Microbialites are an example of complex and diverse microbial assemblages where several metabolic pathways are interconnected for biomass formation coupled to mineral precipitation. Lake Alchichica (Mexico) is an oligotrophic environment where nitrogen (N) and phosphorus alternately limit productivity, and massive microbialite growths are found along the lake's perimeter. Previous studies have described the importance of N2 fixation in these microbialites, although other pathways associated with the N cycle, including denitrification, nitrification and anaerobic ammonium oxidation (anammox), had not been evaluated. This study identified the genetic diversity associated with N cycling in both metagenomic DNA and RNA expression by targeting key genes for nitrogenase (nifH), ammonia monooxygenase (amoA), nitrite oxidoreductase (nxrA, nxrB), hydrazine oxidoreductase (hzo) and nitrite (nirS and nirK) and nitrous oxide (nosZ) reductases. While the genetic potential for N2 fixation, ammonia oxidation, anammox and denitrification was present in the microbialites of Lake Alchichica, the most transcribed pathway was N2 fixation.

Anaerobic digestion of organic residues offers economic benefits via biogas production, still methane (CH₄ ) yield relies on the development of a robust microbial consortia for adequate substrate degradation, among other factors. In this study, we monitor biogas production and changes in the microbial community composition in two semi-continuous stirred tank reactors during the setting process under mesophilic conditions (35°C) using a 16S rDNA high-throughput sequencing method. Reactors were initially inoculated with anaerobic granular sludge from a brewery wastewater treatment plant, and gradually fed organic urban residues (4·0 kg VS m^-3  day^-1 ) . The inocula and biomass samples showed changes related to adaptations of the community to urban organic wastes including a higher relative proportion of Clostridiales, with Ruminococcus spp. and Syntrophomonas spp. as recurrent species. Candidatus Cloacamonas spp. (Spirochaetes) also increased from ~2·2% in the inoculum to >10% in the reactor biomass. The new community consolidated the cellulose degradation and the propionate and amino acids fermentation processes. Acetoclastic methanogens were more abundant in the reactor, where Methanosaeta spp. was found as a key player. This study demonstrates a successful use of brewery treatment plant granular sludge to obtain a robust consortium for methane production from urban organic solid waste in Mexico.

Significance and impact of the study

This study describes the selection of relevant bacteria and archaea in anaerobic digesters inoculated with anaerobic granular sludge from a brewery wastewater treatment plant. Generally, these sludge granules are used to inoculate reactors digesting organic urban wastes. Though, it is still not clearly understood how micro-organisms respond to substrate variations during the reactor start-up process. After feeding two reactors with organic urban residues, it was found that a broader potential for cellulose degradation was developed including Bacteroidetes, Firmicutes and Spirochaetes. These results clarify the bacterial processes behind new reactors establishment for treating organic wastes in urban areas.