Anaerobic Soil Disinfestation and Vermicompost to Manage Bottom Rot in Organic Lettuce

Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris [Frank] Donk) is an aggressive soilborne pathogen with a wide host range, survives saprophytically between crops presenting a challenge for organic vegetable farmers that lack effective management tools. A two-year field experiment was conducted at two organic farms to compare anaerobic soil disinfestation (ASD) and worm-cured compost (vermicompost) to manage bottom rot caused by R. solani subspecies AG1-IB in field-grown organic lettuce (Lactuca sativa). At each farm, four replicate plots of seven treatments were arranged in a randomized complete block design. Randomization was restricted by grouping treatments to evaluate ASD, and treatments to evaluate vermicompost in starter plugs. ASD experiment treatments were three different ASD carbon sources that are commonly used and widely available to local farmers in Vermont: compost, cover crop residues, and poultry manure fertilizer, and a tarped control. Vermicompost experimental treatments were vermicompost compared to two types of controls: a commercial biocontrol product (RootShield® PLUS+G), and unamended (untarped control). This study demonstrated that the ASD method is achievable in a field setting on Vermont farms. However, neither ASD nor vermicompost produced significant disease suppression or resulted in higher marketable yields than standard growing practices. Given the laborious nature of ASD, it is likely more appropriate in a greenhouse setting with high value crops that could especially benefit from being grown in plastic tarped beds (e.g., tomatoes, strawberries). This study is the first known attempt of field-implemented ASD for soil pathogen control in the northeastern USA.

Rhizoctonia solani AG1-IB, AG1-IC, and AG4-HGII cause bottom rot of field lettuce in Vermont

Members of Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) species complex cause bottom rot on lettuce (Latuca sativa) and yield losses up to 70% (Subbarao et al. 2017). Severe symptoms include necrosis, stem rot, and/or discoloration especially on the leaf midrib. In Vermont, vegetable farms are small (0.5-30 acres) and grow lettuce concurrently with other vegetable crops in the same field but the AG(s) that causes the disease in Vermont has not been determined. Isolates (n = 157) were collected from 31 fields with reported history of bottom rot between July 10 and October 8, 2019, across Addison, Caledonia, Chittenden, Franklin, Lamoille, and Orleans counties. Isolates were collected from lettuce tissue or potato (Solanum tuberosum), a common rotation crop, or uncropped soil baited using radish (Raphanus sativus). Pieces of tissue (5-10 mm) were cut from the leading margin of lesions, surface disinfested with 0.1% NaClO for 1 min followed by 2 rinses with sterile water, blotted dry, and plated onto acidified 2% water agar (0.085% lactic acid, pH 4.8). After incubation for 48 to 72 h, mycelia resembling Rhizoctonia were examined for morphological characteristics including hyphal branching at ca. 90o angles, a septum near the branching point, multiple nuclei per cell, and lack of both clamp connections and conidia (Sneh et al. 1991). Colonies were white to dark brown, and some produced small sclerotia. Koch's postulates were performed by inoculating nine 8-week-old (9 leaf pairs) romaine lettuce plants (Johnny's Seeds, Winslow, ME, cv. Monte Carlo) per isolate. Isolates were grown on 2% potato dextrose agar for 1 week, from which a 5-mm agar plug was placed on the adaxial leaf surface at the base of a petiole. Plants were enclosed in a plastic bag to maintain high humidity and grown under a 16-hour photoperiod at 24 °C. Disease severity was rated 4 days after inoculation (0: healthy, 1: isolated lesions, 2: lesions across multiple petioles, and 3: systemic disease). Putative AG were determined by Sanger sequencing of the internal transcribed spacer (ITS) region using the ITS1F and ITS4B primer pair (758 bp) (Gardes and Bruns 1993). Contigs were assembled using CAP3 software (Huang and Madan 1999). Taxonomy was assigned to each OTU via the NCBI BLASTn database with criteria as 0.0 E and nucleotide match of at least 97%. Of the 10 isolates sequenced with sufficient coverage (735 to 784 bp alignment length) and definitive resolution (96.7 to 99.9% identity), 5 were putative AG 1-IB (Genbank Accession HG934430.1), 2 AG 1-IC (Genbank Accession AF354058.1), 2 AG 3 (Genbank Accession AF354064.1), and 1 AG 4-HGII (Genbank Accession AF354074.1). Fasta files and metadata are archived at 10.6084/m9.figshare.20301324, 10.6084/m9.figshare.20301375. Putative AG 1-IB was highly virulent on lettuce plants whether it originated from potato (mean 2.6) or lettuce (mean 1.3 to 3). AG 4-HGII and AG 1-IC isolated from lettuce and radish, respectively, were moderately severe (mean 1.4 to 2.2) on lettuce with identical symptoms. The two potato isolates (AG3) were not pathogenic on lettuce. Similarly, higher incidence of AG 1-IB is reported on lettuce in Quebec (Wallon et al. 2021), Ohio (Herr 1993), and Germany (Grosch et al. 2004). Because AG vary in their host range (Sneh et al. 1991), knowing the AG will inform management decisions such as crop rotation and weed control. This is the first report of the causal agent of bottom rot of lettuce or any AG of R. solani in Vermont.

