Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

BACKGROUD

The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated.

RESULTS

The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus.

CONCLUSION

The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Response of sulfide autotrophic denitrification process and microbial community to oxytetracycline stress

The coexistence of antibiotics with sulfide and nitrate is common in sewage. Thus, this study explored the removal performance of nitrate and sulfide, and the response of extracellular polymer substances (EPS) and the microbial community to the sulfide autotrophic denitrification (SAD) process under oxytetracycline (OTC) stress. In Phase Ⅰ, the SAD system showed favouranle performance (nitrate removal rate ＞ 92.57%, sulfide removal rate ＞ 97.75%). However, in Phase Ⅳ, at OTC concentrations of 10, 15, and 20 mg/L, the NRE decreased to 76.13%, 40.71%, 11.37%, respectively, and the SRE decreased to 97.58%, 97.09%, 92.84%, respectively. At OTC concentrations of 0, 10, 15, and 20 mg/L, the EPS content were 1.62, 1.75, 2.03, and 1.42 mg/gVSS, respectively. The results showed that SAD performance gradually deteriorated under OTC stress. In particular, when the OTC concentration was 20 mg/L, the EPS content was lower than that of the control test, which could be attributed to the occurrence of microbial death. Finally, high-throughput sequencing results showed that OTC exposure led to gradual domination by heterotrophic denitrifying bacteria.

Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications

The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.

Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"

Anaerobic ammon ium oxidizing (anammox) bacteria oxidize ammonium and reduce nitrite, producing N₂, and could play a major role in energy-optimized wastewater treatment. However, sensitivity to various environmental conditions and slow growth currently hinder their wide application. Here, we attempted to determine online the effect of environmental stresses on anammox bacteria by using an overnight batch activity test with whole cells, in which anammox activity was calculated by quantifying N₂ production via headspace-pressure monitoring. A planktonic mixed culture dominated by "Candidatus Kuenenia stuttgartiensis" strain CSTR1 was cultivated in a 30-L semi-continuous stirring tank reactor. In overnight resting-cell anammox activity tests, oxygen caused strong inhibition of anammox activity, which was reversed by sodium sulfite (30 µM). The tested antibiotics sulfamethoxazole, kanamycin, and ciprofloxacin elicited their effect on a dose-dependent manner; however, strain CSTR1 was highly resistant to sulfamethoxazole. Anammox activity was improved by activated carbon and Fe₂O₃. Protein expression analysis from resting cells after anammox activity stimulation revealed that NapC/NirT family cytochrome c (KsCSTR_12840), hydrazine synthase, hydrazine dehydrogenase, hydroxylamine oxidase, and nitrate:nitrite oxidoreductase were upregulated, while a putative hydroxylamine oxidoreductase HAO (KsCSTR_49490) was downregulated. These findings contribute to the growing knowledge on anammox bacteria physiology, eventually leading to the control of anammox bacteria growth and activity in real-world application. KEY POINTS: • Sulfite additions can reverse oxygen inhibition of the anammox process • Anammox activity was improved by activated carbon and ferric oxide • Sulfamethoxazole marginally affected anammox activity.

Draft Genome Sequence of a Sulfur-Oxidizing Bacterium, Aquamicrobium lusatiense NLF2-7, Isolated from Livestock Wastewater

Here, we report the draft genome sequence of Aquamicrobium lusatiense NLF2-7, a Gram-negative, aerobic, non-flagellum-forming, rod-shaped bacterium that was isolated from livestock wastewater in South Korea. The assembled genome sequence is 5,201,486 bp, with 4,972 protein-coding sequences in 12 contigs, and possess the genes for the sulfur oxidation pathway.

Aerobic naphthenic acid-degrading bacteria in petroleum-coke improve oil sands process water remediation in biofilters: DNA-stable isotope probing reveals methylotrophy in Schmutzdecke

