Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics

Abstract

Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM’s aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C–N and C–S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.

Acesulfame Anoxic Biodegradation Coupled to Nitrate Reduction by Enriched Consortia and Isolated Shinella spp.

“…It consisted of 83 nodes (MAGs) and 777 edges, with an average node degree connectivity of 9.59, an average path length of 1.75, and an average clustering coefficient of 0.265 (Figure a). All the proposed ACE-degrading species were classified into peripherals ( z < 2.5 and P < 0.62), implying that the direction of energy flow in ACE-degrading consortia may be distinct from that of consortia assembled under nutrient-rich environments (Figure b) . This result was also consistent with the findings that peripherals were potential degraders of recalcitrant matter .…”

“…All the proposed ACE-degrading species were classified into peripherals (z < 2.5 and P < 0.62), implying that the direction of energy flow in ACE-degrading consortia may be distinct from that of consortia assembled under nutrient-rich environments (Figure 5b). 54 This result was also consistent with the findings that peripherals were potential degraders of recalcitrant matter. 54 Interestingly, those ACE degraders were generally large genome species and could dominate in this nutrient-limited environment, probably because they occupied an indispensable niche where there was little penalty for slow growth.…”

“…54 This result was also consistent with the findings that peripherals were potential degraders of recalcitrant matter. 54 Interestingly, those ACE degraders were generally large genome species and could dominate in this nutrient-limited environment, probably because they occupied an indispensable niche where there was little penalty for slow growth. 55,56 The remaining microbes in the enriched consortia mainly fed on the metabolites or extracellular polymeric substances of the above degraders.…”

Changes of Soil Dissolved Organic Matter and Its Relationship with Microbial Community along the Hailuogou Glacier Forefield Chronosequence

“…Such negative interactions imply microbial utilization or consumption of DOM, while positive interactions imply metabolic production. This provided evidence for microbial degradation and transformation of DOM, as molecules with higher H/C ratios are generally more bio-available . Moreover, significantly increased DBE and AI mod values indicated greater aromaticity after microbial transformation …”

In Vivo Solid-Phase Microextraction and Applications in Environmental Sciences

“…The extension of reaction/structure directed analysis, namely, PMD-based reactomics, further provides the qualification and quantification methods for PMD analysis . In this case, evaluating changes in certain PMDs enables researchers to determine the reaction level changes within the sample ,, and skip the annotation of specific compounds. In addition, such reactomics analysis can also be used to generate in vivo metabolic pathways composed of connections among metabolites based on high-frequency PMDs.…”