Metabolic network analysis reveals microbial community interactions in anammox granules

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.

Accumulation of NO2‐cobalamin in nutrient‐stressed ammonia‐oxidizing archaea and in the oxygen deficient zone of the eastern tropical North Pacific

“…We hypothesized that anaerobic ammonium oxidizing (anammox) bacteria (Schmid et al, 2000) are another likely source of NO 2 -cobalamin within the ODZ. Anammox bacteria are one of the most active populations within the ODZ (Ulloa et al, 2012), possess the genetic capacity for cobalamin biosynthesis Lawson et al, 2017), and process RNS such as NO (Strous et al, 2006;Kartal et al, 2011). Together, these factors strongly support the possibility for NO 2cobalamin production by anammox bacteria.…”

“…Thus, considering both their environmental distribution and activity in culture, AOA are a plausible source of the observed NO 2 -cobalamin in the oxycline and the upper ODZ. Anammox bacteria are one of the most active populations within the ODZ (Ulloa et al, 2012), possess the genetic capacity for cobalamin biosynthesis Lawson et al, 2017), and process RNS such as NO (Strous et al, 2006;Kartal et al, 2011). Anammox bacteria are one of the most active populations within the ODZ (Ulloa et al, 2012), possess the genetic capacity for cobalamin biosynthesis Lawson et al, 2017), and process RNS such as NO (Strous et al, 2006;Kartal et al, 2011).…”

The social network of microorganisms — how auxotrophies shape complex communities

“…Although auxotrophies and the role of amino acid and vitamin exchange have been identified recently in several microbial communities 5,6,31,32,61 , the dynamics of these complex interaction networks have only been revealed in simple co-culture experiments. However, interactions between multiple species can change over time according to nutrient availability and proteome allocation 4 .…”

“…Increased expression of genes involved in pathways for B 1 , B 7 and B 12 synthesis in Brocadia spp. indicates that these bacteria may support the B vitamin requirements of the entire community 61 . A host-associated study evaluated the long-term persistence of the microbiota after faecal transplantation in patients infected with C. difficile 62 and identified Bacteroides spp.…”

OscoNet: Inferring oscillatory gene networks

“…Indeed, in biological networks, communities often correspond to functional units of a system. For example in metabolic networks [9], such functional groups correspond to cycles or pathways whereas in the protein-protein interaction networks [7], communities correspond to proteins with similar functionality inside a biological cell.…”