Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil

Polluticaenibacter yanchengensis gen. nov., sp. nov., A Novel Taxon Within the Family Chitinophagaceae Isolated from Activated Sludge

A Gram-stain-negative bacterium, designated strain LY-5 T, was isolated from an activated sludge sample collected from a river in Yancheng city, Jiangsu province, China. Cells of strain LY-5 T, were strictly aerobic, non-motile and rod-shaped. Growth occurred at 15-37 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum 7.0) and at 0-3% (w/v) NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strain LY-5 T formed a distinct phyletic branch within the family Chitinophagaceae, with closest relatives being members of the genera Phnomibacter, Aurantisolimonas, and Chitinophaga, sharing 88.5-90.3% sequence similarity. Moreover, the average amino acid identity (AAI) between strain LY-5 T and its closed phylogenetic neighbors was below 70%, indicating it belongs to a novel genus. The predominant cellular fatty acids of LY-5 T were iso-C15:0, iso-C15:1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and the only isoprenoid quinone was menaquinone-7 (MK-7). The major polar lipids identified in strain LY-5 T comprised phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The genome size of strain LY-5 T was 4.8 Mbp with a G + C content of 38.9%. Based on the evidence presented in this study, strain LY-5 T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Polluticaenibacter yanchengensis gen. nov., sp. nov. (Type strain LY-5 T = CCTCC AB 2023260 T = KCTC 102218 T) is proposed.

Performance of single PN/A reactor under wide fluctuation of nitrogen load

Partial nitritation-anammox (PN/A) is a cost-effective technology in high ammonia-nitrogen wastewater treatment. However, PN/A is prone to instability as the ammonia-nitrogen sharply fluctuates. In this study, a packed bed reactor is employed to construct a single-stage PN/A system to investigate the operational characteristics and explore the denitrification mechanism. The effluent NH4+-N concentration, ammonia nitrogen removal rate (ARE), and total nitrogen removal rate (TNR) could be sustained at about 60 mg/L, 80%, and over 70%, respectively, when the influent nitrogen load rate (NLR) is changed from 0.733 to 0.879 kg-N/m3/day. Both ARE and TNR are decreased when NLR continues increasing to 1.026 kg-N/m3/day. The influent NLR decreases from 0.879 to 0.147 kg-N/m3/day, and ARE and TNR reached 98% and 85.4%, respectively. Therefore, the denitrification effect of the reactor could be recovered, and the excellent nitrogen removal capacity could be obtained within a wide range of influent NLR. Moreover, the high-throughput sequencing and metagenomic testing indicate that the Proteobacteria and Planctomycetes that the PN/A functional strains (i.e., ammonia-oxidizing bacteria (AOB) and anammox bacteria (AnAOB)) account for 38.8% in the sludge. The relative abundance of Nitrospira containing the nitrite-oxidizing bacteria (NOB) has dropped to 0.01%, and the functional gene nxr of the nitrite oxidation process is also inhibited. The relative expression of the functional gene is dominated by the short-range nitritation and anammox oxidation, which demonstrates that the nitrogen removal is mainly dominated by nitritation-anammox.

Mycovorax composti gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from button mushroom compost

Two Gram-stain-negative, aerobic, rod-shaped, orange-coloured bacterial strains, designated strain C216T and strain M2295, were isolated from mature mushroom compost from composting facilities in Victoria and South Australia, Australia, respectively. External structures such as flagella or pili were not observed on the cells under scanning electron microscopy. Optimal growth was found to occur at 45 °C, at pH 7.25 and in the absence of NaCl on Emerson's 350 YpSs medium. The genome sequence of strain C216T was 3 342 126 bp long with a G+C content of 40.5 mol%. Functional analysis of the genome of strain C216T revealed genes encoding chitinolytic and hemi-cellulolytic functions, with 166 predicted genes associated with carbohydrate metabolism (8.9% of the predicted genes). These functions are important for survival in the mushroom compost environment, which is rich in hemicelluloses. No antibiotic resistance genes were found in the genome sequence. The major fatty acids of strain C216T were iso-C15 : 0 (56.7%), iso-C17 : 0 3-OH (15.6%), C16 : 1  ω7c/iso-C15 : 0 2-OH (7.3%) and iso-C15 : 1 G (6.1%). The only respiratory quinone was MK-7. The major polar lipid of strain C216T was phosphatidylethanolamine, but three unidentified phospholipids, four unidentified aminophospholipids/aminolipids and one unidentified glycolipid were also detected. Phylogenetic analysis based on proteins encoded by the core genome (bac120, 120 conserved bacterial genes) showed that strain C216T forms a distinct lineage in the family Chitinophagaceae and that the closest identified relative is Niabella soli (69.69% ANI). These data demonstrate that strain C216T represents a novel genus and novel species within the family Chitinophagaceae, for which we propose the name Mycovorax composti. The type strain is C216T (=DSM 114558T=LMG 32998T).

Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil

A taxonomic investigation was conducted on four bacterial strains isolated from soil contaminated with polycyclic aromatic hydrocarbons and heavy metals. Phylogenetic analysis revealed that these strains belonged to the family Chitinophagaceae. Examination of the 16S rRNA genes indicated that their sequence identities were below 97.6 % compared to any known and validly nominated bacterial species. The genomes of the four strains ranged from 4.12 to 8.76 Mb, with overall G + C molar contents varying from 41.28 % to 50.39 %. Predominant cellular fatty acids included iso-C15:0, iso-C15:1 G, and iso-C17:0 3-OH. The average nucleotide identity ranged from 66.90 % to 74.63 %, and digital DNA-DNA hybridization was 12.5-12.8 %. Based on the genomic and phenotypic features of the new strains, four novel species and two new genera were proposed within the family Chitinophagaceae. The ecological distributions were investigated by data-mining of NCBI databases, and results showed that additional strains or species of the newly proposed taxa were widely distributed in various environments, including polluted soil and waters. Functional analysis demonstrated that strains H1-2-19XT, JS81T, and JY13-12T exhibited resistance to arsenite (III) and chromate (VI). The proposed names for the four novel species are Paraflavitalea pollutisoli (type strain H1-2-19XT = JCM 36460T = CGMCC 1.61321T), Terrimonas pollutisoli (type strain H1YJ31T = JCM 36215T = CGMCC 1.61343T), Pollutibacter soli (type strain JS81T = JCM 36462T = CGMCC 1.61338T), and Polluticoccus soli (type strain JY13-12T = JCM 36463T = CGMCC 1.61341T).

