Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing

<div><p>Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using <i>q</i>PCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 10⁶ and (0.4±0.0) x 10⁷ g^-1, and the <i>Rhodospiralles</i> and <i>Lactobacialles</i> orders dominated. Fungal communities had (2.9±0.0) x10⁵ and (6.1±0.2) x10⁵ ITS copies g^-1, and the <i>Saccharomycetales</i> order dominated. At the end of the thermophilic stage on the 30^th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included <i>Flavobacteriales</i>, <i>Chitinophagaceae</i> and <i>Bacterioidetes</i> for bacteria and <i>Microascaceae</i>, <i>Dothideomycetes</i>, <i>Eurotiomycetes</i>, <i>Sordariomycetes</i>, and <i>Agaricomycetes</i> for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.</p></div

The most abundant bacterial OTUs found in I and IH composts.

<p>The most abundant bacterial OTUs found in I and IH composts.</p

Dynamics of temperature, DOC and GI in the process of composting.

<p>Dynamics of temperature, DOC and GI in the process of composting.</p

Alpha diversity indices of the fungal and bacterial communities of I and H composts.

<p>Alpha diversity indices of the fungal and bacterial communities of I and H composts.</p

The most abundant fungal OTUs found in I and IH composts.

<p>The most abundant fungal OTUs found in I and IH composts.</p

The chemical characteristics of the raw wastes and composting mixtures.

<p>The chemical characteristics of the raw wastes and composting mixtures.</p

Additional file 1: of High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1

A main spectra profiles (MSP) dendrogram generated by MALDI Biotyper 3.0 software with the 3.5.1 isolate, 26 Pantoea reference species and 14 E. coli outgroup strains. Each cluster is indicated by different color. Distance level show the phylogenic distance between the selected genus and species. The strain 3.5.1 is highlighted by box. (JPG 182 kb

Additional file 1: Figure S1. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

Quality control process. (PDF 25 kb

Additional file 3: Table S1a. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

List of samples included in “Extended” dataset. Table S1b List of samples included in “Core” dataset. Table S1c List of samples included in “Ancient” dataset. Table S2 Results of ADMIXTURE for K = 9. Table S3 Results of ADMIXTURE for K = 6, 7, 8. Table S4 Results of f3 test. Table S5 Results of IBD sharing analysis in 1–3 cM and 4–10 cM bins. Table S6 Total amount of shared IBD between populations. Table S7 Standard residue of linear regression analysis of distance-IBD sharing. Table S8 Distance and shared IBD between pairs of populations. Table S9: Results of f3 outgroup test with ancient samples. (XLSX 482 kb