Abstract
Compost has been widely used in agriculture in recent years, but the nutrients it provides are far from enough for plant growth. Therefore, it is necessary to systematically explore the fermentation process of composting. In this study, the succession of microbial community and metabolite characteristics in compost were analyzed by using microbial sequencing and metabolomics techniques. The results showed that compared with mesophilic phase and cooling phase, the richness and diversity of bacterial community decreased in thermophilic phase. At the genus level, Pseudomonas (8.90%), Lactobacillus (3.99%), Bacteroidetes (3.39%), Flavobacterium (3.25%) and Prevotella (Prevotella_9, 2.33%, Prevotellaceae_NK3B31_group, 2.44%) were the dominant genera in the pig manure composting. The abundance of Pseudomonas and Flavobacterium increased significantly while Lactobacillus and Prevotella were significantly decreased after composting, and the abundance of Bacteroidetes increased first and then decreased. Fatty acyls, sterol lipids, glycerophospholipids, polyketides and prenol lipids were common microbial metabolites in compost. Moreover, the linoleic acid metabolic pathway was significantly enriched in the three stages of composting, and linoleic acid metabolism might be the primary function of the microbial community in composting. The network analysis showed that between the microbial communities or between the microbial community and metabolites were closely related to each other.
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References
Antunes LP, Martins LF, Pereira RV, Thomas AM, Barbosa D, Lemos LN, Silva GMM, Moura LMS, Epamino GWC, Digiampietri LA, Lombardi KC, Ramos PL, Quaggio RB, De Oliveira JCF, Pascon RC, Da Cruz JB, Da Silva AM, Setubal JC (2016) Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Sci Rep 6:38915. https://doi.org/10.1038/srep38915
Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Evol Microbiol 46:128–148. https://doi.org/10.1099/00207713-46-1-128
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinform 30:2114–2134. https://doi.org/10.1093/bioinformatics/btu170
Brodhun F, Gobel C, Hornung E, Feussner I (2009) Identification of PpoA from Aspergillus nidulans as a fusion protein of a fatty acid heme dioxygenase/peroxidase and a cytochrome P450. J Biol Chem 284:11792–11805. https://doi.org/10.1074/jbc.M809152200
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303
Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270. https://www.jstor.org/stable/4615964
De Gannes V, Eudoxie G, Hickey WJ (2013) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Bioresour Technol 133:573–580. https://doi.org/10.1016/j.biortech.2013.01.138
Garscha U, Jernerén F, Chung D, Keller NP, Hamberg M, Oliw EH (2007) Identification of dioxygenases required for Aspergillus development. Studies of products, stereochemistry, and the reaction mechanism. J Biol Chem 282:34707–34718. https://doi.org/10.1074/jbc.M705366200
Huang YX (2015) Studies on gene expression related to carbon and nitrogen metabolism and microbial diversty during composting process. Dissertation, University of Guangxi.