Effects of Different Mulching Practices on Soil Environment and Fruit Quality in Peach Orchards

Mulching practices have been used to improve peach growth and production across the globe. However, the impact of mulching on the physiochemical properties and soil characteristics of orchards remains largely unknown. This study aimed to decipher the impacts of various mulching patterns on the soil environment and the quality of Prunus persica fruit in "Zijinhuangcui". Three treatments were set up, which included black ground fabric mulch (BF) and two living grass mulch treatments (HV: hairy vetch and RG: ryegrass). The results showed that different mulching treatments have different effects on soil, plant growth, and fruit quality. Living grass mulch treatments, especially the HV treatment, significantly improved soil nutrients by enhancing nitrogen-related indicators. Of note, the BF treatment had higher total phosphorus and available phosphorus contents than the HV and RG treatments. The HV treatment had the highest relative abundance of Proteobacteria (33.49%), which is associated with symbiotic nitrogen fixation, followed by RG (25.62%), and BF (22.38%) at the young fruit stage. Similarly, the abundance of Terrimonas, which has a unique nitrogen fixation system at the genus level, was significantly higher in the living grass mulch (HV, 1.30-3.13% and RG, 2.27-4.24%) than in the BF treatment. Living grass mulch also promoted tree growth, increased fruit sugar content, sugar-related components, and sugar-acid ratio, and reduced the acid content. Collectively, the findings of this study show that living grass mulch can promote tree growth and improve fruit quality by improving soil fertility, bacterial diversity, and richness.

Performance and mechanism of pilot-scale carbon fibers enhanced ecological floating beds for urban tail water treatment in optimized ecological floating beds water surface coverage

A pilot-scale carbon fibers enhanced ecological floating beds (CF-EFBs) was constructed. Compared to EFBs without carbon fibers enhancement, CF-EFBs have the better removal of total inorganic nitrogen (TIN), total phosphorus (TP), and chemical oxygen demand (COD), the removal efficiencies were 3.19, 3.49, and 2.74 times higher than EFBs. Throughout the pilot test (under three different coverage rates), the concentrations of COD, TIN and TP of effluent were 18.11 ± 4.52 mgL-1, 1.95 ± 0.92 mgL-1 and 0.13 ± 0.08 mgL-1. Meanwhile, the average removal of TIN, TP and COD from tailwater was 0.96 gm-2d-1, 0.07 gm-2d-1 and 2.37 gm-2d-1 respectively. When the coverage was 30 %, the CF-EFBs had better nitrogen removal effectiveness (TIN purification ability of 1.49 gm-2d-1). The enrichment of denitrifying bacteria, such as Aridibacter, Nitrospira, Povalibacter, and Phaeodactylibacter increased denitrification efficiency. These results verified the feasibility of CF-EFBs in tailwater treatment at pilot-scale, which was of great significance for the practical application of CF-EFBs.

Elucidating prioritized factor for mainstream partial nitritation between C/N ratio and dissolved oxygen: Response surface methodology and microbial community shifts

Recently, C/N ratio is suggested as a promising control factor with dissolved oxygen (DO) achieving mainstream partial nitritation (PN); however, their combined effects on mainstream PN are still limited. This study evaluated the mainstream PN with respect to the combined factors, and investigated the prioritized factor affecting the community of aerobic functional microbes competing with NOB. Response surface methodology was performed to assess the combined effects of C/N ratio and DO on the activity of functional microbes. Aerobic heterotrophic bacteria (AHB) played the greatest role in oxygen competition among functional microbes, which resulted in relative inhibition of nitrite-oxidizing bacteria (NOB). The combination of high C/N ratio and low DO had a positive role in the relative inhibition of NOB. In bioreactor operation, the PN was successfully achieved at ≥ 1.5 of C/N ratio for 0.5-2.0 mg/L DO conditions. Interestingly, aerobic functional microbes outcompeting NOB were shifted with C/N ratio rather than DO, suggesting C/N ratio is more prioritized factor achieving mainstream PN. These findings will provide insights into how combined aerobic conditions contribute to achieve mainstream PN.

Improved Denitrification Performance of Polybutylene Succinate/Corncob Composite Carbon Source by Proper Pretreatment: Performance, Functional Genes and Microbial Community Structure

Blending biodegradable polymers with plant materials is an effective method to improve the biodegradability of solid carbon sources and save denitrification costs, but the recalcitrant lignin in plant materials hinders the microbial decomposition of available carbon sources. In the present study, corncob pretreated by different methods was used to prepare polybutylene succinate/corncob (PBS/corncob) composites for biological denitrification. The PBS/corncob composite with alkaline pretreatment achieved the optimal NO₃^--N removal rate (0.13 kg NO₃^--N m^-3 day^-1) with less adverse effects. The pretreatment degree, temperature, and their interaction distinctly impacted the nitrogen removal performance and dissolved organic carbon (DOC) release, while the N₂O emission was mainly affected by the temperature and the interaction of temperature and pretreatment degree. Microbial community analysis showed that the bacterial community was responsible for both denitrification and lignocellulose degradation, while the fungal community was primarily in charge of lignocellulose degradation. The outcomes of this study provide an effective strategy for improving the denitrification performance of composite carbon sources.

