Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns

Formate: A promising electron donor to enhance trichloroethene-to-ethene dechlorination in Dehalococcoides-augmented groundwater ecosystems with minimal bacterial growth

Various substrates have been used to stimulate habitat microbes in chloroethene-contaminated groundwater, however, the specific efficiency and minimum growth of microbes have rarely been studied. This study investigated the effects of seven substrates on trichloroethene (TCE) dechlorination by augmentation of groundwater with Dehalococcoides mccartyi NIT01 and its contribution to the microbial community. Three out of eight test groups completed dechlorination of 1 mM TCE-to-ethene in varying durations; groundwater supplemented with formate (FOR) required 78 days, whereas the microcosms with lactate (LAC) and citrate (CIT) required approximately twice as long (143 days). The calculated efficiency of how much produced H₂ was used in dechlorination indicated a higher efficiency in FOR (36%) compared with LAC (1.9%) or CIT (2.9%). FOR showed lower microbial growth (3.4 × 10⁵ copies/mL) than LAC (1.5 × 10⁶) or CIT (4.4 × 10⁶), and maintained a higher Shannon diversity index (5.65) than LAC (4.97) and CIT (4.30). The rapid and higher H₂ transfer efficiency with lower bacterial growth by using formate was attributed to the slightly positive Gibbs free energy identified in H₂ production requiring a H₂-utilizer, lower carbon in the molecule, and adaptation to metabolic potential of the original groundwater microbiome. Formate is, therefore, a promising electron donor for rapid Dehalococcoides-augmented remediation with minimum bacterial growth. Sequential transferring of the FOR culture successfully maintained TCE-to-ethene dechlorination activity and enriched the members of genera Dehalococcoides (33%), Methanosphaerula (23%), Rectinema (13%), and Desulfitobacterium (5.6%). This suggests that formate is transferred to H₂ and acetate, and provided to Dehalococcoides.

Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes

Soybean root nodules are known to contain a high diversity of both rhizobial endophytes and nonrhizobial endophytes (NREs). Nevertheless, the variation of these bacteria among different root nodules within single plants has not been reported. So far, it is unclear whether the selection of NREs among different root nodules within single plants is a random process or is strictly controlled by the host plant to favor a few specific NREs based on their beneficial influence on plant growth. As well, it is also unknown if the relative frequency of NREs within different root nodules is consistent or if it varies based on the location or size of a root nodule. We assessed the microbiomes of 193 individual soybean root nodules from nine plants using high-throughput DNA sequencing. Bradyrhizobium japonicum strains occurred in high abundance in all root nodules despite the presence of other soybean-compatible rhizobia, such as Ensifer, Mesorhizobium, and other species of Bradyrhizobium in soil. Nitrobacter and Tardiphaga were the two nonrhizobial genera that were uniformly detected within almost all root nodules, though they were in low abundance. DNA sequences related to other NREs that have frequently been reported, such as Bacillus, Pseudomonas, Flavobacterium, and Variovorax species, were detected in a few nodules. Unlike for Bradyrhizobium, the low abundance and inconsistent occurrence of previously reported NREs among different root nodules within single plants suggest that these microbes are not preferentially selected as endophytes by host plants and most likely play a limited part in plant growth as endophytes.IMPORTANCE Soybean (Glycine max L.) is a valuable food crop that also contributes significantly to soil nitrogen by developing a symbiotic association with nitrogen-fixing rhizobia. Bacterial endophytes (both rhizobial and nonrhizobial) are considered critical for the growth and resilience of the legume host. In the past, several studies have suggested that the selection of bacterial endophytes within root nodules can be influenced by factors such as soil pH, nutrient availability, host plant genotype, and bacterial diversity in soil. However, the influence of size or location of root nodules on the selection of bacterial endophytes within soybean roots is unknown. It is also unclear whether the selection of nonrhizobial endophytes within different root nodules of a single plant is a random process or is strictly regulated by the host. This information can be useful in identifying potential bacterial species for developing bioinoculants that can enhance plant growth and soil nitrogen.

