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

Abstract 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

Free fatty acids link metabolism and regulation of the insulin-sensitizing fibroblast growth factor-21

OBJECTIVE—Fibroblast growth factor (FGF)-21 improves insulin sensitivity and lipid metabolism in obese or diabetic animal models, while human studies revealed increased FGF-21 levels in obesity and type 2 diabetes. Given that FGF-21 has been suggested to be a peroxisome proliferator–activator receptor (PPAR) –dependent regulator of fasting metabolism, we hypothesized that free fatty acids (FFAs), natural agonists of PPAR, might modify FGF-21 levels. RESEARCH DESIGN AND METHODS—The effect of fatty acids on FGF-21 was investigated in vitro in HepG2 cells. Within a randomized controlled trial, the effects of elevated FFAs were studied in 21 healthy subjects (13 women and 8 men). Within a clinical trial including 17 individuals, the effect of insulin was analyzed using an hyperinsulinemic-euglycemic clamp and the effect of PPAR activation was studied subsequently in a rosiglitazone treatment trial over 8 weeks. RESULTS—Oleate and linoleate increased FGF-21 expression and secretion in a PPAR-dependent fashion, as demonstrated by small-interfering RNA–induced PPAR knockdown, while palmitate had no effect. In vivo, lipid infusion induced an increase of circulating FGF-21 in humans, and a strong correlation between the change in FGF-21 levels and the change in FFAs was observed. An artificial hyperinsulinemia, which was induced to delineate the potential interaction between elevated FFAs and hyperinsulinemia, revealed that hyperinsulinemia also increased FGF-21 levels in vivo, while rosiglitazone treatment had no effect. CONCLUSIONS—The results presented here offer a mechanism explaining the induction of the metabolic regulator FGF-21 in the fasting situation but also in type 2 diabetes and obesity

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

Mean ± 1 SD of fungal ITS sequences classified to phylum level in a common recipe processed by windrow, aerated static pile or vermicompost.

<p>Values are expressed as percentages.</p><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>Unknown can represent other or unidentified.</p

Principal coordinates analysis biplot for a) bacterial and b) fungal communities in the end product of three compost processes (circle: windrow, square: aerated static pile, inverted triangle: vermicompost), <i>n</i> = 4 per process.

<p>Permutational multivariate analysis of variance indicated that differences between communities were highly significant (<i>p</i>≤0.001). Contrasting superscripts indicate that treatments are significantly different (<i>p</i>≤0.05).</p