Performance enhancement and population structure of denitrifying phosphorus removal system over redox mediator at low temperature

The development of denitrifying polyphosphate accumulating organisms (DPAOs) presents a strategy to carbon competition between denitrifying bacteria and phosphorus removing bacteria. However, low temperature inhibits the rate of enzyme-catalyzed and substrate diffusion during denitrifying phosphorus removal (DPR). Therefore, the present study assessed the addition of NQS (100 μmol/L) for enhancing the removal of TP and TN in DPR reactors operated at alternating anaerobic and anoxic phases and different influent phosphate concentrations. The results showed that the removal efficiency of TP and TN in NQS-DPR system at 10 °C were 99.9% and 42.0%, respectively, which were 2.1 and 2.0 times higher than that of DPR system. Adding NQS significantly alleviated the increase of pH under anoxic condition and decreased the ORP value of the reactor, which in turn enhanced the PHAs accumulation process. The determination of functional genes (nirK, narG and phoD) showed that Dechloromonas, Lentimicrobium, and Terrimonas were the dominant functional bacteria in NQS-DPR system at 10 °C with the relative abundance of 3.09%, 2.99% and 2.28%, respectively. This study can provide valuable information for the effects of the addition of the redox mediator on denitrifying phosphorus removal technology.

Effect of aerobic microbes' competition for oxygen on nitrogen removal in mainstream nitritation-anammox systems

The effects of C/N ratio in mainstream partial nitritation (PN)-anaerobic ammonia oxidation (ANAMMOX) considering competitive relationship of aerobic microbes competing for oxygen were investigated. Thy system was operated for 501 d with various C/N ratio. Competitive growth of aerobic heterotrophic bacteria (AHB) at ≥ 1 of C/N ratio acted effectively on the selective inhibition of nitrite-oxidizing bacteria (NOB) while contributing to stable PN-A. In-depth kinetic analysis indicated oxygen affinity of aerobic microbes was in the order of AHB > ammonia-oxidizing bacteria (AOB) > NOB. In addition, potential of denitritation by AHB could contributed to improving nitrogen removal up to 87.5 ± 4.3%. AHB was comparatively clustered into two groups with a C/N ratio of 1. Nitrosomonas sp. PY1 became predominant while Nitrospira spp. were the major NOB. The potential of AHB in establishing selective inhibition of NOB was identified, which could be a novel approach to stabilze the mainstream PN-A.

Use of sponge iron as an indirect electron donor to provide ferrous iron for nitrate-dependent ferrous oxidation processes: Denitrification performance and mechanism

Sponge iron (SI) can serve as an indirect electron donor to provide Fe(II) for the nitrate-dependent ferrous oxidation (NDFO) process, producing OH^- and magnetite. The SI-NDFO system mainly uses Fe(OH)₂ as an electron donor, achieving a TN reduction rate of 0.42 mg-TN/(gVSS·h) for a period of at least 90 days. The enrichment of iron-oxidizing bacteria and the competition of iron-carbon micro-electrolysis for reaction sites on the surface of SI are the main reasons for the improvement of total nitrogen removal efficiency (TNRE). With an influent NO₃^--N concentration of 50 mg/L and a SI concentration of 50 g/L (at pH 5.0 and 30 °C), the TNRE reached a maximum level of 38.28%. In addition, reducing the pH environment was found to improve the denitrification efficiency of the SI-NDFO system, although denitrification stability was also reduced as a result. Overall, the SI-mediated NDFO process is a promising technique.

Hanamia caeni gen. nov., sp. nov., a Member of the Family Chitinophagaceae Isolated from Activated Sludge in Korea

A novel Gram-stain-negative, aerobic, yellowish-pigmented, non-motile, rod-shaped bacterial strain, designated strain BO-59^T, was isolated from the activated sludge of a wastewater treatment plant in Hanam City, South Korea. Phylogenetic study based on the 16S rRNA gene sequence positioned BO-59^T in a distinct lineage in the family Chitinophagaceae, sharing less than 92.8% sequence similarity with members of the closely related genera Ferruginibacter, Flavitalea, Pseudoflavitalea, Flavisolibacter, Niastella, and Terrimonas. Phylogenomic- and genomic relatedness analyses revealed that strain BO-59^T is clearly distinguished from other genera in the family Chitinophagaceae by average nucleotide identity < 66.9%) and the genome-to-genome distance (< 29.5%) values. The strain BO-59^T contained MK-7 as the predominant quinone, and iso-C_15:0, iso-C_17:0 3OH, and iso-C_15:1 G as major fatty acids (> 10%). The DNA G + C content was 39.1 mol% based on genome sequence analysis. The polar lipids of strain BO-59^T were phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified polar lipids. 16S rRNA gene sequence similarity, physiological, and biochemical characteristics indicated that strain BO-59^T represents a novel species of a new genus, for which the name Hanamia caeni gen. nov., sp. nov. is proposed. The type strain is BO-59^T (= KACC 19646^T = LMG 30865 ^T).

Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26^T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7-1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26^T was able to grow at 10-40 °C, at pH 6.0-9.0 and with 0-1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria-Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26^T was closely related to Flavihumibacter sediminis CJ663^T and Parasegetibacter terrae SGM2-10^T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae. Strain MAH-26^T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C_15:0, iso-C_15:1 G and iso-C_17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26^T represents a novel species of a novel genus of the family Chitinophagaceae, for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26^T (=KACC 19749^T=CGMCC 1.13701^T).

Limnovirga soli gen. nov., sp. nov., isolated from river sediment

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6^T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0-8.0 (optimum, pH 7.0) and 10-37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6^T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550^T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6^T were iso-C_15:0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6^T represents a novel species in a new genus in the family Chitinophagaceae, for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6^T=KCCM 43337^T=NBRC 114336^T) is proposed.

Applications of food waste-derived black soldier fly larval frass as incorporated compost, side-dress fertilizer and frass-tea drench for soilless cultivation of leafy vegetables in biochar-based growing media

Black soldier fly (BSF) larval bioconversion can recycle nutrients in organic wastes into larval biomass and frass. While the frass has been commonly marketed as a soil amendment, its usefulness in soilless cultivation remains largely unexplored. Growth experiments were conducted to investigate the effectiveness of surplus food-derived and okara-derived BSF larval frass as an incorporated compost, side-dress fertilizer and frass-tea drench for the cultivation of pak choi and lettuce in waste-wood derived biochar growing media. Pak choi yields from treatments with surplus food-derived frass and biochar at a 10:90 (v/v) ratio and inorganic fertilizer were comparable to those of the control which consisted of soil, peat-based compost and inorganic fertilizer. However, yields decreased with increasing frass incorporation rates owing to high salinity and potentially low oxygen conditions in the growing media. When used as a fertilizer on biochar-coir growing media, the direct application of frass as a side-dress fertilizer was 1.6-6.8 times more effective in promoting lettuce growth than the application as a frass-tea drench. Frass fertilizers derived from surplus food outperformed those derived from okara by 1.3-5.3 times. Lettuce yields were not significantly different between the treatment with surplus food-derived frass applied as a side-dress fertilizer and the control of liquid inorganic fertilizer. Variations in fertilizing potential were attributed to nutrient availability and the presence of plant growth promoting microbes in the growing media. BSF larval frass derived from food waste shows promise in partially replacing unsustainable agricultural inputs for leafy vegetable cultivation, including soil and inorganic fertilizers.

