Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

Abstract

24Remediation of industrial wastewater is important for preventing environmental 25 contamination and enabling water reuse. Biological treatment for one industrial 26 contaminant, thiocyanate (SCN -), relies upon microbial hydrolysis, but this process is 27 sensitive to high loadings. To examine the activity and stability of a microbial community 28 over increasing SCN -loadings, we established and operated a continuous-flow bioreactor 29 fed increasing loadings of SCN -. A second reactor was fed ammonium sulfate to mimic 30 breakdown products of SCN -. Biomass was sampled from both reactors for 31 metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one 32 rotifer that constituted the abundant community in both reactors. We analyzed the 33 metabolic potential and temporal dynamics of these organisms across the increasing 34 loadings. Microbial communities in biotechnology have historically been treated as black boxes, 46 but as molecular methods have improved, our knowledge of these systems has deepened. 47Increasingly, 'meta-omics' methods are being used to investigate critical processes and 48 potential weak points in biotechnology, such as nitrogen and phosphorus removal or 49 bulking in wastewater treatment. [1][2][3] In particular, specialized treatment of industrial 50 wastewater has benefited from a genome-resolved meta-omics approach 4-7 using high-51 throughput sequencing of community genomic DNA (metagenomics) or RNA 52 (metatranscriptomics), or spectral characterization of proteins (metaproteomics). These 53 data can be used to identify the key species involved in processes of interest. Improved 54 understanding of the activities and abundances of these organisms under varying 55 conditions could inform design and operation of these systems. (Figure 1) and small amounts of 5 N KOH were added directly to reactors if 100 observed pH was ≤ 6.5. Bicarbonate (4 g/L) was added to the feed to buffer the system 101 from day 112 to day 136. 102The reactors were run in batch-fed mode until SCN -degradation was stably 103 observed in the SCN -reactor, at which time both reactors were switched to continuous 104 feeding at a residence time of 42 hours (day 5). The hydraulic retention time (HRT) of 105 both reactors was lowered from 42 hours to 12 hours (days 5-68) and then maintained at 106 12 hours while the feed concentration of SCN -or equivalent NH 4 (SO 4 ) 1/2 was increased 107 stepwise. The reactor was allowed to stabilize between each step to reach steady state 108 ( Figure S1). 109 110Sampling: Samples of biomass from each reactor were taken for metagenomic 111 sequencing just before increases in feed concentration (Figure 1 and Table S1). 112Approximately 0.5 g (wet-weight) of biofilm was scraped from the wall of each reactor 113 with sterile spatula and stored at -60 C. Paired samples of planktonic biomass were 114

Genome-reconstruction for eukaryotes from complex natural microbial communities

“…(Figure 3). As previously reported (Kantor et al 2017), the Rotifer was present in seven different samples (Rotifer_A-G, Figure 3), consistent with its persistence in the thiocyanate reactor community. All seven bins shared greater than 99% ANI (Supplemental Figure S4B) indicating they are likely the same species.…”

“…To test the broader application of EukRep, we applied the method to infant fecal samples and thiocyanate reactor samples in which eukaryotes had previously been identified , Raveh-Sadka et al 2015, Kantor et al 2015, Raveh-Sadka et al 2016, Kantor et al 2017.…”

“…When the DNA sequences are assembled, tens of thousands of genome fragments may be generated, some of which derive from eukaryotes. Exceedingly few metagenomic studies have systematically identified such fragments as eukaryotic, although some genomes for microbial eukaryotes have been reconstructed , Quandt et al 2015, Kantor et al 2015, Mosier et al 2016, Raveh-Sadka et al 2016, Kantor et al 2017. In almost all cases, these genomes were recovered from relatively low diversity communities where binning of genomes is typically less challenging than in complex environments.…”

Accurate and Complete Genomes from Metagenomes

“…Case three, curation of a published incomplete genome to completion. Here we completed a published curated but incomplete genome belonging to the order Rickettsiales (Kantor et al 2017) . This genome was assembled de novo into a single circularizable 988 kbp scaffold, with two closely spaced gaps ( Figure S9a ).…”

Voltammetric Behaviors and Determination of Thiocyanate on Multiwalled Carbon Nanotubes‐Cetyltrimethylammonium Bromide Modified Electrode

“…Moreover, thiocyanate has been wildly employed in recovery of noble metals in metallurgy . It has been a widespread industrial contaminant found at especially high concentrations (up to 4000 mg/L) in gold mining effluents . Although the toxicity of thiocyanate is much smaller than that of cyanide , it can seriously influence the life of aquatic plants and animals and destroy the ecological environment when its concentration exceeds a certain degree.…”