Differential Survival of Escherichia coli and Listeria spp. in Northeastern U.S. Soils Amended with Dairy Manure Compost, Poultry Litter Compost, and Heat-Treated Poultry Pellets and Fate in Raw Edible Radish Crops

ABSTRACT

Composted or heat-treated biological soil amendments of animal origin (BSAAOs) can be added to soils to provide nutrients for fresh produce. These products lower the risk of pathogen contamination of fresh produce compared with the use of untreated BSAAOs; however, meteorological conditions, geographic location, and soil properties can influence the presence of pathogenic bacteria or their indicators (e.g., generic Escherichia coli) and allow potential for produce contamination. Replicated field plots of loamy or sandy soils were tilled and amended with dairy manure compost (DMC), poultry litter compost (PLC), or no compost (NoC) over two field seasons and noncomposted heat-treated poultry pellets (HTPPs) during the second field season. Plots were inoculated with a three-strain cocktail of rifampin-resistant E. coli (rE. coli) at levels of 8.7 log CFU/m2. Direct plating and most-probable-number methods measured the persistence of rE. coli and Listeria spp. in plots through 104 days postinoculation. Greater survival of rE. coli was observed in PLC plots in comparison to DMC plots and NoC plots during year 1 (P < 0.05). Similar trends were observed for year 2, when rE. coli survival was also greater in HTPP-amended plots (P < 0.05). Survival of rE. coli depended on soil type, and water potential and temperature were significant covariables. Listeria spp. were found in NoC plots, but not in plots amended with HTPPs, PLC, or DMC. Radish data demonstrate that PLC treatment promoted the greatest level of rE. coli translocation compared with DMC and NoC treatments (P < 0.05). These results are consistent with findings from studies conducted in other regions of the United States, and they inform northeast produce growers that composted and noncomposted poultry-based BSAAOs support greater survival of rE. coli in field soils. This result has the potential to affect the food safety risk of edible produce grown in BSAAO-amended soils as a result of pathogen contamination.

HIGHLIGHTS

Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments varying in animal origin: dairy manure (DMC), poultry litter (PLC), or neither (NoC). The composition and function of bacterial and fungal communities were characterized by the amplicon sequencing of marker genes and by the ecoenzyme activity, respectively. The temporal autocorrelation within and among years was adjusted by principal response curves (PRC) to analyze the effect of compost on community composition among treatments. Bacteria in the phylum Bacteriodetes, classes Flavobacteriia and Spingobacteriales (Fluviicola, Flavobacteriia, and Pedobacter), were two to four times more abundant in soils amended with PLC than DMC or NoC consistently among fields and years. Fungi in the phylum Ascomycota were relatively abundant, but their composition was field-specific and without treatment differences. The ecoenzyme data verify that the effects of PLC and DMC on soil communities are based on their microbial composition and not a response to the C source or nutrient content of the compost.