Insam H, Franke-Whittle IH, Goberna M (2010) Microbes at Work. Springer, Netherlands. https://doi.org/10.1007/978-3-642-04043-6_1
Jia W, Qin W, Zhang Q, Wang X, Ma Y, Chen Q (2018) Evaluation of crop residues and manure production and their geographical distribution in China. J Clean Prod 188:954–965. https://doi.org/10.1016/j.jclepro.2018.03.300
Jiang J, Bjorck L, Fonden R (1998) Production of conjugated linoleic acid by dairy starter cultures. J Appl Microbiol 85:95–102. https://doi.org/10.1046/j.1365-2672.1998.00481.x
Jurado M, López MJ, Suárez-Estrella F, Vargas-García MC, López-González JA, Moreno J (2014) Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting. Bioresour Technol 162:283–293. https://doi.org/10.1016/j.biortech.2014.03.145
Kishino S, Ogawa J, Omura Y, Matsumura K, Shimizu S (2002) Conjugated linoleic acid production from linoleic acid by lactic acid bacteria. J Am Oil Chem Soc 79:159–163. https://doi.org/10.1007/s11746-002-0451-4
Li R, Wang Q, Zhang Z, Zhang G, Li Z, Wang L, Zheng J (2015) Nutrient trans formation during aerobic composting of pig manure with biochar prepared at different temperatures. Environ Technol 36:815–826. https://doi.org/10.1080/09593330.2014.963692
Liu N, Hou T, Yin H, Han L, Huang G (2019) Effects of amoxicillin on nitrogen transformation and bacterial community succession during aerobic composting. J Hazard Mater 362:258–265. https://doi.org/10.1016/j.jhazmat.2018.09.028
López-González JA, Suárez-Estrella F, Vargas-García MC, López MJ, Jurado MM, Moreno J (2015) Dynamics of bacterial microbiota during lignocellulosic waste composting: studies upon its structure, functionality and biodiversity. Bioresour Technol 175:406–416. https://doi.org/10.1016/j.biortech.2014.10.123
Ma S, Fang C, Sun X, Han L, He X, Huang G (2018) Bacterial community succession during pig manure and wheat straw aerobic composting covered with a semi-permeable membrane under slight positive pressure. Bioresour Technol 259:221–227. https://doi.org/10.1016/j.biortech.2018.03.054
Maeda K, Hanajima D, Toyoda S, Yoshida N, Morioka R, Osada T (2011) Microbiology of nitrogen cycle in animal manure compost. Microb Biotechnol 4:700–709. https://doi.org/10.1111/j.1751-7915.2010.00236.x
Martin M, Barbeyron T, Martin R, Portetelle D, Michel G, Vandenbol M (2015) The cultivable surface microbiota of the brown alga ascophyllum nodosumis enriched in macroalgal-polysaccharide-degrading bacteria. Front Microbiol 6:1487–1500. https://doi.org/10.3389/fmicb.2015.01487
Mason IG, Milke MW (2005) Physical modelling of the composting environment: a review. Part 1: reactor systems. Waste Manage 25:481–500. https://doi.org/10.1016/j.wasman.2005.01.016
Meng X, Liu B, Xi C, Luo X, Yuan X, Wang X, Zhu W, Wang H, Cui Z (2018) Effect of pig manure on the chemical composition and microbial diversity during cocomposting with spent mushroom substrate and rice husks. Bioresour Technol 251:22–30. https://doi.org/10.1016/j.biortech.2017.09.077
Rawoteea SA, Mudhoo A, Kumar S (2017) Co-composting of vegetable wastes and carton: effect of carton composition and parameter variations. Bioresour Technol 227:171–178. https://doi.org/10.1016/j.biortech.2016.12.019
Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30:460–465. https://doi.org/10.1038/nbt.2170
Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: a versatile open source tool for metagenomics. Peer J 4:e2584. https://doi.org/10.7717/peerj.2584
Sánchez OJ, Ospina DA, Montoya S (2017) Compost supplementation with nutrients and microorganisms in composting process. Waste Manage 69:136–153. https://doi.org/10.1016/j.wasman.2017.08.012
Shen Z, Zhong S, Wang Y, Wang B, Mei X, Li R, Ruan Y, Shen Q (2013) Induced soil microbial suppression of banana fusarium wilt disease using compost and biofertilizers to improve yield and quality. Eur J Soil Biol 57:1–8. https://doi.org/10.1016/j.ejsobi.2013.03.006
Shulaev V (2006) Metabolomics technology and bioinformatics. Brief Bioinform 7:128–139. https://doi.org/10.1093/bib/bbl012
Simonin M, Le Roux X, Poly F, Lerondelle C, Hungate BA, Nunan N, Niboyet A (2015) Coupling between and among ammonia oxidizers and nitrite oxidizers in grassland mesocosms submitted to elevated CO2 and nitrogen supply. Microb Ecol 70:809–818. https://doi.org/10.1007/s00248-015-0604-9
