Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov

Integrated use of electrochemical anaerobic reactors and genomic based modeling for characterizing methanogenic activity in microbial communities exposed to BTEX contamination

In soil polluted with benzene, toluene, ethylbenzene, and xylenes (BTEX), oxygen is rapidly depleted by aerobic respiration, creating a redox gradient across the plume. Under anaerobic conditions, BTEX biodegradation is then coupled with fermentation and methanogenesis. This study aimed to characterize this multi-step process, focusing on the interactions and functional roles of key microbial groups involved. A reactor system, comprising an Anaerobic Bioreactor (AB) and two Microbial Electrolysis Cell (MEC) chambers, designed to represent different spatial zones along the redox gradient, operated for 160 days with intermittent exposure to BTEX. The functional differentiation of each chamber was reflected by the gas emission profiles: 50%, 12% and 84% methane in the AB, anode and cathode chambers, respectively. The taxonomic profiling, assessed using 16S amplicon sequencing, led to the identification chamber-characteristic taxonomic groups. To translate the taxonomic shift into a functional shift, community dynamics was transformed into a simulative platform based on genome scale metabolic models constructed for 21 species that capture both key functionalities and taxonomies. Representatives include BTEX degraders, fermenters, iron reducers acetoclastic and hydrogenotrophic methanogens. Functionality was inferred according to the identification of the functional gene bamA as a biomarker for anaerobic BTEX degradation, taxonomy and literature support. Comparison of the predicted performances of the reactor-specific communities confirmed that the simulation successfully captured the experimentally recorded functional variation. Variations in the predicted exchange profiles between chambers capture reported and novel competitive and cooperative interactions between methanogens and non-methanogens. Examples include the exchange profiles of hypoxanthine (HYXN) and acetate between fermenters and methanogens, suggesting mechanisms underlying the supportive/repressive effect of taxonomic divergence on methanogenesis. Hence, the platform represents a pioneering attempt to capture the full spectrum of community activity in methanogenic hydrocarbon biodegradation while supporting the future design of optimization strategies.

Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov., marine anaerobic laminarin and xylan degraders in the phylum Bacteroidota

The bacterial group of the phylum Bacteroidota greatly contributes to the global carbon cycle in marine ecosystems through its specialized ability to degrade marine polysaccharides. In this study, it is proposed that two novel facultative anaerobic strains, DS1-an-13321T and DS1-an-2312T, which were isolated from a sea squirt, represent a novel genus, Halosquirtibacter, with two novel species in the family Prolixibacteraceae. The 16S rRNA sequence similarities of these two strains were 91.26% and 91.37%, respectively, against Puteibacter caeruleilacunae JC036T, which is the closest recognized neighbor. The complete genomes of strains DS1-an-13321T and DS1-an-2312T each consisted of a single circular chromosome with a size of 4.47 and 5.19 Mb, respectively. The average amino acid identity and the percentage of conserved proteins against the type species of the genera in the family Prolixibacteraceae ranged from 48.33 to 52.35% and 28.34-37.37%, respectively, which are lower than the threshold for genus demarcation. Strains DS1-an-13321T and DS1-an-2312T could grow on galactose, glucose, maltose, lactose, sucrose, laminarin, and starch, and only DS1-an-2312T could grow on xylose and xylan under fermentation conditions. These strains produced acetic acid and propionic acid as the major fermentation products. Genome mining of the genomes of the two strains revealed 27 and 34 polysaccharide utilization loci, which included 155 and 249 carbohydrate-active enzymes (CAZymes), covering 57 and 65 CAZymes families, respectively. The laminarin-degrading enzymes in both strains were cell-associated, and showed exo-hydrolytic activity releasing glucose as a major product. The xylan-degrading enzymes of strain DS1-an-2312T was also cell-associated, and had endo-hydrolytic activities, releasing xylotriose and xylotetraose as major products. The evidence from phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of a novel genus with two novel species in the family Prolixibacteraceae, for which the names Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov. are proposed. The type strain of Halosquirtibacter laminarini is DS1-an-13321T (= KCTC 25031T = DSM 115329T) and the type strain of Halosquirtibacter xylanolyticus is DS1-an-2312T (= KCTC 25032T = DSM 115328T).

