Stenotrophobium rhamnosiphilum gen. nov., sp. nov., isolated from a glacier, proposal of Steroidobacteraceae fam. nov. in Nevskiales and emended description of the family Nevskiaceae

Cleavage of natural rubber by rubber oxygenases in Gram-negative bacteria

Bacterial degradation of natural rubber (NR) in an oxic environment is initiated by oxidative cleavage of double bonds in the NR-carbon backbone and is catalyzed by extracellular haem-containing rubber oxygenases. NR-cleavage products of sufficiently low molecular mass are taken up by the cells and metabolized for energy and biomass formation. Gram-negative and Gram-positive NR-degrading bacteria (usually) employ different types of rubber oxygenases such as RoxA and/or RoxB (most Gram-negative NR-degraders) or latex clearing protein Lcp (most Gram-positive NR-degraders). In order to find novel orthologues of Rox proteins, we have revisited databases and provide an update of Rox-like proteins. We describe the putative evolution of rubber oxygenases and confirm the presence of a third subgroup of Rox-related proteins (RoxCs), the biological function of which remains, however, unclear. We summarize the knowledge on the taxonomic position of Steroidobacter cummioxidans 35Y and related species. Comparison of genomic and biochemical features of strain 35Y with other species of the genus Steroidobacter suggests that strain 35Y represents a species of a novel genus for which the designation Aurantibaculum gen. nov. is proposed. A short summary on the capabilities of NR-degrading consortia, that could be superior in biotechnological applications compared to pure cultures, is also provided. KEY POINTS: • Three types of rubber oxygenases exist predominantly in Gram-negative microbes • S. cummioxidans 35Y contains RoxA and RoxB which are superior in activity • S. cummioxidans 35Y represents a species of a novel genus.

Remediation of the black-odor water body by aquatic plants with plant growth-promoting Rhizobacteria: Lab and pilot tests

To explore an effective, environmental, rapid operating method to repair black and odor water bodies, water samples and sediment samples collected from a polluted municipal lake in Daqing, China, were directly tested in transparent barrels (10 L). Seven groups of optimizing parameters obtained the optimal operating method, and the max removal rate of COD, NH₄⁺-N, NO₃^--N, and TP were achieved (89.18%, 59.65%, 69.50%, and 75.61%) by using aquatic plants with plant growth-promoting Rhizobacteria (PGPR). To further verify the method's effectiveness, lager scale tests were conducted based on a water tank (216 L), and similar removal rates were obtained within 48 h. The water quality index and microbial community structure analysis revealed the mechanisms of the interaction among plants, microorganisms, and pollutants and the main biological processes during water body remediation. Finally, the cost of water body remediation by using this method was estimated.

Phylogenomics and molecular marker-based analyses of the order Nevskiales: Proposal for the creation of Steroidobacterales ord. nov. and Peristeroidobacter gen. nov

The order Nevskiales, class Gammaproteobacteria, encompasses four families Algiphilaceae, Salinisphaeraceae, Nevskiaceae, and Steroidobacteraceae. The taxonomy of this order is structured from the inferences derived from the 16S rRNA gene and genome-based phylogenetic tree analyses. However, previous taxonomic studies of the order failed to incorporate most of the representatives from other established orders within the class Gammaproteobacteria. Other divergent members within the class Gammaproteobacteria were therefore overlooked. In this study, the taxonomy of the order Nevskiales was revisited using genome-based analyses with an expanded scope of outgroups representing the vast majority of the diversity within the class Gammaproteobacteria. Results from the phylogenetic analyses strongly supported the exclusion of the family Steroidobacteraceae from the order Nevskiales and further implied the assignment of the family into a novel order. In addition, the analyses also supported the reclassification of Steroidobacter gossypii, Steroidobacter soli, Steroidobacter agariperforans, and Steroidobacter agaridevorans into a novel genus. The identified conserved signature indels in 33 protein sequences further reinforced the new taxonomic assignments. Furthermore, the results of the average nucleotide identity and average amino acid identity analyses, together with the phenotypic and genomic characteristics among the members of the genus Steroidobacter also provided evidence supporting the reclassification of the four Steroidobacter species. Based on these results, the family Steroidobacteraceae is proposed to be assigned into a novel order Steroidobacterales ord. nov., and the species S. gossypii, S. soli, S. agariperforans, and S. agaridevorans are proposed to be moved into a novel genus Peristeroidobacter gen. nov. within the family Steroidobacteraceae.