Phnomibacter ginsenosidimutans gen. nov., sp. nov., a novel glycoside hydrolase positive bacterial strain with ginsenoside hydrolysing activity

The conversion of major ginsenosides into minor ginsenosides attracts a lot of interest because of their biological and pharmaceutical activities. Therefore, for the conversion of ginsenosides, finding a novel competent glycoside hydrolase-producing bacterial strain is useful for future research studies and the mass production of minor ginsenosides. Wastewater samples were collected and screened for novel glycoside hydrolase bacterial strains using Reasoner's 2A+aesculin agar medium. As a result, a novel glycoside hydrolase positive bacterial strain (SB-02^T) was identified and subjected to a polyphasic taxonomic analysis. Based on genome analysis, strain SB-02^T was found to be affiliated with the family Chitinophagaceae and have less than 92.8 % sequence similarity to other members of the same family. Functional analysis indicated that SB-02^T was able to hydrolyse the ginsenosides Rb1, Rc and Rd to F2 and C-K. Due to the conversion of ginsenosides, the strain's genome was sequenced and the genes were annotated by the NCBI. The average amino acid identity and average nucleotide identity values between SB-02^T and the available reference genomes were 65.7 and 65.9 %, respectively. The novel isolate contained MK-7 as the predominant menaquinone, the major polyamine putrescine, and iso-C_15 : 0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH as major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Thus, based on the data presented here, strain SB-02^T represents a novel species within a new genus in the family Chitinophagaceae, for which the name Phnomibacter ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of Phnomibacter ginsenosidimutans is SB-02^T (=KACC 21266^T=LMG 31707^T). The genome annotation of SB-02^T shows many glycoside hydrolase genes, which may be responsible for the efficient production of many kinds of minor ginsenosides and will be very helpful for future research (target gene cloning) and mass production of either F2 or C-K.

Responses of bacterial communities and organic matter degradation in surface sediment to Macrobrachium nipponense bioturbation

The excessive accumulation of organic matter (OM) in sediments in aquaculture ponds is a potential environmental threat due to the risk of endogenous water pollution and eutrophication. From the perspective of inhibiting OM accumulation to prevent endogenous water pollution, the present study investigated the OM degradation states, variations of bacterial communities and basic environmental factors in sediments with/without Macrobrachium nipponense treatment/control groups in triplicate for effects of bioturbation on OM degradation in 90-day incubation. The total organic carbon (TOC) and total nitrogen (TN) in the M. nipponense treatment were higher than in the control at the 30th and 60th days, while no significant differences between treatment and control were found at the end of the experiment. Significantly higher oxidation-reduction potential (ORP) and more extensively degraded OM were observed in the M. nipponense treatment. Eleven significantly differential bacterial taxa were enriched in the sediments of M. nipponense treatment, of which eight (Actinobacteria, Chitinophagales, Chitinophagaceae, Flavihumibacter, Marinilabiliaceae, Cytophaga xylanolytica group, Christensenellaceae, and Christensenellaceae R-7 group) were significantly correlated with at least two OM degradation indicators. The functional groups chemoheterotrophy, aerobic chemoheterotrophy, xylanolysis, ureolysis, and intracellular parasites were enhanced by M. nipponense and were negatively correlated with OM degradation indictors. Overall, the M. nipponense bioturbation effectively increased the ORP to provide better conditions for OM degradation, altered the taxonomic composition and functional groups to enhance the bacterial ability for OM degradation, and finally promoted the OM degradation of the surface sediment in an artificial aquaculture system.

Pilot study on urban sewage treatment with micro pressure swirl reactor

This study aimed to propose a new type of micro-pressure swirl reactor (MPSR) to treat urban sewage. The MPSR could form a stable swirl in the reactor, and realized the coexistence of anaerobic, anoxic, and aerobic zones in a single aeration tank. The pilot study showed that MPSR achieved high removal efficient of SS, COD, NH₄⁺-N, TN, TP under the conditions of drastic fluctuation in influent quality and temperature, and the average removal rate were 88.58%, 93.32%, 94.47%, 73.19%, 96.16%. The relative high abundance of Thermomonas, Thaurea, and Dechloromonas, etc, guaranteed the denitrification efficiency of the MPSR, and Dechloromonas was the main phosphorus removal bacteria in the system. The study confirmed the rationality of the structural design of the MPSR, and it was excellent in sewage treatment and stability.

Simultaneous nitrification and denitrification process using novel surface-modified suspended carriers for the treatment of real domestic wastewater

Moving-bed biofilm reactor (MBBR) is a well-established technology for simultaneous nitrification and denitrification (SND). In MBBR, biofilm development and pollutant removal performance are strictly governed by the physico-chemical properties of the carriers. In this study, novel surface-modified carriers with enhanced hydrophilicity (surface contact angle of 60.2 ± 2.3°) and positively-charged surfaces (+11.7 ± 1.1 mV, pH 7.0) had been prepared successfully via polymer blending, and they had also been implemented in SND system for the treatment of real domestic wastewater. Results showed that accelerated startup of SND with more biomass on the carriers was observed in MBBR system filled with surface-modified carriers. At low DO level (0.6-0.8 mg L^-1) and low C/N ratio (≤5), highly efficient organics removal and SND performance could be achieved with COD removal, TN removal and SND efficiencies of 79.3-85.7%, 62.0-75.9% and 58.5-71.8%, respectively. The efficient performance of SND in MBBR system filled with surface-modified carriers was mainly attributed to the coexistence of enriched mixtrophic nitrifiers and denitrifiers like autotrophic nitrifers (Nitrosomonas, Nitrospira, Nitrobacter), heterotrophic nitrifers (Rudaea), aerobicdenitrifiers (Dokdonella, Terrimonas), anoxic denitrifiers (Gemmobacter, Ottowia, Methyloversatilis, Thermomonas) and N₂O producer (Mesorhizobium).

