Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks

Felix Matheri; Anne Kelly Kambura; Maina Mwangi; Edward Karanja; Noah Adamtey; Kennedy Wanjau; Edwin Mwangi; Chrysantus Mbi Tanga; David Bautze; Steven Runo

doi:10.1371/journal.pone.0286320

Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks

PLoS One. 2023 May 31;18(5):e0286320. doi: 10.1371/journal.pone.0286320. eCollection 2023.

Authors

Affiliations

¹ Department of Biochemistry, Microbiology, and Biotechnology, Kenyatta University (KU), Nairobi, Kenya.
² International Centre for Insect Physiology and Ecology (icipe), Nairobi, Kenya.
³ Department of Agricultural Sciences, Taita Taveta University (TTU), Voi, Kenya.
⁴ Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
⁵ International Livestock Research Institute (ILRI), Department Animal and Human Health, Nairobi, Kenya.

Abstract

Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials' influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost's biological and chemical stability.

Copyright: © 2023 Matheri et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Composting*
Eukaryota
Manure / microbiology
Microbiota* / genetics
Mycobiome*
Nitrogen / analysis
Soil

Substances

Nitrogen
Soil
Manure

Grants and funding

This research received partial financial support from Biovision Foundation (Grant No: 1040), Coop Sustainability Fund (Grant No: 1040), Liechtenstein Development Service (LED) (Grant No: 1040) and Swiss Agency for Development and Cooperation (SDC) (Grant No: 1040),. The authors also acknowledge partial financial support from the DAAD-Africa through the "In-Country/ In-Region Scholarship Programmes Eastern Africa" (Grant No: 91712524) We also gratefully acknowledge the support of icipe core funding provided by United Kingdom’s Foreign, Commonwealth and Development Office (FCDO); the Swedish International Development Cooperation Agency (Sida); the Swiss Agency for Development and Cooperation (SDC); the Federal Democratic Republic of Ethiopia; and the Government of the Republic of Kenya.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript”.