Analysis of bacterial community distribution characteristics in the downstream section of a cross confluence in a polluted urban channel

Channel confluences are common in urban rivers and caused complex hydrodynamic conditions in the downstream section, significantly influencing the distribution of pollutants and the microbial community. So far, the principles of bacterial community assembly and their linkages with environmental factors are poorly understood. In the present study, the hydrodynamic and pollution conditions were investigated in a typical channel confluence of an urban river in the Yangtze River delta area, China, and their impacts on the bacterial community structure in the water and sediment were characterized using 16S rRNA gene high-throughput sequencing technology. Based on the results, the flow velocity was the crucial factor influencing the dispersal of nutrients, organic compounds, and bacterial communities in the river water. Moreover, the sediments exhibited higher α-diversity and bacterial richness for nitrogen and sulfur cycling than the water. In addition to flow velocity, the contents of total organic carbon, total phosphorus, and heavy metals determined the sediment bacterial communities at varying depths. The predictive analysis of functional gene category indicated differences between the water and sediment communities in metabolic potentials and pathogen risk and provided guidance for water pollution control and the eco-remediation of urban rivers.

Elemental composition and microbial community differences between wastewater treatment plant effluent and local natural surface water: A Zhengzhou city study

Wastewater treatment plant (WWTP) effluent is discharged into rivers as supplemental water, which may result in ecological risk. This study compares the element composition and microbial community of WWTP effluent and natural surface water (NSW) and reveals the potential ecological risk of WWTP effluent discharge. Twenty recently upgraded WWTPs and three relatively large reservoirs in Zhengzhou city, China, were selected. The contents of N, P, S, K, Ca, Mg, B, Si, Na, Fe, Mn, Co, Ni and Sn were significantly higher in WWTP effluent than in NSW, while those of Mo, V, Pb and Cd were significantly lower. There was no significant difference between WWTP effluent and NSW in terms of the element imbalance index (IMI) (representing the extent of imbalance of element proportions) relative to the class IV surface water quality standard (the control standard for most Chinese rivers). The macronutrient IMI relative to the Hoagland formula was significantly lower in WWTP effluent than in NSW, and WWTP effluent discharge could significantly lower this index in NSW; this may be an important cause of primary productivity explosion. The microbial diversity was significantly higher in WWTP effluent than in NSW. The predicted relative abundances of mobile genetic elements and oxidative-stress-tolerant phenotypes were significantly higher in WWTP effluent than in NSW, whereas the abundance of gram-negative phenotypes was significantly lower, and that of potential pathogenic phenotypes was slightly lower. The effluent from upgraded WWTPs exhibited a low risk of pathogen diffusion but a high risk of antibiotic resistance gene diffusion. The element composition and microbial community should be considered when evaluating the ecological risk of WWTP effluent discharge.