Organohalide-Respiring Bacteria in Polluted Urban Rivers Employ Novel Bifunctional Reductive Dehalogenases to Dechlorinate Polychlorinated Biphenyls and Tetrachloroethene

Polluted urban river sediments could be a sink of persistent and toxic polychlorinated biphenyls (PCBs) in urban areas and provide desired growth niches for organohalide-respiring bacteria (OHRB). In this study, microcosms were set up with surface sediments of nationwide polluted urban rivers in China, of which 164 cultures could dechlorinate tetrachloroethene (PCE) to dichloroethenes (DCEs) and to vinyl chloride and/or ethene. Further in vivo tests showed extensive PCB dechlorination with different pathways in 135 PCE pregrown cultures. Taking reductive dechlorination of PCB180 (2345-245-CB) as an example, 121 and 14 cultures preferentially removed flanked para- and meta-chlorines, respectively. Strikingly, all in vitro assays with the 135 PCE pregrown cultures showed identical PCB dechlorination pathways with their living cultures, implying the involvement of bifunctional reductive dehalogenases (RDases) to dechlorinate both PCBs and PCE. Further 16S rRNA and RDase gene-based analyses, together with enantioselective dechlorination of chiral PCBs, suggested that Dehalococcoides and Dehalogenimonas in the 135 cultures largely employed distinctively different novel bifunctional RDases to catalyze PCB/PCE dechlorination. Quantitative assessment of the community assembly process with the modified stochasticity ratio (MST) indicated three different stages in enrichment of OHRB. The second stage, as the only one controlled by stochastic processes (MST > 0.5), required extra attention in monitoring community successional patterns to minimize stochastic variance for enriching the PCB/PCE-dechlorinating OHRB.

Transport and release of electron donors and alkalinity during reductive dechlorination by combined emulsified vegetable oil and colloidal Mg(OH)2: Laboratory sand column and microcosm tests

Emulsified vegetable oil combined with colloidal Mg(OH)₂ (EVO-CM) can slowly release electron donors and OH^- into groundwater and is therefore regarded as a promising amendment for enhanced in situ treatment of chlorinated solvents, such as tetrachloroethene (PCE) and trichloroethene (TCE). However, its migration ability in different porous media and the simultaneous release of electron donor and pH buffer during enhanced reductive dechlorination (ERD) have never been evaluated in detail. In this study, EVO-CM with uniform drop size and desirable stability was prepared. Laboratory-scale column tests were conducted to investigate the transport and spatial distribution of the EVO-CM in different porous media. Batch microcosm experiments were carried out to study the dechlorination efficiency under different EVO:Mg(OH)₂ ratios. Experimental results indicate that prepared EVO-CM emulsions can be transported effectively through different porous media with grain size ranging from 0.1-1.0 mm. The emulsified vegetable oil (EVO) and colloidal Mg(OH)₂ showed synchronous movement through the porous media column systems, providing both electron donor and alkalinity at the same location. The retention degree of EVO-CM is greater in the finer grained media and decreases with increasing distance from the inlet. The injection of EVO-CM lead to a significant mobilization of TCE in the column. The reductive dechlorination of TCE in the microcosms was remarkably enhanced in the presence of EVO-CM. The coaddition of sufficient colloidal Mg(OH)₂ effectively limits the deleterious pH decline caused by acid release. The microcosm achieves an optimum dechlorination efficiency when the EVO:Mg(OH)₂ ratio is 1:1.

Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor

A trichloroethene (TCE)-dechlorinating community (CANAS) maintained in a completely mixed flow reactor was established from a semi-batch enrichment culture (ANAS) and was monitored for 400 days at a low solids retention time (SRT) under electron acceptor limitation. Around 85% of TCE supplied to CANAS (0.13 mmol d^-1) was converted to ethene at a rate of 0.1 mmol d^-1, with detection of low production rates of vinyl chloride (6.8 × 10^-3 mmol d^-1) and cis-dichloroethene (2.3 × 10^-3 mmol d^-1). Two distinct Dehalococcoides mccartyi strains (ANAS1 and ANAS2) were stably maintained at 6.2 ± 2.8 × 10⁸ cells mL^-1 and 5.8 ± 1.2 × 10⁸ cells mL^-1, respectively. Electron balance analysis showed 107% electron recovery, in which 6.1% were involved in dechlorination. 16 S rRNA amplicon sequencing revealed a structural regime shift between ANAS and CANAS while maintaining robust TCE dechlorination due to similar relative abundances of D. mccartyi and functional redundancy among each functional guild supporting D. mccartyi activity. D. mccartyi transcriptomic analysis identified the genes encoding for ribosomal RNA and the reductive dehalogenases tceA and vcrA as the most expressed genes in CANAS, while hup and vhu were the most critical hydrogenases utilized by D. mccartyi in the community.