Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine

Abstract

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability.

Response of lotic microbial communities to altered water source and nutritional state in a glaciated alpine floodplain

“…PCR products were subjected to electrophoresis on a 2% agarose gel with a 100 base pair (bp) ladder (Promega) and stained with ethidium bromide to verify successful amplification. ARISA fragments were processed as previously described (Bü rgmann et al 2011). A 1 mL aliquot of PCR product was mixed with 9 mL highly deionized (HiDi) formamide and 0.5 mL Liz1200 size standard (Applied Biosystems) followed by denaturation on a PCR thermocycler for 3 min at 95uC.…”

Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake

“…In all, 1:10 dilutions of DNA extracts were subjected to ARISA using general bacterial primers (Supplementary Table S1) and PCR conditions according to Yannarell et al (2003) with slight modifications (Bü rgmann et al, 2011). A total of 10 ng ml À 1 of Escherichia coli DNA served as a positive control, 10 ng ml À 1 of salmon sperm DNA and nuclease-free water served as no template control and PCR blank, respectively.…”

“…Samples were run on an ABI 3130xl capillary sequencer as described previously (Bü rgmann et al, 2011). Data analysis was performed using Gene Mapper Software version 4.0 (Applied Biosystems) considering only peaks with sizes between 350 and 1250 bp and a minimum peak height of 125 fluorescence units.…”

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

“…DNA was amplified using the fluorescein (6-FAM)-labeled universal forward primer 1406f-6FAM and the bacteria-specific reverse primer 23Sr (Yannarell et al, 2003). ARISA fragment analysis was performed as described in Bü rgmann et al (2011).…”