Fate of dissolved inorganic nitrogen in turbulent rivers: The critical role of dissolved oxygen levels

Dissolved inorganic nitrogen (DIN) is considered the main factor that induces eutrophication in water, and is readily influenced by hydrodynamic activities. In this study, a 4-year field investigation of nitrogen dynamics in a turbulent river was conducted, and a laboratory study was performed in the approximately homogeneous turbulence simulation system to investigate potential mechanisms involved in DIN transformation under turbulence. The field investigation revealed that, contrary to NO^-₃ dynamics, the NH⁺₄ concentrations in water were lower in flood seasons than in drought seasons. Further laboratory results demonstrated that limitation of dissolved oxygen (DO) caused inactive nitrification and active denitrification in static river sediment. In contrast, the increased DO levels in turbulent river intensified the mineralization of organic nitrogen in sediment; moreover, ammonification and nitrification were activated, while denitrification was first activated and then depressed. Turbulence therefore decreased NH⁺₄ and NO^-₂ concentrations, but increased NO^-₃ and total DIN concentrations in the overlying water, causing the total DIN to increase from 0.4 mg/L to maximum of 1.0 and 1.7 mg/L at low and high turbulence, respectively. The DIN was maintained at 0.7 and 1.0 mg/L after the 30-day incubation under low and high turbulence intensities (ε) of 3.4 × 10^-4 and 7.4 × 10^-2 m²/s³, respectively. These results highlight the critical role of DO in DIN budgets under hydrodynamic turbulence, and provide new insights into the DIN transport and transformation mechanisms in turbulent rivers.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves.

IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum

A Gram-stain-negative, aerobic, rod-shaped strain (R2A-3^T) was isolated from the toxin-producing dinoflagellate Centrodinium punctatum and identified as a novel genus and new species based on a polyphasic taxonomic approach. The optimum conditions for growth of the strain were at 25 °C, pH 8.0 and in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes and 92 core genes sets revealed that strain R2A-3^T belongs to the family Nevskiaceae in the class Gammaproteobacteria and represented an independent taxon separated from other genera. The 16S rRNA gene of strain R2A-3^T showed the highest sequence similarity to Polycyclovorans algicola TG408^T (95.2%), Fontimonas thermophila HA-01^T (94.1%) and Sinimarinibacterium flocculans NH6-24^T (93.2%), and less than 92.8 % similarity to other genera in the family Nevskiaceae. The genome length of strain R2A-3^T was 3608892 bp with 65.2 mol% G+C content. Summed feature 8 (comprising C_18 : 1  ω7c and/or C_18 : 1  ω6c) was the major fatty acid (>10 %). Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected as the major polar lipids. The major respiratory quinone was ubiquinone-8. According to its phylogenetic, phenotypic, chemotaxonomic and genomic features, strain R2A-3^T represents a new species in the new genus of the family Nevskiaceae. It is recommended to name it Flagellatimonas centrodinii gen. nov., sp. nov. The type strain is R2A-3^T (=KCTC 82469^T=GDMCC 1.2523^T).

Characterization and Distribution of Agar-degrading Steroidobacter agaridevorans sp. nov., Isolated from Rhizosphere Soils

The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-BT was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-BT and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-BT. However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-BT, indicating that they are different species from S. agariperforans KA5-BT. To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-BT and YU21-B grew at 15-40°C and pH 6.0-12 and contained C16:0 as the dominant cell fatty acid, whereas KA5-BT showed no growth at 40°C and pH 12 and contained a moderate amount of C16:0. Based on these characteristics, SA29-BT (JCM 333368T=KCTC 72223T) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.

Rule 24b of the International Code of Nomenclature of Prokaryotes and regulating the priority of names and epithets considered to be associated with heterotypic synonyms

Rule 24b of the International Code of Nomenclature of Prokaryotes regulates the priority of names that are considered to be heterotypic synonyms. However, the rule is imperfect because it caters only for names that compete for priority that were only included on the Approved Lists of Bacterial Names or for names that were only validly published in the International Journal of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology, either in an original article or via the Validation Lists. Although this should be self-explanatory, Rule 24b does not cater for what happens when one or more names considered to be heterotypic synonyms have appeared on the Approved Lists of Bacterial Names while other names also considered to be heterotypic synonyms were validly published in the International Journal of Systematic Bacteriology or the International Journal of Systematic and Evolutionary Microbiology, either in an original article or via the Validation Lists. Formal changes to the International Code of Nomenclature of Prokaryotes are required.