Simpson EH (1949) Measurement of diversity Nat 163:688. https://doi.org/10.1038/163688a0
Sun ZY, Zhang J, Zhong XZ, Tan L, Tang YQ, Kida K (2016) Production of nitrate-rich compost from the solid fraction of dairy manure by a lab-scale composting system. Waste Manage 51:55–64. https://doi.org/10.1016/j.wasman.2016.03.002
Walkley A, Black IA (1934) An examination of the degtjareff method for determining soil organic matter and a proposed modification of the chromic acid titration method. Soil Sci 37:29–38. https://doi.org/10.1097/00010694-193401000-00003
Wang Q, Wang Z, Awasthi MK, Jiang Y, Li R, Ren X, Zhao J, Shen F, Wang M, Zhang Z (2016) Evaluation of medical stone amendment for the reduction of nitrogen loss and bioavailability of heavy metals during pig manure composting. Bioresour Technol 220:297–304. https://doi.org/10.1016/j.biortech.2016.08.081
Wang K, Mao H, Wang Z, Tian Y (2018) Succession of organics metabolic function of bacterial community in swine manure composting. J Hazard Mater 360:471–480. https://doi.org/10.1016/j.jhazmat.2018.08.032
Wei H, Wang L, Hassan M, Xie B (2018) Succession of the functional microbial communities and the metabolic functions in maize straw composting process. Bioresour Technol 256:333–341. https://doi.org/10.1016/j.biortech.2018.02.050
White PJ, Brown PH (2010) Plant nutrition for sustainable development and global health. Ann Bot 105:1073–1080. https://doi.org/10.1093/aob/mcq085
Whittaker RH (1972) Evolution and measurement of species diversity. Taxon 21:213–251. https://doi.org/10.2307/1218190
Wu J, Zhao Y, Zhao W, Yang T, Zhang X, Xie X, Cui H, Wei Z (2017a) Effect of precursors combined with bacteria communities on the formation of humic substances during different material composting. Bioresour Technol 226:191–199. https://doi.org/10.1016/j.biortech.2016.12.031
Wu J, Zhao Y, Qi H, Zhao X, Yang T, Du Y, Zhang H, Wei Z (2017b) Identifying the key factors that affect the formation of humic substance during different materials composting. Bioresour Technol 244:1193–1196. https://doi.org/10.1016/j.biortech.2017.08.100
Xu X, Li H, Zhang D (2010) Microbiological priciples of composting and cultion of agaricus bisporus. Science Publishers, Beijing
Yamamoto N, Otawa K, Nakai Y (2010) Diversity and Abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting. Microb Ecol 60:807–815. https://doi.org/10.1007/s00248-010-9714-6
Zhang X, Cao Y, Tian Y, Li J (2014) Short-term compost application increases rhizosphere soil carbon mineralization and stimulates root growth in long-term continuously cropped cucumber. Sci Hortic 175:269–277. https://doi.org/10.1016/j.scienta.2014.06.025
Zhang L, Zhang H, Wang Z, Chen G, Wang L (2016) Dynamic changes of the dominant functioning microbial community in the compost of a 90 m3 aerobic solid state fermentor revealed by integrated meta-omics. Bioresour Technol 203:1–10. https://doi.org/10.1016/j.biortech.2015.12.040
Zhong X, Ma S, Wang S, Wang T, Sun Z, Tang Y, Deng Y, Kida K (2017) A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics. Bioresour Technol 247:443–452. https://doi.org/10.1016/j.biortech.2017.09.116
Zhou J (2017) Effect of turning frequency on co-composting pig manure and fungus residue. J Air Waste Manage Assoc 67:313–321. https://doi.org/10.1080/10962247.2016.1232666
Acknowledgements
This work was supported by the Key Program of Key Research and Development Project of Shanxi Province of China (Grant No. 201703D211001-05-01) and Shanxi Province Key Research and Development Projects (Grant No. 201903D221011).
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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by LL, TW and SL. The first draft of the manuscript was written by LL, The professors RH and QL commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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Liu, L., Wang, T., Li, S. et al. Combined analysis of microbial community and microbial metabolites based on untargeted metabolomics during pig manure composting. Biodegradation 32, 217–228 (2021). https://doi.org/10.1007/s10532-021-09935-0
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DOI: https://doi.org/10.1007/s10532-021-09935-0