Improved insights into the adaptation and selection of Nitrosomonas spp. for partial nitritation under saline conditions based on specific oxygen uptake rates and next generation sequencing

Partial nitritation (PN) is a bioprocess that is essential for developing cost-effective biological nitrogen removal processes. Understanding the abundant bacterial communities responsible for nitrification under salt stress conditions is important to achieve a stable PN system for treating saline wastewater. Therefore, in this study, we identified the core nitrifying communities and investigated their correlations with the process parameters in a nitrifying bioreactor that was used for treating saline high-strength ammonia wastewater. A PN system worked efficiently under saline conditions with varying operational factors, such as temperature, dissolved oxygen (DO), and alkalinity. Interestingly, the specific oxygen uptake rate (SOUR) became similar under salt-free and saline media after the salt adaption. Next generation sequencing results suggested that the inactivation of Nitrobacter winogradskyi was a key factor for the PN reaction under salt stress conditions. We also found that Nitrosomonas europaea, a freshwater type ammonia-oxidizing bacteria (AOB), was predominantly found under both salt-free and saline conditions, whereas other halotolerant or halophilic AOB species, including Nitrosomonas nitrosa and Nitrosomonas mobilis, became selectively abundant under saline conditions. This implies that adaptation (training of N. europaea) and selection (presence of N. nitrosa and N. mobilis) were simultaneously attributed to selective ammonia conversion for the PN reaction. The redundancy analysis showed that the salinity and ammonia loading rates were statistically significant process parameters that determined the nitrifying bacterial community, suggesting that these parameters drive the adaptation and selection of the core AOB species during the PN reaction. Furthermore, the correlation analysis revealed that the abundance of N. nitrosa and N. mobilis was critically correlated with the specific oxygen uptake rates in saline media containing ammonia.

Gelidibacter maritimus sp. nov., isolated from marine sediment

A Gram-stain-negative, yellow, strictly aerobic, non-flagellated, gliding, rod-shaped bacterial strain, was isolated from costal sediment, designated as F6074^T. The strain F6074^T grows optimally at 30 °C, pH 7.5, and 3.0% (w/v) NaCl. Cells of strain F6074^T are 0.2-0.5 µm wide and 1.0-2.0 µm long. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain F6074^T belonged to the genus Gelidibacter, with the highest sequence similarity to Gelidibacter japonicus JCM 31967^T (98.0%), followed by G. flavus JCM 31135^T (97.7%), and similarity between strain F6074^T and the type species G. algens DSM 12408^T was 96.0%. Genome sequencing results revealed a genome size of 47,07,621 bp. The DNA G + C content was 37.8 mol%. The ANI and dDDH values between strain F6074^T and G. japonicus JCM 31967^T were 83.9 and 27.8%, the values between strain F6074^T and G. algens DSM 12408^T were 77.5% and 31.5%, and the values between strain F6074^T and G. flavus JCM 31135^T were 84.3 and 27.9%, respectively. The predominant quinone was MK-6 and the major fatty acids were iso-C_15:0, iso-C_15:1G, iso-C_17:0 3-OH, anteiso-C_15:0 and summed feature 3. The polar lipids were consisted of phosphatidylethanolamine (PE), two unidentified aminolipids (AL) and three unidentified lipids (L1, L2, L3). Based on the phenotypic, phylogenetic and chemotaxonomic data, strain F6074^T was considered to represent a novel species of the genus Gelidibacter, for which the name Gelidibacter maritimus sp. nov., is proposed. The type strain is F6074^T (MCCC 1H00427^T = KCTC 72942^T).

Gelidibacter pelagius sp. nov., Isolated from Coastal Sediment

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated, and gliding bacterial strain, designated DF109^T, was isolated from the coastal sediment of Jingzi Wharf, Weihai, China. The optimal growth occurs at 28°C, pH 7.0-7.5, and 1.0% (w/v) NaCl environment. The colony was yellow-colored, convex, non-transparent, and circular on 2216E Agar. Phylogenetic analyses of the 16S rRNA gene and genome sequence of this newly isolated strain revealed that it is a member of the genus Gelidibacter within the family Flavobacteriaceae. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DF109^T has the highest sequence similarity to Gelidibacter japonicus JCM 31967^T (98.0%). The average nucleotide identity (ANI) values between genomes of DF109^T and G. japonicus JCM 31967^T and G. algens DSM 12408^T were 86.3% and 78.7% and the digital DNA-DNA hybridization (dDDH) values were 31.4% and 22.4%, respectively. The sole isoprenoid quinone was MK-6 and the major cellular fatty acids were iso-C_15:1G, iso-C_17:0 3-OH, anteiso-C_15:0, and iso-C_16:0 3-OH. The major polar lipids of strain DF109^T were an aminolipid, a phosphatidylethanolamine, and four unidentified lipids. The genomic DNA G+C content was 37.5 mol%. Strain DF109^T is suggested to represent a novel species in the genus Gelidibacter, for which the name Gelidibacter pelagius sp. nov. is proposed. The type strain is DF109^T (=MCCC 1H00454^T=KCTC 82420^T).

