO's must be done cautiously, as raw manure commonly contains enteric foodborne pathogens that can potentially contaminate edible produce that may be consumed without cooking. USDA National Organic Program (NOP) certified production systems follow the 90-or 120-day interval standards between applications of untreated BSAAOs and crop harvest, depending on whether the edible portions of the crops are in indirect or direct contact with the soil, respectively. This study was conducted to evaluate the survival of four foodborne pathogens in soils amended with BSAAOs and to examine the potential for bacterial transfer to fresh produce harvested from USDA NOP certified organic farms (19) from four states. Only 0.4% (2/527) of produce samples were positive for L. monocytogenes. Among the untreated manure and compost samples, 18.0% (42/233) were positive for at least one of the tested and culturable bacterial foodborne pathogens. The prevalence of non-O157 STEC and Salmonella in untreated manure was substantially > that of E. coli O157:H7 and L. monocytogenes. Of the 2,461 soil samples analyzed in this study, 12.9% (318) were positive for at least one pathogen. In soil amended with untreated manure, the prevalence of non-O157 STEC [7.7% (190) and L. monocytogenes (5.0% (122), was > that of Salmonella (1.1% (26)] or E. coli O157 [0.04% (1)]. Foodborne pathogen prevalence in the soil peaked after manure application and decreased significantly 30 days post-application (dpa). However, non-O157 STEC and L. monocytogenes were recovered from soil samples after 90 and 120 dpa. Results indicate that produce contamination by tested foodborne pathogens was infrequent, but these data should not be generalized outside of the specific wait-time regulations for organic crop production and the farms studied. Moreover, other sources of contamination, e.g., irrigation, wildlife, environmental conditions, cropping and management practices, should be considered. This study also provides multi-regional baseline data relating to current NOP application intervals and development of potential risk mitigation strategies to reduce pathogen persistence in soils amended with BSAAOs. These findings contribute to filling critical data gaps concerning occurrence of fecal pathogens in NOP-certified farming systems used for production of fresh produce in different US regions.

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“…Based on the results of the study reported here, there are several candidate Salmonella strains to use in challenge and validation studies as worst-case contamination scenarios. Prior literature ( Harris et al, 2013 ; Andino and Hanning, 2015 ; Harrand et al, 2019 ; Ramos et al, 2019 ) has described the importance of using worst-case contamination scenarios (i.e., conservative approach) and a diverse set of strains, as survival and behavior can vary considerably by factor (e.g., soil-type). For example, S. Saintpaul survived 168 days in sandy- and clay-loam amended soils exposed to daily irrigation, and according to the cTree model had one of the longest times to detect Salmonella .…”

Section: Discussionmentioning

confidence: 99%

“…However, it is unclear (i) if existing data support the National Organic Program guidelines and (ii) if a one-size-fits all guideline is appropriate for all commodities, management practices (e.g., type of BSAAO used and irrigation regimen), produce-growing regions, and even fields within a single operation. Indeed, past studies have shown that soil characteristics, environmental and laboratory conditions (e.g., temperature), and amendment type can all affect Salmonella survival in soil ( Himathongkham et al, 1999 ; You et al, 2006 ; Semenov et al, 2009 ; Ramos et al, 2019 ). Similarly, past studies ( Strawn et al, 2014 ; Weller et al, 2015 ; Sharma et al, 2020 ) indicates that factors that vary between produce-growing regions, between farms within the same region, and between fields on the same farm can affect pathogen dynamics in farm environments.…”

Section: Introductionmentioning

confidence: 99%

Strain, Soil-Type, Irrigation Regimen, and Poultry Litter Influence Salmonella Survival and Die-off in Agricultural Soils

et al. 2021

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The use of untreated biological soil amendments of animal origin (BSAAO) have been identified as one potential mechanism for the dissemination and persistence of Salmonella in the produce growing environment. Data on factors influencing Salmonella concentration in amended soils are therefore needed. The objectives here were to (i) compare die-off between 12 Salmonella strains following inoculation in amended soil and (ii) characterize any significant effects associated with soil-type, irrigation regimen, and amendment on Salmonella survival and die-off. Three greenhouse trials were performed using a randomized complete block design. Each strain (~4 log CFU/g) was homogenized with amended or non-amended sandy-loam or clay-loam soil. Salmonella levels were enumerated in 25 g samples 0, 0.167 (4 h), 1, 2, 4, 7, 10, 14, 21, 28, 56, 84, 112, 168, 210, 252, and 336 days post-inoculation (dpi), or until two consecutive samples were enrichment negative. Regression analysis was performed between strain, soil-type, irrigation, and (i) time to last detect (survival) and (ii) concentration at each time-point (die-off rate). Similar effects of strain, irrigation, soil-type, and amendment were identified using the survival and die-off models. Strain explained up to 18% of the variance in survival, and up to 19% of variance in die-off rate. On average Salmonella survived for 129 days in amended soils, however, Salmonella survived, on average, 30 days longer in clay-loam soils than sandy-loam soils [95% Confidence interval (CI) = 45, 15], with survival time ranging from 84 to 210 days for the individual strains during daily irrigation. When strain-specific associations were investigated using regression trees, S. Javiana and S. Saintpaul were found to survive longer in sandy-loam soil, whereas most of the other strains survived longer in clay-loam soil. Salmonella also survived, on average, 128 days longer when irrigated weekly, compared to daily (CI = 101, 154), and 89 days longer in amended soils, than non-amended soils (CI = 61, 116). Overall, this study provides insight into Salmonella survival following contamination of field soils by BSAAO. Specifically, Salmonella survival may be strain-specific as affected by both soil characteristics and management practices. These data can assist in risk assessment and strain selection for use in challenge and validation studies.

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Assessment of Biological Soil Amendments of Animal Origin Use, Research Needs, and Extension Opportunities in Organic Production

Cited by 21 publications

References 35 publications

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

Effects of Organic Fertilizers on the Soil Microorganisms Responsible for N2O Emissions: A Review

Survival and Persistence of Foodborne Pathogens in Manure-Amended Soils and Prevalence on Fresh Produce in Certified Organic Farms: A Multi-Regional Baseline Analysis

Strain, Soil-Type, Irrigation Regimen, and Poultry Litter Influence Salmonella Survival and Die-off in Agricultural Soils

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