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status

Infections of the cow udder leading to mastitis and reducing milk quality are a critical challenge facing all dairy farmers. Mastitis may be linked to the ecological disruption of an endogenous mammary microbial community, suggesting an ecosystems approach to management and prevention of this disease. The teat end skin represents a first point of host contact with mastitis pathogens and may offer an opportunity for microbially mediated resistance to infection, yet we know little about the microbial community of teat end skin or its potential interaction with the microbial community of intramammary milk of organic dairy cattle. High-throughput sequencing of marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected gland (i.e., udder quarter) and to assess the sharing of microbial DNA between these tissue habitat sites. The mammary microbiome varied among cows, through time, and between skin and milk. Microbiomes of milk from healthy and infected quarters reflected a diverse group of microbial DNA sequences, though milk had far fewer operational taxonomic units (OTUs) than skin. Milk microbiomes of infected quarters were generally more variable than healthy quarters and were frequently dominated by a single OTU; teat end skin microbiomes were relatively similar between healthy and infected quarters. Commonly occurring genera that were shared between skin and milk of infected glands included Staphylococcus spp. bacteria and Debaryomyces spp. fungi. Commonly occurring genera that were shared between skin and milk of healthy glands included bacteria SMB53 (Clostridiaceae) and Penicillium spp. fungi. Results support an ecological interpretation of the mammary gland and the notion that mastitis can be described as a dysbiosis, an imbalance of the healthy mammary gland microbiome.

Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach

AIMS

The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources.

METHOD AND RESULTS

Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH₄ -N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful.

CONCLUSIONS

Dairy-based composts are less likely to support E. coli survival than poultry-based composts.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results aid in risk assessment of the use of different types of manure-based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.

A Plate Competition Assay As a Quick Preliminary Assessment of Disease Suppression

The goal was to develop and optimize a simple, affordable, and effective bioassay to detect disease suppressive ability of a specific compost against soilborne fungus Rhizoctonia solani. R. solani is a pathogen of a wide range of plant hosts worldwide. The fungus survives in soils as a saprophyte and grows rapidly on simple water agar media. The plate assay is a rapid method to compare composts for their ability to slow the growth of R. solani. The assay also correlates well with suppression of other soilborne fungal pathogens that survive as saprophytes in soils such as Alternaria early blights, Fusarium wilt, Phytophthora root rot, and Pythium root rot.

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Nematode Genera in Forest Soil Respond Differentially to Elevated CO2

Previous reports suggest that fungivorous nematodes are the only trophic group in forest soils affected by elevated CO2. However, there can be ambiguity within trophic groups, and we examined data at a genus level to determine whether the conclusion remains similar. Nematodes were extracted from roots and soil of loblolly pine (Pinus taeda) and sweet gum (Liquidambar styraciflua) forests fumigated with either ambient air or CO2-enriched air. Root length and nematode biomass were estimated using video image analysis. Most common genera included Acrobeloides, Aphelenchoides, Cephalobus, Ditylenchus, Ecphyadorphora, Filenchus, Plectus, Prismatolaimus, and Tylencholaimus. Maturity Index values and diversity increased with elevated CO2 in loblolly pine but decreased with elevated CO2 in sweet gum forests. Elevated CO2 treatment affected the occurrence of more nematode genera in sweet gum than loblolly pine forests. Numbers were similar but size of Xiphinema decreased in elevated CO2. Abundance, but not biomass, of Aphelenchoides was reduced by elevated CO2. Treatment effects were apparent at the genus levels that were masked at the trophic level. For example, bacterivores were unaffected by elevated CO2, but abundance of Cephalobus was affected by CO2 treatment in both forests.