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

The role of salinity on the changes of the biomass characteristics and on the performance of an OMBR treating tannery wastewater

Tannery wastewaters are difficult to treat biologically due to the high salinity and organic matter concentration. Conventional treatments, like sequential batch reactors (SBR) and membrane bioreactors (MBR), have showed settling problems, in the case of SBR, and ultrafiltration (UF) membrane fouling in the case of MBR, slowing their industrial application. In this work, the treatment of tannery wastewater with an osmotic membrane bioreactor (OMBR) is assessed. Forward osmosis (FO) membranes are characterized by a much lower fouling degree than UF membranes. The permeate passes through the membrane pores (practically only water by the high membrane rejection) from the feed solution to the draw solution, which is also an industrial wastewater (ammonia absorption effluent) in this work. Experiments were carried out at laboratory scale with a FO CTA-NW membrane from Hydration Technology Innovations (HTI). Tannery wastewater was treated by means of an OMBR using as DS an actual industrial wastewater mainly consisting of ammonium sulphate. The monitoring of the biological process was carried out with biological indicators like microbial hydrolytic enzymatic activities, dissolved and total adenosine triphosphate (ATP) in the mixed liquor and microbial population. Results indicated a limiting conductivity in the reactor of 35 mS cm^-1 (on the 43th operation day), from which process was deteriorated. This process performance diminution was associated by a high decrease of the dehydrogenase activity and a sudden increase of the protease and lipase activities. The increase of the bacterial stress index also described appropriately the process performance. Regarding the relative abundance of bacterial phylotypes, 37 phyla were identified in the biomass. Proteobacteria were the most abundant (varying the relative abundance between 50.29% and 34.78%) during the first 34 days of operation. From this day on, Bacteroidetes were detected in a greater extent varying the relative abundance of this phylum between 27.20% and 40.45%.

Aquaticitalea lipolytica gen. nov., sp. nov., isolated from Antarctic seawater

A Gram-stain-negative, rod-shaped bacterium, designated Ar-125^T, was isolated from Antarctic seawater. It produced carotenoid-like pigments and did not produce Bchl a. Ar-125^T was positive for hydrolysis of DNA, aesculin, gelatin, starch, Tween 40 and Tween 60. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and two unidentified lipids. The principal fatty acids were branched-chain fatty acids, including iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C16 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH, as well as C15 : 0. The genomic DNA G+C content was 31.8 mol%. On the basis of 16S rRNA gene sequence analysis, Ar-125^T is closely related to the species of the genera Bizionia(with 16S rRNA gene pairwise sequence similarity of 93.7-96.5 %), Formosa(94.3-95.8 %), Gaetbulibacter(94.2-95.7 %), Geojedonia(95.5 %), Gelidibacter (93.3-95.4 %), Meridianimaribacter(95.3 %) and Psychroserpens (94.8-95.3 %), of the family Flavobacteriaceae. Phylogenetic analysis indicated that it represented an independent lineage and that the closest relatives were members of the genus Gelidibacter. Differential phenotypic properties and chemotaxonomic differences, together with phylogenetic distinctiveness, revealed that Ar-125^T could be differentiated from members of closely related genera. Therefore, it is proposed that Ar-125^T represents a novel species in a new genus, for which the name Aquaticitalea lipolytica gen. nov., sp. nov. (type strain Ar-125^T =CGMCC 1.15295^T =JCM 30876^T) is proposed.

Gelidibacter flavus sp. nov., Isolated from Activated Sludge of Seawater Treatment System

A Gram-stain-negative bacterial strain designated Con4^T was isolated from activated sludge in a seawater treatment system. The strain was rod-shaped, motile, aerobic, and formed yellow-colored colonies on agar medium. Cells contained carotenoid pigments, but flexirubin-type pigments were absent. Based on 16S rRNA gene sequence analysis, the strain was assigned to the genus Gelidibacter. Optimum growth occurred at 20 °C, pH 7.0, and 1-2% (w/v) NaCl. Prominent fatty acid types were iso-C_15:0, anteiso-C_15:0, and iso-C_16:0 3OH. Diphosphatidylglycerol and phosphatidylethanolamine were present as the major polar lipids. MK-6 was present as major menaquinone. Strain Con4^T showed the highest sequence similarity with Gelidibacter mesophilus KCTC 12106^T (96.5%), Gelidibacter gilvus IC158^T (96.4%), and Gelidibacter algens ACAM 536^T (95.8%). The G+C mol% contents of the strain Con4^T were 37.7%. Distinct morphological, physiological, and genotypic differences from the previously described taxa support the classification of strain Con4^T as a representative of a novel species in the genus Gelidibacter, for which the name Gelidibacter flavus sp. nov. is proposed. The type strain is Con4^T (=KEMB 41-198^T = JCM 31135^T).