Ecoenzymes as Indicators of Compost to Suppress Rhizoctonia solani

Reports of disease suppression by compost are inconsistent likely because there are no established standards for feedstock material, maturity age for application, and application rate. The overall goal of the study was to evaluate a suite of biological indicators for their ability to predict disease suppression. Indicators included both commercial available methods for compost stability (Solvita™, respiration) and metrics of soil ecology not yet adopted by the compost industry (e.g., ecoenzymes, nematode community index). Damping-off by Rhizoctonia solani on radish was chosen as a model system given its global importance, competitiveness affected by carbon quality, and lack of disease management options for organic production. Biological indicators were evaluated for their ability to consistently differentiate among curing process, maturity, and feedstock material as a function of disease severity of a seedling bioassay and a compost extract assay to test competition with R. solani growth. Compost processed as vermicompost and anaerobic digestate were more suppressive against R. solani than windrow or aerated static pile. Mature composts were more suppressive than immature components. Feedstocks containing dairy manure and/or hardwood bark tended to have suppressive qualities. In contrast, poultry manure-based components were conducive to disease. Microbial ecoenzymes active on chitin and cellulose and nematode community indices were better predictors of disease suppressiveness than microbial respiration. These indicators are quicker than plant bioassays and could be adopted as tools to certify commercial products

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

Grazing in a porous environment. 2. Nematode community structure

The influence of soil matrix potential on nematode community composition and grazing associations were examined. Undisturbed cores (5 cm diameter, 10 cm depth) were collected in an old field dominated by perennial grasses on a Hinckley sandy loam at Peckham Farm near Kingston, Rhode Island. Ten pairs of cores were incubated at -3, -10, -20 and -50 kPa matric potential after saturation for 21-28 or 42-58 days. Nematodes were extracted using Cobb\u27s decanting and sieving method followed by sucrose centrifugal-flotation and identified to family or genus. Collembola and enchytraeids present were also enumerated because they are grazers that reside in air-filled spaces. Direct counts of bacteria and fungi were made to estimate biovolume using fluorescein isothiocyanate and fluorescein diacetate stains, respectively. Trophic diversity and maturity indices were calculated for nematode communities. Three patterns of matric potential effect were observed for nematode taxa. One, there was a consistent effect of matric potential for all season for Alaimus, Monhysteridae, Prismatolaimus, Paraxonchium and Dorylaimoides. Two, some effects of matric potential were consistent among seasons and other effects were inconsistent for Aphelenchoides, Aphelenchus, Cephalobidae, Coomansus, Eudorylaimus, Huntaphelenchoides, Panagrolaimide, Paraphelenchus, Sectonema, and Tripyla. Third, effects of matric potential were always inconsistent among seasons for Aphanolaimus, Aporcelaimellus, Bunonema, Rhabditidae, and Tylencholaimus. As predicted, fungal and bacterial biomass responded oppositely to matric potential. Total bacterial biomass was greater at -3 kPa than -10, -20 and -50 kPa (P=0.0095). Total fungal biomass was greater at -50, -20 and -10 kPa than -3 kPa (P=0.0095). Neither bacterial-feeding, fungal-feeding nor predacious nematodes correlated significantly with bacterial or fungal biomass. Omnivorous and predacious nematodes correlated positively with number of bacterial-feeding nematodes; predacious nematodes also correlated positively with fungal-feeding nematodes. Numbers of Collembola and enchytraeids were more often correlated positively with microbial-grazing nematode numbers in drier than moist soils. From this study, we propose two mechanisms that may explain nematode community structure changes with matric potential: differential anhydrobiosis and/or enclosure hypotheses. The later suggests that drying of soil generates pockets of moisture in aggregates that become isolated from one another enclosing nematodes and their food in relatively high concentrations creating patches of activity separated by larger areas of inactivity

Organic Farm Bedded Pack System Microbiomes: A Case Study with Comparisons to Similar and Different Bedded Packs

Animal housing and bedding materials influence cow and farm worker exposure to microbial pathogens, biocontrol agents, and/or allergens. This case study represents an effort to characterize the bacterial and fungal community of bedding systems using an amplicon sequencing approach supplemented with the ecological assessment of cultured Trichocomaceae isolates (focusing on Penicillium and Aspergillus species) and yeasts (Saccharomycetales). Bedding from five certified organic dairy farms in northern Vermont USA were sampled monthly between October 2015 and May 2016. Additional herd level samples from bulk tank milk and two bedding types were collected from two farms to collect fungal isolates for culturing and ecology. Most of the microorganisms in cattle bedding were microbial decomposers (saprophytes) or coprophiles, on account of the bedding being composed of dead plant matter, cattle feces, and urine. Composition of bacterial and fungal communities exhibited distinct patterns of ecological succession measured through time and by bedding depth. Community composition patterns were related to management practices and choice of bedding material. Aspergillus and Penicillium species exhibited niche differentiation expressed as differential substrate requirements; however, they generally exhibited traits of early colonizers of bedding substrates, typically rich in carbon and low in nitrogen. Pichia kudriavzevii was the most prevalent species cultured from milk and bedding. P. kudriavzevii produced protease and its abundance directly related to temperature. The choice of bedding and its management represent a potential opportunity to curate the microbial community of the housing environment

