Monitoring the Microbiomes of Agricultural and Food Waste Treating Biogas Plants over a One-Year Period  
[PERSON]  
1 Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE),  
Waste to Roproducts-Lab, University of Padova, Agripolis, Vale dell'Universita 16, 35020 Legnaro, PD, Italy;  
[EMAIL_ADDRESS] (S.A.); [EMAIL_ADDRESS] (L.F)  
[PERSON]  
2 Department of Biology (DIBio), University of Padova, Via U. Bassi 58/b, 35121 Padova, PD, Italy;  
[EMAIL_ADDRESS] (F.M.); [EMAIL_ADDRESS] (S.C.)  
[PERSON]  
3S.E.S.A. S.P.A., Via Comuna 5/b, 35042 Este, PD, Italy; [EMAIL_ADDRESS] (M.Z.);  
padoandeseseseste1 (D.P)  
3 Cited for 3 Cited  
The efficiency of the process is heavily reliant on the composition of the microbiome, making the understanding of microbial structure a crucial aspect for optimizing digestion and increasing methane yield [6]. Therefore, extensive research has been conducted to comprehend anaerobic communities and elucidate the biological roles of the species involved [7]. The emergence of new generation sequencing (NGS) technologies and the advancements in the field of bioinformatics facilitated the exploration of microbial population structures and the study of metabolic potential within the anaerobic microbiomes. Specifically, this approach can examine the evolution of communities under specific process conditions, and it can follow the dynamicity of populations through a snapshot analysis [8]. 16S rRNA gene sequencing provides a rapid response on the most abundant species in the biogas system, while the whole genome analysis (metagenomic) offers a deeper knowledge on the bacteria and archaea populating the community by assembling genomes to Metagenome Assembled Genomes (MAGs) [9]. However, despite the numerous studies, a more extensive comprehension of the functional activity of single microbes and the microbial interactions in the AD system remains a relevant challenge.  
AD community and performance efficiency are influenced by the source of inoculum, as well as the processed substrates [8; 10]. However, [PERSON] et al. [11] have revealed the existence of a functional core of microorganisms common to various biogas plants. As such, the exploration of AD ecology may help in the comprehension of the correlation between substrate and anaerobic microbiomes. Changes in substrate composition or organic source overload can cause alterations in the microbial structure, resulting in process imbalances and modification of the microbiome's stability [12; 13]. As a result, ongoing studies are focused on understanding the relationship between feedstock macrostructure and the bacterial and archaeal communities [14; 15].  
Nowadays, in Italy, most biogas plants co-digest residues from farms and agro-food industries, such as sewage, manure, silages, or vegetables [16; 17]. As such, to investigate the microbiome compositions of anaerobic digestors treating feedstocks mostly adopted in Italy, four full-scale anaerobic biogas digesters, three treating agricultural and zootechnical residues into biogas, and one dealing with the organic fraction of municipal solid waste (OFMSW) were specifically selected in this study. The final goal is to elucidate at what level the different substrates shape the microbial compositions of AD plants. Such insight will be relevant towards a deeper understanding of the role of microbes in boosting biogas yields from different waste streams.