Characterization of microbial populations in two distinct dairy manure management systems: seasonal effect and implications for pollutant gases emissions

Following an increase of the demand of dairy products, higher quantities of manure are consequently produced, with the subsequent pollutant gas emission charge associated with its management. The two mostly used housing systems in the northeast of Spain, cubicles (CUB) and compost-bedded pack (CBP), entail different manure management techniques; thus, our main objective was to describe the microbiota present in manure of both systems during two distinct climatic situations (winter, mean temperature of 6.2ºC; and summer, mean temperature of 36.4ºC). The secondary aim was to correlate these microbiological profiles with literature findings on the emission of certain well-known pollutant gases from manure. CBP showed to have higher alpha biodiversity as well as presenting a remarkable clustering by season, but showed lower network complexity than CUB. Firmicutes/Bacteroidetes ratio was found superior in CUB, which also presented a significantly higher abundance of methanogenic genera belonging to Euryarchaeota phylum, such as Methanobrevibacter, Methanosaeta or Methanosarcina. On the other hand, CBP manure presented a significant presence of Corynebacterium, Pseudomonas or Truepera, among other genera, which activity has been linked to nitrogen (N) transformation pathways in manure. Season also had a relevant role to play on the fluctuation of these populations within each housing system under study. These results show how microbial populations change when manure is differently managed, and how these variations can be related to the synthesis of certain pollutant gases upon housing systems.

This research was mainly funded by Generalitat de Catalunya, Department of Agriculture, Livestock, Fisheries, and Food (S-18017). Esperanza Fuertes is the recipient of a grant from Agencia de Gestión de Ayudas Universitarias y de Investigación of Spain (FI-SDUR 2020/00031) as well as currently receiving Investigo Programme funding (2022 INV-1 00010).