Grazing in a porous environment: 1. The effect of soil pore structure on C and N mineralization. Plant Soil 212

Abstract The porous soil environment constrains grazing of microorganisms by microbivorous nematodes. In particular, at matric potentials at which water-filled pore spaces have capillary diameters less than nematode body diameters the effect of grazing, e.g. enhanced mineralization, should be reduced ('exclusion hypothesis') because nematodes cannot access their microbial forage. We examined C and N mineralization, microbial biomass C (by fumigationextraction), the metabolic quotient (C mineralization per unit biomass C), nematode abundance, and soil water content in intact soil cores from an old field as a function of soil matric potential (−3 to −50 kPa). We expected, in accordance with the exclusion hypothesis, that nematode abundance, N and C mineralization would be reduced as matric potential decreased, i.e. as soils became drier. N mineralization was significantly greater than zero for −3 kPa but not for −10, −20 and −50 kPa. Microbial biomass C was less at −50 kPa than at −10 kPa, but not significantly different from biomass C at −3 and −20 kPa. The metabolic quotient was greatest at −50 kPa than any of the other matric potentials. From the exclusion hypothesis we expected significantly fewer nematodes to be present at −50 and −20 kPa representing water-filled capillary pore sizes less than 6 and 15 µm, respectively, than at −3 and −10 kPa. Microbivorous (fungivorous+bacterivorous) nematode abundance per unit mass of soil was not significantly different among matric potentials. Body diameters of nematodes ranged from 9 µm to 40 µm. We discuss several alternatives to the exclusion hypothesis, such as the 'enclosure hypothesis' which states that nematodes may become trapped in large water-filled pore spaces even when capillary pore diameters (as computed from matric potential) are smaller than body diameters. One of the expected outcomes of grazing in enclosures is the acceleration of nutrient cycling

Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

<div><p>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 <i>Epicoccum</i>, <i>Thermomyces</i>, <i>Eurotium</i>, <i>Arthrobotrys</i>, and <i>Myriococcum</i>. 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.</p></div

Mean ± 1 SD (<i>n</i> = 4) of total sequences classified as bacteria in a common recipe processed by windrow, aerated static pile or vermicompost.

<p>Values are expressed as percentages.</p>*<p>: <i>p</i>≤0.05 false discovery rate (adjusted) from KW and unadjusted P-values.</p>∧<p>: <i>p</i>≤0.05 for unadjusted <i>P</i>-value, but ≤0.1 for false discovery rate (adjusted).</p

Mean ± 1 SD of fungal genera, expressed as percentage of sequences classified to phylum level in cured manure, hay, and hardwood compost recipes.

<p>False Discovery Rate (FDR) <i>p</i>-values from Kruskal-Wallis test,</p>n.s.<p>: <i>p</i>_FDR>0.05,</p>*<p>:0.01<<i>p</i>_FDR<0.05,</p>**<p>: 0.001<<i>p</i>_FDR<0.01.</p>a<p>: rank order of <i>Epicoccum</i> species abundance: <i>E.</i> sp_CHTAM7, <i>E.</i> sp_TMS_2011.</p>b<p>represents a) a sequence from an undescribed taxon, b) from an environmental sequence were the organism was not identified, or c) a sequence matches a described species that is not represented in the reference database.</p>c<p>: rank order of <i>Arthrobotrys</i> species abundance: <i>A. amerospora</i>><i>A. flagrans</i>><i>A. oligospora</i>.</p>d<p>: rank order of <i>Scedosporium</i> species abundance: <i>S. prolificans</i>><i>S. aurantiacum</i>><i>S. apiospermum</i>.</p>e<p>: dominant species: <i>Myriococcum thermophilum</i>.</p>f<p>: rank order of <i>Smittium</i> species abundance: <i>Smittium</i> sp.><i>S. orthocladii</i>.</p

Shannon diversity of a) bacteria and b) fungal communities within a standardized recipe finished by windrow, aerated static pile (ASP) or vermicompost.

<p>Shannon diversity is computed as H′ = −Σ(p_i ln p_i) where <i>p</i> represents the proportion of taxon <i>i</i> in the community. Box-whisker plots are illustrated.</p

Heat map illustrating changes in A) bacterial and B) fungal composition through time for the same recipe composted by three processes: windrow, aerated static pile or vermicompost.

<p>All fungi illustrated are ascomycota. Time is expressed as days of decomposition. The thermophillic phase occurred prior to sampling in windrow, days 22–56 for aerated static pile, and day 53 for vermicompost. Units illustrated as mean percentages of total sequences (bacteria) and percentage of taxa classified to phylum (fungi). Dots represent missing samples. Each column is colored so that taxa with high relative abundance are red, intermediate abundances are white and low abundances are blue.</p