Novel nitrifiers and comammox in a full-scale hybrid biofilm and activated sludge reactor revealed by metagenomic approach

Abstract

Biofilms are widely used in wastewater treatment for their particular enhancement of nitrogen removal and other significant advantages. In this study, the diversity and potential functions of nitrogen removal bacteria in suspended activated sludge (AS) and biofilm of a full-scale hybrid reactor were uncovered by metagenomes (∼34 Gb), coupled with PCR-based 454 reads (>33 K reads). The results indicated that the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in AS, while more nitrification and denitrification genes were indeed found in biofilm than AS, suggesting that the increased nitrogen removal ability by applying biofilm might be attributed to the enhancement of removal efficiency, rather than the biomass accumulation of nitrogen removal bacteria. The gene annotation and phylogenetic analysis results revealed that AS and biofilm samples consisted of 6.0 % and 9.4 % of novel functional genes for nitrogen removal and 18 % and 30 % of new Nitrospira species for nitrite-oxidizing bacteria, respectively. Moreover, the identification of Nitrospira-like amoA genes provided metagenomic evidence for the presence of complete ammonia oxidizer (comammox) with the functional potential to perform the complete oxidation of ammonia to nitrate. These findings have significant implications in expanding our knowledge of the biological nitrogen transformations in wastewater treatment.

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

“…Furthermore, it is possible that the Nitrospira co-occurring with Candidatus Brocadia were Nitrospira species with the genetic potential for comammox, as a fluorescence in-situ hybridization study confirmed the extensive aggregation of the 2 phylotypes in hypoxic conditions (<3.1 µM O 2 ) (Van Kessel et al, 2015). Despite Nitrospira comammox being identified in numerous aquatic environments (Chao et al, 2016; Daims et al, 2015; Pinto et al, 2016), we cannot conclusively identify comammox without sequencing the ammonia monooxygenase gene (Pinto et al, 2016; Van Kessel et al, 2015). …”

The pH dependency of N‐converting enzymatic processes, pathways and microbes: effect on net N2O production

“…NirK, the gene for Cu-NIR, is also present in comammox, but no evidence of NO accumulation in comammox enrichments cultures suggests that nitrite reduction may not be particularly robust (Daims et al, 2015). Comammox have been found in different water engineered systems, including WWTPs (Chao et al, 2016;Gonzalez-Martinez et al, 2016;Pjevac et al, 2017). However, their abundance in wastewater treatment plants is lower than AOB, which is likely due to the competitive advantage of AOB in systems with high substrate concentrations (Costa et al, 2006;Kits et al, 2017).…”

User Response – Based Sustainable Solutions to Traffic Congestion Problem using Public Transport: The Case of Uttara, Dhaka

“…In the latter case, Chao et al (2016) [3], have emphasized that the biofi lm in aerobic reactors is exposed to the dissolved oxygen (DO) concentration gradient, which may induce the growth of comammox bacteria. Earlier cross-section studies of biomass distribution in nitrifying biofi lm systems (Okabe et al 1999) found the highest NOB abundance in deeper zones with less DO availability.…”

“…All comammox organisms identifi ed to date belong to "Candidatus Nitrospira nitrosa", "Candidatus Nitrospira nitrifi cans", "Candidatus Nitrospira inopinata", and Nitrospira sp. strain Ga0074138 [2,13] [3,13]. However, the metagenomics analysis does not provide information about the activity of those bacteria.…”

“…In contrast, in biofi lms and other microbial aggregates with low substrate diffusion gradients and low mixing of biomass (clonal clusters), a higher yield of biomass per amount of substrate consumed (which is equivalent to a more economical use of resources) would benefi t only the neighborhood. Therefore, under a broad range of favourable conditions in biofi lms, more economical (but slower-growing organisms) would have a higher fi tness than resource-wasting, fast-growing competitors.The hypothesis of Costa et al [1], was supported by the very recent discoveries of bacteria capable of performing comammox (complete ammonia oxidation) in an aquaculture system (van Kessel et al 2015) and deep subsurface pipe [2], and subsequently in a bioactive fi lter at a drinking water treatment plant (Pinto et al 2015) and a WWTP [3]. In the latter case, Chao et al (2016) [3], have emphasized that the biofi lm in aerobic reactors is exposed to the dissolved oxygen (DO) concentration gradient, which may induce the growth of comammox bacteria.…”