There is an increasing interest in treatment of oil sands process water (OSPW) via biofiltration with petroleum coke (PC) as a substratum. In fixed bed biofilters (FBBs) with PC, the dominance of anaerobic digestion of dissolved organics results in poor removal of naphthenic acids (NAs) along with a high degree of methanogenesis. In this study, the operation of FBBs was modified to improve OSPW remediation by supporting the filtering bed with aerobic naphthenic acid-degrading bacteria treating aerated OSPW (FBB_{bioaugmentation}). The results were compared with a biofilter operated under controlled conditions (FBB_control). To this end, a consortium of three aerobic NAs-degrading bacterial strains was immobilized on PC as a top layer (10 cm). These bacteria were pre-screened for growth on 15 different NAs surrogates as a sole carbon source, and for the presence of catabolic genes coding alkane hydroxylase (CYP153) and alkane monooxygenase (alkB) enzymes. The results illustrated that biofiltration in FBB_{bioaugmentation} removed 32% of classical NAs in 15 days; while in the FBB_control, degradation was limited to 19%. The degradation of fluorophore (aromatic) compounds was also improved from 16% to 39% for single ring (O_I), 22% to 29% for double ring (O_II), and 15% to 23% for three rings (O_III) compounds. DNA-Stable Isotope Probing revealed that potential hydrocarbons degraders such as Pseudomonas (inoculated), Pseudoxanthomonas (indigenous) were present up to 9.0% in the ¹³C-labelled DNA fraction. Furthermore, a high abundance of methylotrophs was observed in the Schmutzdecke, with Methylobacillus comprising more than two-third of the total community. This study shows that bioaugmentation rapidly improved OSPW remediation. Aeration mostly contributed to methane consumption in the top layer, thus minimizing its release into the environment.

Aquamicrobium zhengzhouense sp. nov., a Bacterium Isolated from Farmland Soil Applied with Amino Acid Fertilizer

A novel Gram-stain-negative, rod-shaped, strictly aerobic, non-motile bacterium, designated strain cd-1^T, was isolated from a farmland soil applied with amino acid fertilizer in Zhengzhou, Henan province, China. The optimum growth of strain cd-1^T occurred at 30 °C, pH 7.0 in Luria-Bertani (LB) broth without NaCl supplement. Phylogenetic analysis based on 16S rRNA gene sequences indicated that cd-1^T is member of the genus Aquamicrobium, and formed a separate branch with Aquamicrobium aerolatum DSM 21857^T (96.5%) and Aquamicrobium soli KCTC 52165^T (95.7%). The draft genome sequencing revealed a DNA G + C content of 59.2 mol% and Q-10 was the predominant respiratory quinone. The major cellular fatty acids were identified as C_18:1 ω7c (35.8%), C_19:0 cyclo ω8c (32.1%), and C_18:1 ω7c 11-methyl (5.2%). The polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. Average nucleotide identity (ANI) and the digital DNA-DNA hybridizations (dDDH) for draft genomes between strain cd-1^T and KCTC 52165^T were 71.0% and 19.9%, respectively, the values for strain cd-1^T and DSM 21857^T were 73.4% and 20.6%. Based on the physiological and biochemical characteristics, phylogenetic and chemotaxonomic analysis, strain cd-1^T is considered to represent a novel species of the genus Aquamicrobium, for which the name Aquamicrobium zhengzhouense sp. nov. is proposed. The type strain is cd-1^T (= KCTC 82182^T = CCTCC M 2018904^T).

Chronic endophthalmitis from Aquamicrobium lusatiense

Purpose

To report a case of chronic endophthalmitis caused by Aquamicrobium lusatiense following phacoemulsification surgery.

Observations

A 71 year-old woman was referred for chronic ocular inflammation after cataract surgery. Serologic testing was negative for common infectious etiologies. Her condition deteriorated on immune-modulating therapy prompting vitreous biopsy, which confirmed infection with A. lusatiense. She was managed successfully with intravitreal antibiotic pharmacotherapy and intraocular lens explantation.

Conclusion and Importance

This is the first reported case of A. lusatiense causing endophthalmitis, or disease in a human, in the literature.

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods

Water and soil contamination by industrial wastes is a global concern. Biological treatment of industrial wastewater using bioreactors allows the removal of organic matter and nutrients and enables either reuse or safe discharge. Wastewater bioremediation depends in part on the microbial communities present in the bioreactor. To ascertain which communities may play a role in the remediation process, the present study investigates the microbial community structure and diversity of microorganisms found in a full-scale membrane bioreactor (MBR) for industrial wastewater treatment. The study was carried out using high-throughput data observations following a failure (crash) of the MBR and during the extended recovery of the process. Results revealed a positive correlation between the MBR's ability to remove organic matter and its microbial community richness. The significant changes in relative microbial abundance between crash and recovery periods of the MBR revealed the important role of specific bacterial genera in wastewater treatment processes. A whole-genome metagenomics based comparison showed a clear difference in microbial makeup between two functional periods of MBR activity. The crash period was characterized by abundance in bacteria belonging to Achromobacter, Acinetobacter, Halomonas, Pseudomonas and an uncultured MBAE14. The recovery period on the other hand was characterized by Aquamicrobium and by Wenzhouxiangella marina. Our study also revealed some interesting functional pathways characterizing the microbial communities from the two periods of bioreactor function, such as Nitrate and Sulfate reduction pathways. These differences indicate the connection between the bacterial diversity of the MBR and its efficiency to remove TOC.