Simultaneously enhancement of methane production and active phosphorus transformation by sludge-based biochar during high solids anaerobic co-digestion of dewatered sludge and food waste: Performance and mechanism

Biochar has been proved to improve methane production in high solids anaerobic co-digestion (HS-AcoD) of dewatered sludge (DS) and food waste (FW), but its potential mechanism for simultaneous methane production and phosphorus (P) transformation has not been sufficiently revealed. Results showed that the optimal preparation temperature and dosage of sludge-based biochar were selected as 300 °C and 0.075 g·g-1, respectively. Under this optimized condition, the methane production of the semi-continuous reactor increased by 54%, and the active phosphorus increased by 18%. The functional microorganisms, such as Methanosarcina, hydrogen-producing, sulfate-reducing, and iron-reducing bacteria, were increased. Metabolic pathways associated with sulfate reduction and methanogenesis, especially hydrogenotrophic methanogenesis, were enhanced, which in turn promoted methanogenesis and phosphorus transformation and release. This study provides theoretical support for simultaneously recovery of carbon and phosphorus resources from DS and FW using biochar.

Tracking the extracellular and intracellular antibiotic resistance genes across whole year in wastewater of intensive dairy farm

Monitoring the annual variation of antibiotic resistance genes (ARGs) in livestock wastewater is important for determining the high-risk period of transfer and spread of animal-derived antibiotic resistance into the environment. However, the knowledge regarding the variation patterns of ARGs, especially intracellular ARGs (iARGs) and extracellular ARGs (eARGs), over time in livestock wastewater is still unclear. Herein, we conducted a year-round study to trace the profiles of ARGs at a Chinese-intensive dairy farm, focusing on the shifts observed in different months. The results showed significant differences in the composition and variation between iARGs and eARGs. Tetracycline, sulfonamide, and macrolide resistance genes were the major types of iARGs, while cfr was the major type of eARG. The environmental adaptations of the host bacteria determine whether ARGs appear as intracellular or extracellular forms. The total abundance of ARGs was higher from April to September, which can be attributed to the favorable climatic conditions for bacterial colonization and increased antibiotic administration during this period. Integron was found to be highly correlated with most iARGs, potentially playing a role in the presence of these genes within cells and their similar transmission patterns in wastewater. The intracellular and extracellular bacterial communities were significantly different, primarily because of variations in bacterial adaptability to the high salt and anaerobic environment. The intracellular co-occurrence network indicated that some dominant genera in wastewater, such as Turicibacter, Clostridium IV, Cloacibacillus, Subdivision5_genera_incertae_sedis, Saccharibacteria_genera_incertae_sedis and Halomonas, were potential hosts for many ARGs. To the best of our knowledge, this study demonstrates, for the first time, the annual variation of ARGs at critical points in the reuse of dairy farm wastewater. It also offers valuable insights into the prevention and control of ARGs derived from animals.

Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment

A Gram-stain-negative, facultative anaerobic, motile, rod-shaped and orange bacterium, designated A06^T, was obtained off the coast of Weihai, PR China. Cells were 0.4-0.5×0.6-1.0 µm in size. Strain A06^T grew at 20-40 °C (optimum, 33 °C), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and in the presence of 0-8 % NaCl (w/v) (optimum, 2 %). Cells were oxidase and catalase positive. Menaquinone-7 was detected as the major respiratory quinone. The dominant cellular fatty acids were identified as C_15:0 2-OH, iso-C_15:0, anteiso-C_15:0 and iso-C_15:1  ω6c. The DNA G+C content of strain A06^T was 46.1 mol%. The polar lipids were phosphatidylethanolamine, one aminolipid, one glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A06^T is a member of the family Prolixibacteraceae and exhibited the highest sequence similarity to Mangrovibacterium diazotrophicum DSM 27148^T (94.3 %). Based on its phylogenetic and phenotypic characteristics, strain A06^T is considered to represent a novel genus in the family Prolixibacteraceae, for which the name Gaoshiqia gen. nov. is proposed. The type species is Gaoshiqia sediminis sp. nov., with type strain A06^T (=KCTC 92029^T=MCCC 1H00491^T). The identification and acquisition of microbial species and genes in sediments will help broaden the understanding of microbial resources and lay a foundation for its application in biotechnology. Strain A06^T uses an enrichment method, so the isolation of strain A06^T is of great significance to the enrichment of marine microbial resources.

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.

Polystyrene nanoplastics shape microbiome and functional metabolism in anaerobic digestion

Nanoplastics (NPs) and microplastics (MPs) are ubiquitous in the natural environment, social production, and life. However, our understanding of the effects of NPs and MPs on shaping the microbiome and functional metabolism of anaerobic microorganisms is limited. We investigated the response of core microbiomes and functional genes to polystyrene (PS) NPs and MPs exposure in a representative anaerobic micro-ecosystem of waste activated sludge. Independent anaerobic digestion (AD) experiment indicated that PS nanobeads suppressed acidogenesis by inhibiting the activity of acetate kinase, and subsequently reduced methane production. Our findings confirmed that MPs (1 and 10 μm) had no perceptible effect on methane production, yet 50 nm NPs resulted in a 15.5% decrease in methane yield, perhaps driven by the behavior of dominant genera Sulfurovum, Candidatus Methanofastidiosum, and Methanobacterium. Assays revealed that NPs contributed to the simplest network assemblies in bacterial communities, contrary to empirical networks in archaeal communities. NPs significantly reduced the abundance of genes involved in carbon degradation: lig, naglu and xylA, as well as gcd and phnK related to phosphorus cycling. The absolute abundance of mcrA encoding methyl-coenzyme M reductase was 54.4% of the control assay. PS NPs might adversely affect the biodiversity and biogeochemical cycles in natural and artificial ecosystems through their negative impact on biomass energy conversion by anaerobic microorganisms.

Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea

A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070T were 4–37 °C (optimum, 16 °C), pH 6.0–9.0 (optimum, pH 7.0) and 1.0 –6.0% (w/v; optimum, 3.0%). The predominant isoprenoid quinone of strain JC070T was identified as menaquinone-7. The dominant fatty acids (>10%) were iso-C15:0 (59.6%) and iso-C17:0 3-OH (17.2%). The major polar lipids were aminophospholipid, aminolipid, two unknown phospholipids and two unidentified lipids. The genomic DNA G+C content was determined to be 37.0 mol%. Based on the results of polyphasic analysis, a new species, named Marinifilum caeruleilacunae sp. nov., within the genus Marinifilum was proposed. The type strain is JC070T (= JCM 39045T=MCCC 1K03774T).

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

Mechanisms Driving Microbial Community Composition in Anaerobic Co-Digestion of Waste-Activated Sewage Sludge

