Metabolic network analysis reveals microbial community interactions in anammox granules - PubMed (original) (raw)
Metabolic network analysis reveals microbial community interactions in anammox granules
Christopher E Lawson et al. Nat Commun. 2017.
Abstract
Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions. We find that Chlorobi-affiliated bacteria may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate to nitrite. Other heterotrophs may also contribute to scavenging of detritus and peptides produced by anammox bacteria, and potentially use alternative electron donors, such as H2, acetate and formate. Our findings improve the understanding of metabolic activities and interactions between anammox and heterotrophic bacteria and offer the first transcriptional insights on ecosystem function in anammox granules.
Conflict of interest statement
The authors declare no competing financial interests.
Figures
Figure 1. Phylogenetic tree of all recovered draft genomes from the anammox bioreactor.
Tree includes MAGs recovered from this study (red) and closely related genomes downloaded from the NCBI genome repository. GenBank accession numbers for each genome are provided in parentheses. Branch node numbers represent bootstrap support values. The tree was constructed using RAxML based on a set of 37 concatenated universal single-copy marker genes.
Figure 2. Abundance and gene expression of organisms represented by the MAGs recovered from the anammox bioreactor.
Abundance and gene expression estimates were based on RPKM values of metagenomic reads and transcripts that mapped to each MAG, respectively. See Supplementary Table 2 for mapping details.
Figure 3. Presence and expression of denitrification genes across the recovered heterotrophic genomes.
Purple arrows indicate gene presence. Colour intensity represents gene expression (log2 RPKM), based on mapping of metatranscriptomic reads to the metagenomic assembly. An outlined white arrow indicates one or more enzyme subunits had no detectable gene expression. A summary of genes involved in denitrification across the recovered genomes can be found in Supplementary Data 4.
Figure 4. Relative gene expression of major carbon and energy metabolic pathways encoded by each MAG.
Colour intensity represents gene expression, based on mapping of metatranscriptomic reads to the metagenomic assembly. Gene expression was relativized by median RPKM values calculated across each ORF in a given MAG (Methods section). A value of 1 equals median expression in a given genome. Yellow box indicates pathway absence. Anammox metabolic pathway in the AMX1 genome had a relative expression value of 15. See Supplementary Data 3 for a detailed summary of all reconstructed metabolic pathways.
Figure 5. Predicted peptidases and amino acid transporters recovered from the MAGs.
(a) Number (bubble diameter) and relative gene expression (bubble colour intensity) of selected peptidases possibly involved in EPS matrix protein degradation. Peptidases were annotated against the MEROPS database. The subcellular location (extracellular, outer membrane or peroplasm) of each peptidase was predicted using the subcellular localization predictor (CELLO). A summary of all predicted peptidases can be found in Supplementary Data 5. (b) Number (bubble diameter) and relative gene expression (bubble colour intensity) of amino acid and peptide transporters predicted across the recovered genomes. Transporters were annotated against the transporter classification database (TCDB) and can be found in Supplementary Data 2.
Figure 6. Relative gene expression of amino acid biosynthetic and degradation pathways encoded by each MAG.
Red colour intensity represents gene expression, which was relativized by median RPKM values calculated across each ORF in a given MAG. A value of 1 equals median expression. Top, middle and bottom panels separate amino acids by hydrophilic, hydrophobic and special structured side chains, respectively. Bracketed numbers rank the metabolic cost of amino acid biosynthesis based on values reported by Akashi and Gojobori, with 1 being the most costly.
Figure 7. Proposed metabolic interactions between Brocadia (AMX1) and Chlorobi (CHB1) in anammox granules.
AMX1 fixes CO2 and synthesizes amino acids and EPS. CHB1 degrades proteins bound in EPS using extracellular peptidases and subsequently transports and catabolizes short peptides (circles) to central carbon intermediates. Nitrite oxidation and reduction by AMX1 and CHB1, respectively, results in a distributed nitrite loop. Purple arrows indicate nitrogen cycling; orange arrows indicate carbon cycling; light blue arrows indicate vitamin B metabolite exchange. Hatched ovals indicate peptidases. BCAA, branched-chain amino acids. Met(?), methionine synthase present in genome but other steps involved in Met biosynthesis not identified. The presence of a periplasm has been ignored for clarity of the schematic.
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