Trimethylamine abatement in algal-bacterial photobioreactors

Trimethylamine (TMA) is an odorous volatile organic compound emitted by industries. Algal-based biotechnologies have been proven as a feasible alternative for wastewater treatment, although their application to abate polluted air emissions is still scarce. This work comparatively assessed the removal of TMA in a conventional bacterial bubble column bioreactor (BC) and a novel algal-bacterial bubble column photobioreactor (PBC). The PBC exhibited a superior TMA abatement performance compared to the conventional BC. In this sense, the BC reached a removal efficiency (RE) and an elimination capacity (EC) of 78% and 12.1 g TMA m^-3 h^-1, respectively, while the PBC achieved a RE of 97% and a EC of 16.0 g TMA m^-3·h^-1 at an empty bed residence time (EBRT) of 2 min and a TMA concentration ~500 mg m^-3. The outstanding performance of the PBC allowed to reduce the operating EBRT to 1.5 and 1 min while maintaining high REs of 98 and 94% and ECs of 21.2 and 28.1 g m^-3·h^-1, respectively. Moreover, the PBC improved the quality of the gas and liquid effluents discharged, showing a net CO₂ consumption and decreasing by ~ 30% the total nitrogen concentration in the liquid effluent via biomass assimilation. A high specialization of the bacterial community was observed in the PBC, Mumia and Aquamicrobium sp. being the most abundant genus within the main phyla identified. GraphicalAbstract.

Paracoccus sediminilitoris sp. nov., isolated from a tidal flat sediment

A novel marine Gram-stain-negative, non-spore-forming, motile, aerobic, coccoid or ovoid bacterium, designated as strain DSL-16T, was isolated from a tidal flat sediment on the East China Sea and characterized phylogenetically and phenotypically. Optimal growth of the strain occurred at 35 °C (range 4–40 °C), at pH 6 (range 5–11) and with 4 % (w/v) NaCl (range 1–14 %). The nearest phylogenetic neighbour was Paracoccus seriniphilus DSM 14827T (98.2 % 16S rRNA gene sequence similarity). The digital DNA–DNA hybridization value between strain DSL-16T and P. seriniphilus DSM 14827T was 19.5±2.2 %. The average nucleotide identity value between strain DSL-16T and P. seriniphilus DSM 14827T was 83.6 %. The sole respiratory ubiquinone was Q-10. The major polar lipids were phosphatidylmonomethylethanolamine (PME), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidyglycerol (DPG) and glycolipid (GL). The predominant cellular fatty acids of strain DSL-16T were C18 : 1ω7c, C18 : 0 and 11-methyl C18 : 1ω7c. The G+C content of the genomic DNA was 64.5 mol%. The combined genotypic and phenotypic data indicated that strain DSL-16T represents a novel species of the genus Paracoccus , for which the name Paracoccus sediminilitoris sp. nov. is proposed. The type strain is DSL-16T (=KCTC 62644T=MCCC 1K03534T).

Enhancement of surfactant biodegradation with an anaerobic membrane bioreactor by introducing microaeration

In controlled ecological life support system (CELSS), 100% water recycle efficiency is needed. Both water and nutrients in wastewater needs reclaiming. In an anaerobic membrane bioreactor (AnMBR) designed to hydrolyze organic matters and convert organic nitrogen, accumulation of anionic surfactants and organic compounds was observed in the supernatant. To solve the problem, microaeration which had rarely been reported to enhance surfactants biodegradation in anaerobic process was introduced and it was proved to be an effective approach that resulted in concentrations of surfactants and soluble chemical oxygen demand (SCOD) in the supernatant decreasing from 9000 mg/L and 40000 mg/L to 2000 mg/L and 10000 mg/L, respectively. And the degradations followed the kinetic characteristics of zero order reaction with R² values of 0.9472 and 0.949. Three-dimensional excitation emission matrix (3D-EEM) analysis revealed that some activities of microbes were activated and enhanced by microaeration, which resulted in the disintegration of aggregates of large molecules, indicated by the size exclusion chromatography (SEC). After the introduction of microaeration, the emerging genera Aquamicrobium, Flaviflexus, Pseudomonas and Thiopseudomonas in the microbial community might be responsible for the effective biodegradation of the surfactants.