Effect of periodic temperature shock on nitrogen removal performance and microbial community structure in plug-flow microaerobic sludge blanket

The positive effects nitrogen removal capability in a plug-flow microaerobic sludge blanket at low temperature are confirmed by inducing periodic high temperature shocks. This method enables enhancement of metabolic activity and an optimized bacterial community structure of microbes under the conditions of low C/N ratio and temperature. The control reactor was operated at a constant temperature of 20 °C, and the plug-flow microaerobic sludge blanket was subjected to a high temperature shock treatment with three cycles for 94 d. Starting with the initial temperature of 20 °C, after three cycles at temperature (30 °C) shock, the removal efficiencies of ammonium and total nitrogen at the terminal period increased to 68.0% and 54.7% from 51.1% to 35.6%, respectively. The activity and relative abundance of ammonia oxidizing bacteria, nitrite oxidizing bacteria, and anammox bacteria, dominated by Candidatus Brocadia at low temperature, were accordingly enhanced after periodic temperature shocks.

Cultivation and stable operation of aerobic granular sludge at low temperature by sieving out the batt-like sludge

Aerobic granules were successfully cultivated at 10 °C with relatively low strength substrate. Stable granules coexisted with the batt-like sludge (BLS) were obtained in 60 days. After removing the BLS, nutrient removal performance was greatly improved and stable removal efficiencies of 99% phosphorous, 98% ammonia and 60% TN were achieved. The bacterial community structure revealed that it was an unclassified-Comamonadaceae genus dominant in the BLS, which represented for low relative abundance in mature granules. Overgrowth of unclassified-Comamonadaceae genus was considered to be the key factor for inhibiting the performance of granules. The final configuration of granules was dominated by DPAO genus Flavobacterium and polysaccharide nutritional genus Chryseolinea. This study showed that stable aerobic granules with superior performance under low temperature could be successfully cultivated by sieving out the BLS.

Sludge reduction and microbial structures of aerobic, micro-aerobic and anaerobic side-stream reactor coupled membrane bioreactors

An anoxic/oxic membrane bioreactor (MBR) and three side-stream reactor (SSR) coupled membrane bioreactors were operated in parallel to investigate effects of dissolved oxygen (DO) level in SSR on sludge reduction and microbial community structure of SSR-MBRs. The four MBRs were equally efficient in COD and ammonium nitrogen removal. The anaerobic and micro-aerobic SSR favored nitrogen removal through denitrification, simultaneous nitrification and denitrification and autochthonous substrate release as carbon source. The micro-aerobic SSR achieved greatly higher sludge reduction efficiency (61.1%) than anaerobic (37.3%) and aerobic SSR (7.9%). Micro-aerobic SSR obtained the highest endogenous decay constant (0.035 d^-1) compared to anaerobic (0.023 d^-1) and aerobic SSR (0.015 d^-1). High-throughput sequencing results revealed that anaerobic SSR enriched hydrolytic and fermentative bacteria, aerobic environment favored the growth of slow-growing bacteria, and micro-aerobic SSR stimulated biological activities of both anaerobic and aerobic bacteria.

Terrimonas soli sp. nov., isolated from farmland soil

A Gram-staining-negative, aerobic, non-motile and rod-shaped bacterium that produced yellow viscous colonies, designated FL-8^T, was isolated from farmland soil in Chuzhou, Anhui province, PR China. 16S rRNA gene sequence similarities between strain FL-8^T and the type strains of species of the genus Terrimonas with validly published names ranged from 94.6 to 96.1 %. Strain FL-8^T contained iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH as the predominant fatty acids. The predominant polar lipid of strain FL-8^T was phosphatidylethanolamine. The sole respiratory quinone of strain FL-8^T was MK-7 and the DNA G+C content was 44.8 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain FL-8^T is considered to represent a novel species of the genus Terrimonas, for which the name Terrimonassoli sp. nov. is proposed. The type strain is FL-8^T (=CCTCC AB 2017059^T=JCM 32095^T).

Morphology, composition and aggregation mechanisms of soft bioflocs in marine snow and activated sludge: A comparative review

Conditions that lead to marine snow formation and aggregates that constitute the marine snow have similarities with the soft bioflocs that form during wastewater treatment by activated sludge process. Analysis of the conditions and similarities of the soft bioflocs in these two aquatic environments provide insight for the processes that lead to formation and growth of hydrated aggregates consisting of both living and nonliving particles, their chemical and biolocial composition, settling/suspension behavior, and contributing factors for their structure and morphology. This literature review provides a comparative analysis of the soft aggregates that form in marine and wastewater environments to characterize the conditions for formation and growth of highly hydrated aggregates consisting of microorganisms, suspended solids and large molecules. The marine snow and bioflocs that form in wastewater are visually similar and even contain microorganisms that are of similar type (i.e., Zoogloea, filamentous bacteria). During wastewater treatment, the microorganisms are not stressed and exopolymeric substances (EPS) produced have shorter molecules and higher protein content while EPS produced by the marine organisms are significantly larger in molecular size (by orders of magnitude) and have higher carbohydrate content.