Response of soil invertebrates to disturbance across three resource regions in North Carolina

We evaluated the potential of soil microarthropods and enchytraeid worms to be useful as bioindicators of soil condition in forest, wetland, and agricultural ecosystems over a range of ecoregions. Selected mesofauna and soil characteristics in soil and litter in relatively undisturbed and disturbed examples of each of three ecosystems within each of three land resource regions were monitored over two years. Optimal times of year to sample these organisms as indicators of disturbance were April, May, July and September. No single measure reflected disturbance across all three ecosystems. Among forest sites, Simpson's diversity index, evenness, abundance of ants, and proportion of enchytraeids in the mesofauna differed between soils of different disturbance levels. Among agricultural sites, richness, evenness, abundance of mites, and proportions of collembolans and of enchytraeids in the mesofauna differed between disturbance levels. Among wetland sites, Shannon's and Simpson's diversity indices, richness based on the total mesofauna, and abundances of mites, diplurans, ants, and isotomid and onychiurid collembolans differed between disturbance levels. Covariates most frequently associated with abundance and diversity of the measured mesofauna were soil electrical conductivity, available N, organic matter, and pH. Canonical correspondence analysis provided information somewhat different to bivariate analysis. Using both approaches to examine soil and litter taxa that have distinctive responses to disturbance may help to identify candidate groups applicable for use in large-scale environmental monitoring programs.

Nitrogen fixation and leaching of biological soil crust communities in mesic temperate soils

Biological soil crust is composed of lichens, cyanobacteria, green algae, mosses, and fungi. Although crusts are a dominant source of nitrogen (N) in arid ecosystems, this study is among the first to demonstrate their contribution to N availability in xeric temperate habitats. The study site is located in Lucas County of Northwest Ohio. Using an acetylene reduction technique, we demonstrated potential N fixation for these crusts covering sandy, acidic, low N soil. Similar fixation rates were observed for crust whether dominated by moss, lichen, or bare soil. N inputs from biological crusts in northwestern Ohio are comparable to those in arid regions, but contribute substantially less N than by atmospheric deposition. Nitrate and ammonium leaching from the crust layer were quantified using ion exchange resin bags inserted within intact soil cores at 4 cm depth. Leaching of ammonium was greater and nitrate less in lichen than moss crusts or bare soil, and was less than that deposited from atmospheric sources. Therefore, biological crusts in these mesic, temperate soils may be immobilizing excess ammonium and nitrate that would otherwise be leached through the sandy soil. Moreover, automated monitoring of microclimate in the surface 7 cm of soil suggests that moisture and temperature fluctuations in soil are moderated under crust compared to bare soil without crust. We conclude that biological crusts in northwestern Ohio contribute potential N fixation, reduce N leaching, and moderate soil microclimate.

Observed differences in life history characteristics of nematodes Aphelenchus and Acrobeloides upon exposure to copper and benzo(a)pyrene

Maturity index values reflect life history characteristics often inferred by morphology. We tested the hypothesis that Acrobeloides and Aphelenchus are sensitive to chemical pollutants, opposite of what their colonizer-persister (CP) value of 2 suggests. Acrobeloides and Aphelenchus were reared at 19 degrees C and provided diets of Escherichia coli and Rhizoctonia solani, respectively. LC50 values for Aphelenchus exposed to copper or benzo(a)pyrene (BaP) are greater than Acrobeloides. Copper impedes growth of Acrobeloides at 10 microg/g, and results in 100% mortality at 20 microg/g. In contrast, Aphelenchus is more resilient, with no visible impact at 20 microg/g. Acrobeloides and Aphelenchus were sensitive to much lower concentrations of BaP than copper, i.e., 0.5 microg/g inhibited development of Acrobeloides and 2 microg/g for Aphelenchus. Egg size and hatch were unaffected at 15 microg/g copper. In contrast, 0.5 microg/g BaP reduced both egg size and hatch for Aphelenchus but not Acrobeloides. Survival of Acrobeloides and reproduction of Aphelenchus responded differently to copper and BaP, implying the relationship between this classification and their sensitivity to short-term effects may be less straightforward than presumed. Refinement of index values based on empirical evidence can be used to improve sensitivity and interpretation of nematode community indices for environmental monitoring.