Anaerobic co-digestion (Co-AD) is used to increase the effectiveness of anaerobic digestion (AD) using local “wastes”, adding economic and environmental benefits. Since system stability is of existential importance for the operation of wastewater treatment plants, thorough testing of potential co-substrates and their effects on the respective community and system performance is crucial for understanding and utilizing Co-AD to its best capacity. Food waste (FW) and canola lecithin (CL) were tested in mesophilic, lab-scale, semi-continuous reactors over a duration of 120 days with stepwise increased substrate addition. Key performance indicators (biogas, total/volatile solids, fatty acids) were monitored and combined with 16S-rRNA amplicon sequencing to assess the impact of co-substrate addition on reactor performance and microbial community composition (MCC). Additionally, the latter was then compared with natural shifts occurring in the wastewater treatment plant (WWTP, source) at the same time. An almost linear increase in biogas production with both co-substrates at an approximate 1:1 ratio with the organic loading rate (OLR) was observed. The MCCs in both experiments were mostly stable, but also prone to drift over time. The FW experiment MCC more closely resembled the original WWTP community and the observed shifts indicated high levels of functional redundancy. Exclusive to the CL co-substrate, a clear selection for a few operational taxonomic units (OTUs) was observed. There was little evidence for a persistent invasion and establishment of microorganisms from typical primary substrates into the stable resident community of the reactors, which is in line with earlier findings that suggested that the inoculum and history mostly define the MCC. However, external factors may still tip the scales in favor of a few r-strategists (e.g., Prolixibacter) in an environment that otherwise favors K-strategists, which may in fact also be recruited from the primary substrate (Trichococcus). In our study, specialization and diversity loss were also observed in response to the addition of the highly specialized CL, which in turn, may have adverse effects on the system’s stability and reduced resilience and recovery.

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.

Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22^T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5-10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22^T reduced nitrate to nitrite. Major cellular fatty acids were C_15 : 1 ω6c (13.6 %), C_17 : 0 (11.9 %), anteiso-C_15 : 0 (10.6 %) and iso-C_15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22^T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22^T was Sunxiuqinia faeciviva strain JAM-BA0302^T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22^T (=NBRC 112896^T=DSM 106262^T).

Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment

An alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7^T, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7^T were 0.4-0.6 µm wide and 1.0-8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7^T could grow at 10-37 °C (optimum, 25-28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0.5-6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7^T belonged to the genus Mangrovibacterium of the family Prolixibacteraceae. It showed the highest similarity to Mangrovibacterium diazotrophicum JCM 19152^T (96.8 %), followed by Mangrovibacterium marinum KCTC 42253^T (96.1%). The values of average nucleotide identity and DNA-DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7^T with M. diazotrophicum JCM 19152^T and M. marinum KCTC 42253^T, respectively. The major respiratory quinone of strain BM_7^T was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C_15 : 0, anteiso-C_15 : 0, C_15 : 1  ω6c, iso-C_17 : 0 3-OH, C_17 : 1  ω6c, C_17 : 0 3-OH and C_17 : 0. The genome size of strain BM_7^T is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7^T was considered to represent a novel species of the genus Mangrovibacterium, and the name Mangrovibacterium lignilyticum sp. nov. is proposed. The type strain is BM_7^T (=MCCC 1A15882^T=KCTC 72696^T).

Description of Maribellus sediminis sp. nov., a marine nitrogen-fixing bacterium isolated from sediment of cordgrass and mangrove

Two marine bacterial strains designated Y2-1-60^T and GM1-28 were isolated from sediments of cordgrass and mangrove along the Luoyang estuary in Quanzhou Bay, China, respectively. Both strains were Gram-staining-negative, straight rod-shaped, non-flagellum, facultatively anaerobic, nitrogen-fixing, and did not contain carotenoid pigment. Catalase activities were found to be weak positive and oxidase activities negative. The 16S rRNA gene sequences of the two strains were identical and had maximum similarity of 98.0% with Maribellus luteus XSD2^T, and of <94.5% with other species. ANI value (96.9%) and DDH estimate (71.5%) between the two strains supported that they belonged to the same species. ANI value and DDH estimate between the two strains and M. luteus XSD2^T was 74.3% and 19.4%, respectively, indicating that they represent a novel species. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis indicated that strains Y2-1-60^T and GM1-28 formed a monophyletic branch within the genus Maribellus. The respiratory quinone was menaquinone MK-7. The major fatty acid (>10%) consisted of iso-C_15:0, and iso-C_17:0 3-OH. The polar lipids consisted of phosphatidylethanolamine and several unidentified lipids. The genomic G+C contents were 41.9-42.0mol%. Gene annotation revealed that strains Y2-1-60^T and GM1-28 contained a set of nif gene cluster (nifHDKENB) responsible for nitrogen fixation. Based on the above characteristics, strains Y2-1-60^T and GM1-28 represent a novel species within the genus Maribellus. Thus, Maribellus sediminis sp. nov. is proposed with type strain Y2-1-60^T (=MCCC 1K04285^T=KCTC 72884^T), isolated from cordgrass sediment and strain GM1-28 (=MCCC 1K04384=KCTC 72880), isolated from mangrove sediment.

