Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology ofNitrospiraspp.

Abstract

Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammoxNitrospirain the environment

“…The amoA qPCR-based detection of both comammox Nitrospira and AOB, as well as the absence of AOA, in WWTP VetMed are consistent with an earlier analysis of the same sample based on metagenomics and rRNA-targeted FISH (Daims et al, 2015).The qPCR-based dominance of clade A and B comammox Nitrospira over AOB (p < 0.01) in GWW Wolfenbüttel (Figure 2, Table S2) is in line with the previous metagenomic detection of both clades in samples from the same system (Daims et al, 2015). Altogether, the results obtained in this and other studies (Daims et al, 2015;van Kessel et al, 2015;Palomo et al, 2016;Pinto et al, 2016;Bartelme et al, 2017;Wang et al, 2017) for wastewater and drinking water treatment plants suggest that comammox Nitrospira have to be considered in future studies of nitrification in engineered systems. Likewise, the relative abundances of comammox amoA genes in comparison to those of AOA and AOB in the two soils (Figure 2) indicate that comammox organisms should not be neglected in research on terrestrial nitrifiers.…”

“…They are widespread in virtually all oxic natural and engineered ecosystems, and an impressively high diversity of coexisting uncultured Nitrospira strains has been detected in wastewater treatment plants and soils (Pester et al, 2014;GruberDorninger et al, 2015). All known comammox organisms belong to Nitrospira sublineage II (Daims et al, 2015;van Kessel et al, 2015;Palomo et al, 2016;Pinto et al, 2016). This sublineage contains also canonical NOB, which lack the genes for ammonia oxidation (Daims et al, 2001;Koch et al, 2015).…”

Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

“…Demultiplexed contigs were annotated using the UBLAST program in USEARCH v8.1.1861 (69) against the KEGG database (70) for the metabolic pathway prediction and against the carbohydrate active enzyme (CAZy) database (71) for the CAZyme analysis separately. For each contig, the best hit with an E value of Ͻ1eϪ5, bit score of Ͼ60, and sequence identity of Ͼ30% was used for annotation identification (72). For the metabolic pathway analysis, mRNAs were mapped to annotated contigs with KEGG information using the UBLAST program with an E value of 1eϪ5 as the cutoff.…”

Complete nitrification: insights into the ecophysiology of comammox Nitrospira

“…In addition, analyzing metagenome-assembled genomes (MAGs) of clade B comammox Nitrospira gave first genomic insights into this group so far missing a cultured representative (Orellana et al 2018; Palomo et al 2018). Since the discovery of complete nitrifying Nitrospira , numerous studies have addressed their environmental distribution and abundance (e.g., Bartelme et al 2017; Fowler et al 2018; Hu and He 2017; Orellana et al 2018; Pjevac et al 2017) as well as their potential metabolic capabilities by (meta) genomic analyses (e.g., Camejo et al 2017; Orellana et al 2018; Palomo et al 2016; Palomo et al 2018; Wang et al 2017). Additionally, physiological investigations of the first comammox pure culture revealed vital insights into the nitrification kinetics of complete compared to canonical nitrifiers (Kits et al 2017).…”