The Denitrification Characteristics and Microbial Community in the Cathode of an MFC with Aerobic Denitrification at High Temperatures

Microbial fuel cells (MFCs) have attracted much attention due to their ability to generate electricity while treating wastewater. The performance of a double-chamber MFC with simultaneous nitrification and denitrification (SND) in the cathode for treating synthetic high concentration ammonia wastewater was investigated at different dissolved oxygen (DO) concentrations and high temperatures. The results showed that electrode denitrification and traditional heterotrophic denitrification co-existed in the cathode chamber. Electrode denitrification by aerobic denitrification bacterium (ADB) is beneficial for achieving a higher voltage of the MFC at high DO concentrations (3.0–4.2 mg/L), while traditional heterotrophic denitrification is conducive to higher total nitrogen (TN) removal at low DO (0.5–1.0 mg/L) concentrations. Under high DO conditions, the nitrous oxide production and TN removal efficiency were higher with a 50 Ω external resistance than with a 100 Ω resistance, which demonstrated that electrode denitrification by ADB occurred in the cathode of the MFC. Sufficient electrons were inferred to be provided by the electrode to allow ADB survival at low carbon:nitrogen ratios (≤0.3). Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) results showed that increasing the DO resulted in a change of the predominant species from thermophilic autotrophic nitrifiers and facultative heterotrophic denitrifiers at low DO concentrations to thermophilic ADB at high DO concentrations. The predominant phylum changed from Firmicutes to Proteobacteria, and the predominant class changed from Bacilli to Alpha, Beta, and Gamma Proteobacteria.

Identification and characterization of a novel carboxylesterase (FpbH) that hydrolyzes aryloxyphenoxypropionate herbicides

OBJECTIVE

To identify and characterize a novel aryloxyphenoxypropionate (AOPP) herbicide-hydrolyzing carboxylesterase from Aquamicrobium sp. FPB-1.

RESULTS

A carboxylesterase gene, fpbH, was cloned from Aquamicrobium sp. FPB-1. The gene is 798 bp long and encodes a protein of 265 amino acids. FpbH is smaller than previously reported AOPP herbicide-hydrolyzing carboxylesterases and shares only 21-35% sequence identity with them. FpbH was expressed in Escherichia coli BL21(DE3) and the product was purified by Ni-NTA affinity chromatography. The purified FpbH hydrolyzed a wide range of AOPP herbicides with catalytic efficiency in the order: haloxyfop-P-methyl > diclofop-methyl > fenoxaprop-P-ethyl > quizalofop-P-ethyl > fluazifop-P-butyl > cyhalofop-butyl. The optimal temperature and pH for FpbH activity were 37 °C and 7, respectively.

CONCLUSIONS

FpbH is a novel AOPP herbicide-hydrolyzing carboxylesterase; it is a good candidate for mechanistic study of AOPP herbicide-hydrolyzing carboxylesterases and for bioremediation of AOPP herbicide-contaminated environments.

Aquamicrobium soli sp. nov., a bacterium isolated from a chlorobenzoate-contaminated soil

An aerobic, Gram-stain negative, short rod-shaped, asporogenous, non-motile bacterium designated strain NK8^T was isolated from a chlorobenzoate contaminated soil in China. Strain NK8^T was observed to grow optimally at pH 7.0, 30 °C and in the absence of NaCl in LB medium. The G + C content of the total DNA of strain NK8^T was found to be 65.5 mol%. The 16S rRNA gene sequence of strain NK8^T showed high similarity to that of Aquamicrobium aerolatum Sa14^T (97.3%), followed by Aquamicrobium lusatiense S1^T (96.7%) and Mesorhizobium sangali SCAU7^T (96.6%). The DNA-DNA relatedness between strain NK8^T and A. aerolatum Sa14^T was 35.5 ± 0.9%. The major fatty acids of strain NK8^T were determined to be C_19:0 cyclo ω8c (45.6%), C_18:1 ω7c (33.4%) and C_16:0 (8.4%). The respiratory quinone was found to be ubiquinone Q-10. The major polyamine was found to be spermidine. The polar lipid profile include the major compounds phosphatidylcholine and diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminolipid and phospholipid. Based on the differential biochemical and physiological characteristics, the geno-, chemo- and phenotypic characteristics, strain NK8^T is proposed to represent a novel species of the genus Aquamicrobium, Aquamicrobium soli sp. nov. The type strain is NK8^T (=KCTC 52165^T=CCTCC AB2016045^T).

High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning

Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn affected their re-fouling potential.