Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

Abstract

Denitrification and dissimilatory reduction to ammonium (DNRA) are competing nitrate-reduction processes that entail important biogeochemical consequences for nitrogen retention/removal in natural and man-made ecosystems. The nature of the available carbon source and electron donor have been suggested to play an important role on the outcome of this microbial competition. In this study, the influence of lactate as fermentable carbon source on the competition for nitrate was investigated for varying ratios of lactate and nitrate in the influent (Lac/N ratio). The study was conducted in an open chemostat culture, enriched from activated sludge, under strict anoxia. The mechanistic explanation of the conversions observed was based on integration of results from specific batch tests with biomass from the chemostat, molecular analysis of the biomass enriched, and a computational model. At high Lac/N ratio (2.97 mol/mol) both fermentative and respiratory nitrate reduction to ammonium occurred, coupled to partial oxidation of lactate to acetate, and to acetate oxidation respectively. Remaining lactate was fermented to propionate and acetate. At a decreased Lac/N ratio (1.15 mol/mol), the molar percentage of nitrate reduced to ammonium decreased to 58%, even though lactate was supplied in adequate amounts for full ammonification and nitrate remained the growth limiting compound. Data evaluation at this Lac/N ratio suggested conversions were comparable to the higher Lac/N ratio, except for lactate oxidation to acetate that was coupled to denitrification instead of ammonification. Respiratory DNRA on acetate was likely catalyzed by two Geobacter species related to G. luticola and G. lovleyi. Two Clostridiales members were likely responsible for lactate fermentation and partial lactate fermentation to acetate coupled to fermentative DNRA. An organism related to Propionivibrio militaris was identified as the organism likely responsible for denitrification. The results of this study clearly show that not only the ratio of available substrates, but also the nature of the electron donor influences the outcome of competition between DNRA and denitrification. Apparently, fermentative bacteria are competitive for the electron donor and thereby alter the ratio of available substrates for nitrate reduction.

Selective carbon sources influence the end-products of microbial nitrate respiration

“…However, lower pH is associated with more growth which is consistent with organic acid production through fermentation of the sugars (Figure 3B). It is known that fermentation can compete with nitrate respiration to influence nitrate respiratory end-products( 5, 50 ), but in our enrichments this is not a dominant factor.…”

“…A predictive understanding of how environmental perturbations influence the microbially-mediated nitrogen cycle has major implications for sustainable agriculture, wastewater treatment, and toxin remediation( 1, 2 ). Previous work has demonstrated linkages between changes in carbon composition and microbial community composition( 21 - 24 ), carbon composition and respiratory end-products( 5, 10, 53 ), or community composition and respiratory end-products( 6 ). However, few studies to date have examined the dynamics of nitrate respiring microbial communities using metagenomic sequencing ( 6 ), and rarely are the dynamics of genes, strains and respiratory traits systematically linked in a high-throughput format as we have in this study.…”

“…There are some examples of different electron donors (e.g. carbon sources) determining the end-products of nitrate respiration( 5, 8 - 10 ), but less is known about the mechanistic basis for these observations. While thermodynamic calculations predict that higher concentrations of electron donor will favor DNRA over denitrification( 7 ), the specific carbon source available to drive DNRA must be utilized by the DNRA sub-populations in the system.…”

A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway

“…16S-rRNA gene sequences in the enrichment cultures were analyzed by amplicon sequencing on an Illumina HiSeq sequencer (Novogene Bioinformatics Technology Co., Ltd., Beijing, China). Primers 341F (5 -CCTAYGGGRBGCASCAG-3 ) and 805R (5 -GGACTACNNGGGTATCTAAT-3 ) were used to generate 250 bp paired end reads and sequences were analyzed as described previously (van den Berg et al, 2017). Representative sequences for the dominant operational taxonomic unites (OTUs) (>1%) were submitted for taxonomic analysis in the SILVA database (SINA, version 1.2.11 (Pruesse et al, 2012) using default settings.…”

“…The assembled genome was uploaded to the automated Microscope platform (Vallenet et al, 2006. Manual assessment of pathway annotations was assisted by the MicroCyc (Caspi et al, 2008), Kyoto Encyclopedia of Genes and Genomes (KEGG; Kanehisa et al, 2014) and SwissProt alignment (BLASTP version 2.2.28 +; Altschul et al, 1997) databases.…”