Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil

Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the ∼100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process.

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 studyThis 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

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process.

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 studyThis 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

Genetic diversity associated with N-cycle pathways in microbialites from Lake Alchichica, Mexico

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 N 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 N fixation, ammonia oxidation, anammox and denitrification was present in the microbialites of Lake Alchichica, the most transcribed pathway was N fixation. 2 2

Genetic diversity associated with N-cycle pathways in microbialites from Lake Alchichica, Mexico

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

ESICM LIVES 2016: part two : Milan, Italy. 1-5 October 2016.

Meeting abstrac