Terrimonas terrae sp. nov., isolated from the rhizosphere of a tomato plant

A yellow, aerobic, Gram-stain-negative, non-motile, rod-shaped and non-flagellated bacterial strain, designated T16R-129T, was isolated from the rhizosphere of a tomato plant collected at a farm located on Buyeo-gun of Chungcheongnam-do, South Korea. Strain T16R-129T grew at 15-40 °C and pH 7.0-9.0, and did not require NaCl for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T16R-129T clustered with members of the genus Terrimonas, and it shared highest similarity with Terrimonas arctica R9-86T (96.1 %), Terrimonas pekingensis QHT (95.9 %), Terrimonas lutea DYT (94.9 %), Terrimonas crocea M1-33108T (95.4 %) and Terrimonas rhizosphaerae CR94T (95.3 %). The major isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipids of strain T16R-129T were phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and five unidentified polar lipids. The G+C content of the genomic DNA was 46.0 mol%. On the basis of data from this polyphasic taxonomic study, strain T16R-129T represents a novel species in the genus Terrimonas, for which the name Terrimonas terrae sp. nov. is proposed; the type strain is T16R-129T (=KACC 18787T=JCM 31603T).

Terrimonas suqianensis sp. nov., isolated from a tetrabromobisphenol A-contaminated soil

Strain C3-5^T, a Gram-negative, asporogenous, rod-shaped bacterium, was isolated from a tetrabromobisphenol A contaminated soil. Growth was observed at 10-37 °C (optimum 30 °C) and at pH 5.5-9.5 (optimum pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain C3-5^T is a member of the genus Terrimonas and exhibits high sequence similarities with Terrimonas pekingensis QH^T (99.0%) and Terrimonas rhizosphaerae CR94^T (97.3%), and exhibits low (<97%) sequence similarities with other known Terrimonas species. Chemotaxonomic analysis revealed that strain C3-5^T possesses menaquinone-7 (MK-7) as the major isoprenoid quinone and iso-C_15:0, iso-C_15:1 G, iso-C_17:0 3-OH and summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c) as the major (>5% of total) fatty acids. The polar lipids were determined to be a lipid, glycolipid, phospholipid, phosphoaminolipid and phosphatidylethanolamine. The DNA G+C content was found to be 42.6 mol%. The DNA-DNA relatedness values with the closely related strains T. pekingensis QH^T and T. rhizosphaerae CR94^T were 25.2 and 48.5%, respectively. Based on phylogenetic analysis, phenotypic characteristics and chemotaxonomic data, strain C3-5^T is considered to represent a novel species of the genus Terrimonas, for which the name Terrimonas suqianensis sp. nov. is proposed. The type strain is C3-5^T (= CCTCC AB 2017042^T = KCTC 52676^T).

Niveitalea solisilvae gen. nov., sp. nov., isolated from forest soil and emended description of the genus Flavihumibacter Zhang et al. 2010

A Gram-stain-negative and strictly aerobic bacterial strain, designated 6-4T, was isolated from forest soil in Jeju island, South Korea. Cells showing oxidase-positive and catalase-negative reactions were thin and long non-motile rods. Growth of strain 6-4T was observed at 20-35 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, pH 7.0). Strain 6-4T contained iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids and menaquinone-7 (MK-7) as the sole isoprenoid quinone. Phosphatidylethanolamine was the major polar lipid and five unidentified aminolipids, one unidentified aminophospholipid and one unidentified lipid were also detected as minor polar lipids. The G+C content of the genomic DNA was 45.8 mol%. Strain 6-4T was most closely related to Flavihumibacter solisilvae 3-3T with a low 16S rRNA gene sequence similarity (94.2 %) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from members of the genus Flavihumibacter and other closely related genera. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain 6-4T represents a novel species of a new genus of the family Chitinophagaceae, for which the name Niveitalea solisilvae gen. nov., sp. nov. is proposed. The type strain of Niveitalea solisilvae is 6-4T (=KACC 18808T=JCM 31525T). An emended description of the genus Flavihumibacter is also proposed.

Terrimonas crocea sp. nov., isolated from the till of a high Arctic glacier

A yellow-pigmented bacterial strain, designated M1-33108T, was isolated from the till of high Arctic glacier Midtre Lovénbreen near Ny-Ålesund, in the West Svalbard Archipelago, Norway. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M1-33108T belonged to the genus Terrimonas and its closest neighbour was Terrimonas arctica R9-86T with 96.12 % 16S rRNA gene sequence similarity. Cells of strain M1-33108T were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped bacteria that lacked motility. Cells contained iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) as its major cellular fatty acids and menaquinone-7 as the sole respiratory quinone. The polar lipid profile of strain M1-33108T consisted of phosphatidylethanolamine, two unknown aminophospholipids, eight unknown aminolipids, an unknown glycolipid and three unknown polar lipids. The DNA G+C content was 45.0 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain M1-33108T is considered to represent a novel species in the genus Terrimonas, for which the name Terrimonas crocea sp. nov. is proposed. The type strain is M1-33108T (=CCTCC AB 2016103T=KCTC 52448T).

Natural microbial populations in a water-based biowaste management system for space life support

The reutilization of wastewater is a key issue with regard to long-term space missions and planetary habitation. This study reports the design, test runs and microbiological analyses of a fixed bed biofiltration system which applies pumice grain (16-25 mm grain size, 90 m(2)/m(3) active surface) as matrix and calcium carbonate as buffer. For activation, the pumice was inoculated with garden soil known to contain a diverse community of microorganisms, thus enabling the filtration system to potentially degrade all kinds of organic matter. Current experiments over 194 days with diluted synthetic urine (7% and 20%) showed that the 7% filter units produced nitrate slowly but steadily (max. 2191 mg NO3-N/day). In the 20% units nitrate production was slower and less stable (max. 1411 mg NO3-N/day). 84% and 76% of the contained nitrogen was converted into nitrate. The low conversion rate is assumed to be due to the high flow rate, which keeps the biofilm on the pumice thin. At the same time the thin biofilm seems to prevent the activity of denitrifiers implicating the existence of a trade off between rate and the amount of nitrogen loss. Microbiological analyses identified a comparatively low number of species (26 in the filter material, 12 in the filtrate) indicating that urine serves as a strongly selective medium and filter units for the degradation of mixed feedstock have to be pre-conditioned on the intended substrates from the beginning.

Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts

Strain SMR-CT, which was originally isolated from rats as the SMR strain, had been named 'cilia-associated respiratory bacillus' ('CAR bacillus'). 'CAR bacillus' was a Gram-stain-negative, filamentous argentophilic bacterium without flagella. SMR-CT grew at 37 °C under microaerobic conditions, showed gliding activity, hydrolysed urea and induced chronic respiratory diseases in rodents. The dominant cellular fatty acids detected were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 47.7 mol%. 16S rRNA gene sequence analysis revealed SMR-CT and other strains of 'CAR bacillus' isolated from rodents all belonged to the phylum Bacteroidetes. The nearest known type strain, with 86 % 16S rRNA gene sequence similarity, was Chitinophaga pinensis DSM 2588T in the family Chitinophagaceae. Strain SMR-CT and closely related strains of 'CAR bacillus' rodent-isolates formed a novel family-level clade in the phylum Bacteroidetes with high bootstrap support (98-100 %). Based on these results, we propose a novel family, Filobacteriaceae fam. nov., in the order Sphingobacteriales as well as a novel genus and species, Filobacterium rodentium gen. nov., sp. nov., for strain SMR-CT. The type strain is SMR-CT ( = JCM 19453T = DSM 100392T).

Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water

A Gram-negative, oxidase- and catalase-positive bacterium, designated strain EM 4(T), which varied in shape from rod-shaped to curved or helical with frequently observed bulb-shaped protuberances, was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the family Chitinophagaceae within the phylum Bacteroidetes; the closest relative among bacterial species with validly published names was determined to be Sediminibacterium salmoneum NBRC 103935(T), with 93.4 % sequence identity. The main fatty acids of strain EM 4(T) were iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, aminolipids, aminophospholipids and unknown lipids; the quinone system consisted of menaquinone MK-7. 16S rRNA gene sequence analysis and the polar lipid and fatty acid profiles suggest that the strain represents a novel genus and species, for which the name Hydrobacter penzbergensis gen. nov., sp. nov. is proposed. The type strain of Hydrobacter penzbergensis is strain EM 4(T) ( = DSM 25353(T) = CCUG 62278(T)).

Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil

Three novel bacterial strains, designated Vu-144(T), Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144(T) was affiliated with an uncultivated lineage of the phylum Bacteroidetes. Its closest phylogenetic neighbour was the recently described species Niastella populi, a member of the family Chitinophagaceae, with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1-APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1-UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45-60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144(T) represents a novel genus and species in the family Chitinophagaceae, for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144(T) ( = KCTC 22378(T) = NCIMB 14473(T)).

Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil

A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family Chitinophagaceae , and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2–92.6 %), Sediminibacterium (90.8–91.4 %) and Chitinophaga (89.2–91.7 %), Filimonas lacunae YT21T (91.7 %), members of the genus Segetibacter (90.2–91.6 %), Parasegetibacter luojiensis RHYL-37T (90.9 %) and Flavihumibacter petaseus T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).

Terrimonas arctica sp. nov., isolated from Arctic tundra soil

A novel, Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated R9-86(T), was isolated from tundra soil collected near Ny-Ålesund, Svalbard Archipelago, Norway (78° N). Growth occurred at 4-28 °C (optimum, 22-25 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R9-86(T) belonged to the genus Terrimonas in the family Chitinophagaceae. 16S rRNA gene sequence similarities between strain R9-86(T) and the type strains of species of the genus Terrimonas with validly published names ranged from 93.7 to 95.0%. Strain R9-86(T) contained iso-C(15:1)-G (25.7%), iso-C(15:0) (24.5%), iso-C(17:0)-3OH (18.3%) and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c, 8.7%) as its major cellular fatty acids; phosphatidylethanolamine and an unknown polar lipid as its main polar lipids, and MK-7 as its predominant respiratory quinone. The DNA G+C content was 48.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain R9-86(T) is considered to represent a novel species of the genus Terrimonas, for which the name Terrimonas arctica sp. nov. is proposed. The type strain is R9-86(T) ( =CCTCC AB 2011004(T) =NRRL B-59114(T)).

Effect of arsenic on nitrification of simulated mining water

Mining and mineral processing of gold-bearing ores often release arsenic to the environment. Ammonium is released when N-based explosives or cyanide are used. Nitrification of simulated As-rich mining waters was investigated in batch bioassays using nitrifying cultures enriched in a fluidized-bed reactor (FBR). Nitrification was maintained at 100mg AsTOT/L. In batch assays, ammonium was totally oxidized by the FBR enrichment in 48 h. As(III) oxidation to As(V) occurred during the first 3h attenuating arsenic toxicity to nitrification. At 150 and 200mg AsTOT/L, nitrification was inhibited by 25%. Candidatus Nitrospira defluvii and other nitrifying species mainly colonized the FBR. In conclusion, the FBR enriched cultures of municipal activated sludge origins tolerated high As concentrations making nitrification a potent process for mining water treatment.

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation

Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.

Cnuella takakiae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides

A Gram-staining-negative, rod-shaped and non-spore-forming bacterium, designated strain RG1-1T, was isolated from Takakia lepidozioides collected from Gawalong glacier in Tibet, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain RG1-1T were iso-C15 : 0 (19.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 17.0 %), C16 : 0 (9.9 %) and iso-C17 : 0 3-OH (9.4 %); its major polar lipids were phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid, one unidentified aminoglycolipid, one unidentified glycolipid, and three unidentified lipids. Strain RG1-1T contained MK-7 as the dominant menaquinone, and the G+C content of its genomic DNA was 49.1 mol%. Strain RG1-1T exhibited the highest 16S rRNA gene sequence similarity (91.8 %) with Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T. Phylogenetic analysis showed that strain RG1-1T was a member of the family Chitinophagaceae , phylum Bacteroidetes . On the basis of 16S rRNA gene sequence analysis, and phenotypic and chemotaxonomic data, strain RG1-1T is considered to represent a novel species of a novel genus, for which the name Cnuella takakiae gen. nov., sp. nov. is proposed. The type strain is RG1-1T ( = CGMCC 1.12492T = DSM 26897T).

Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring

A thermophilic aerobic bacterium designated strain STH-1-Y1(T) was isolated from sulfur-turf in a Japanese hot spring (Okuhodaka hot spring, Gifu Pref.). Colonies of strain STH-1-Y1(T) were yellow and low convex morphology with a slightly irregular fringe. Cells were slender long rods, 0.4-0.6 µm wide and 1.2-3.0 µm long. The isolate was an obligate aerophilic organism, and could not grow by fermentation or nitrate respiration. The isolate had a thermophilic trait, and could grow at 35-60 °C and pH 5.5-7.5; maximum growth occurred at 55 °C and pH 7.0 with a doubling time of 1.9 h. The Biolog and API tests suggested that strain STH-1-Y1(T) was able to use various sugars such as glucose, lactose, mannose, maltose, trehalose, cellobiose and sucrose, but could not use sugar alcohols other than glycerol, i.e. adonitol, arabitol, erythritol, inositol, mannitol, sorbitol and xylitol. Lactate and glutamate could be used, but other fatty acids, i.e. acetate, citrate, propionate and succinate could not. Gelatin, casein, starch and glycogen were hydrolysed, but neither chitin nor agar was degraded. Cells lacked flexirubin and showed oxidase and catalase activities. The major respiratory quinone was menaquinone-7 (MK-7), and major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 0 and anteiso-C15 : 0. No unsaturated fatty acids were detected. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain STH-1-Y1(T) was closely related to the family Chitinophagaceae within the phylum Bacteroidetes. However, the isolate was evenly distant from all members in this family with sequence similarities of 87-89 %. These significantly low sequence similarities strongly suggested that strain STH-1-Y1(T) represents a novel species in a new genus of the family Chitinophagaceae within the phylum Bacteroidetes. Based on phenotypic and phylogenetic characteristics, the name Crenotalea thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is STH-1-Y1(T) ( = JCM 11541(T) = DSM 14807(T)).

Osmotic membrane bioreactor for wastewater treatment and the effect of salt accumulation on system performance and microbial community dynamics

An osmotic membrane bioreactor was developed for wastewater treatment. The effects of salt accumulation on system performance and microbial community dynamics were investigated. Evident deterioration of biological activity, especially nitrification, was observed, which resulted in significant accumulation of organic matter and NH4(+)-N within the bioreactor. Arising from the elevation of salinity, almost all the dominant species was taken over by high salt-tolerant species. Significant succession among different species of Nitromonas was observed for ammonia-oxidizing bacteria. For nitrite-oxidizing bacteria, Nitrospira was not evidently affected, whereas Nitrobacter was eliminated from the system. Salt accumulation also caused significant shifts in denitrifying bacterial community from α- to γ-Proteobacteria members. Overall, the microbial community adapted to the elevated salinity conditions and brought about a rapid recovery of the biological activity. Membrane fouling occurred but was insignificant. Biofouling and inorganic scaling coexisted, with magnesium/calcium phosphate/carbonate compounds identified as the inorganic foulants.

Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus

A light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 °C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes , exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The only respiratory quinone was MK-7 and the DNA G+C content was 40.3 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain PTJT-5T is considered to represent a novel species of a new genus in the family Chitinophagaceae , for which the name Taibaiella smilacinae gen. nov., sp. nov. is proposed. The type strain of Taibaiella smilacinae is PTJT-5T ( = CCTCC AB 2013017T = KCTC 32316T). An emended description of Flavihumibacter petaseus is also proposed.

Heliimonas saccharivorans gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a mineral water aquifer, and emended description of Filimonas lacunae

Two isolates, with optimum growth temperature and pH of about 30 °C and 6.0–7.0, were recovered from a borehole head of a mineral water aquifer in Portugal. The closest relatives based on 16S rRNA gene sequence analysis were species of genera of the family Chitinophagaceae . Strains L2-4T and L2-109 formed translucent colonies and non-motile pleomorphic cells. Strains were strictly aerobic, and oxidase- and catalase-positive. The major fatty acids of strains L2-4T and L2-109 were 17 : 0 iso 3-OH, 15 : 0 iso and 15 : 1 iso G. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid, four unidentified aminophospholipids, four unidentified aminolipids and three unidentified polar lipids. Menaquinone 7 was the only respiratory quinone. The G+C content of the DNA of strains L2-4T and L2-109 was 42.0 and 41.4 mol%, respectively. Based on 16S rRNA gene sequence analysis, physiological and biochemical characteristics, strains L2-4T ( = CECT 8122T = LMG 26919T) and L2-109 ( = CECT 8121 = LMG 26920) are considered to represent a novel species of a new genus, for which the name Heliimonas saccharivorans gen. nov., sp. nov. is proposed. The type strain of Heliimonas saccharivorans is L2-4T. Due to additional results obtained in this study an emended description of Filimonas lacunae is provided.

Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas , Terrimonas ferruginea , Terrimonas lutea and Terrimonas aquatica

A Gram-negative, strictly aerobic, non-motile and non-spore-forming rod that produced white, viscous colonies, designated QHT, was isolated from bulking sludge collected from a municipal wastewater treatment plant in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QHT belonged to the genus Terrimonas and shared 96.3 % sequence similarity with Terrimonas lutea DYT, 94.1 % with Terrimonas ferruginea ATCC 13524T and 93.8 % with Terrimonas aquatica RIB1-6T. Strain QHT contained iso-C15 : 0, summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH) and iso-C15 : 1 G as the predominant fatty acids. The predominant polar lipid of strain QHT and members of the genus Terrimonas was phosphatidylethanolamine. The major isoprenoid quinone of strain QHT was MK-7 and the DNA G+C content was 41.0 mol%. DNA–DNA relatedness between strain QHT and T. lutea BCRC 17944T, T. ferruginea BCRC 17943T and T. aquatica BCRC 17941T was 32, 23 and 22 %, respectively. On the basis of phylogenetic inference, differential phenotypic data and low DNA–DNA relatedness with members of the genus Terrimonas , strain QHT represents a novel species, for which the name Terrimonas pekingensis sp. nov. is proposed. The type strain is QHT ( = CICC 10452T  = NCCB 100397T). The descriptions of the genus Terrimonas and T. ferruginea , T. lutea and T. aquatica are also emended.