Puteibacter caeruleilacunae gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from Yongle Blue Hole in the South China Sea

Blue holes are unique geomorphological units characterized by steep redox and biogeochemical gradients. Yongle Blue Hole is located on the largest atoll (Yongle Atoll) of the western Xisha Islands in the South China Sea. A Gram-stain-negative, facultatively anaerobic, non-motile, non-flagellated marine bacterium with creamy white colonies, designated JC036T, was isolated from Yongle Blue Hole. Cells were short-rod-shaped and catalase-negative. 16S rRNA gene sequence analysis showed that sequence similarities were lower than 91.6 % against all validly named species in the familyProlixibacteraceae; a reconstructed phylogenetic tree indicated that strain JC036Tformed a lineage with strains in the familyProlixibacteraceae. Growth occurred at 4–37 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum, 7.0) and in the presence of 2–6 % (w/v) NaCl (optimum, 3 %). The prevalent isoprenoid quinone of strain JC036Twas menaquinone-7 (MK-7). Iso-C15 : 0and iso-C17 : 03-OH were the predominant fatty acids. The major polar lipids included a phospholipid, phosphatidylethanolamine, an aminophospholipid and four unidentified lipids. The genomic DNA G+C content of strain JC036Twas 37.8 mol%. Based on physiological and biochemical characteristics and whole genome comparisons, we propose a new genus and species,Puteibacter caeruleilacunaegen. nov., sp. nov., within the familyProlixibacteraceae. The type strain ofPuteibacter caeruleilacunaeis JC036T(=JCM 33128T=MCCC 1K03579T). From this study, a deeper understanding of the community of the microorganism and their roles in biogeochemical cycles, especially anaerobic bacteria, is provided.

Ancylomarina longa sp. nov., isolated from southern Okinawa Trough sediment and emended description of the family Marinifilaceae

A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-C^T, was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-C^T was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae. Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-C^T was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C_{15 : 0} (38.9 %) and anteiso-C_{15 : 0} (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-C^T was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-C^T is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-C^T (=KCTC 15505^T=MCCC 1K01617^T).

Labilibaculum antarcticum sp. nov., a novel facultative anaerobic, psychrotorelant bacterium isolated from marine sediment of Antarctica

A novel facultative anaerobic and facultative psychrophilic bacterium, designated SPP2^T, was isolated from an Antarctic marine sediment. Cells of the isolate were observed to be long rods (0.5 × 5-10 μm), Gram-stain negative and to have gliding motility. For growth, the optimum NaCl concentration was found to be 2-3% and the optimum temperature to be 18-22 °C. Strain SPP2^T cannot use sulfate and nitrate as electron acceptors in the presence of lactate. The G+C content of the genomic DNA was determined to be 36.0 mol%.. The major cellular fatty acids were identified as anteiso-C_15:0 and iso-C_15:0. MK-7 was found to be the predominant respiratory quinone. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belongs to the family Marinifilaceae and to be closely related to Labilibaculum manganireducens 59.10-2M^T with 16S rRNA gene sequence identity of 98%. The OrthoANI and dDDH values between the genome sequences of strain SPP2^T and its close relative were 84% and 27.3%, which are lower than the threshold values for species delineation. On the basis of phylogenetic and phenotypic characterisation, Labilibaculum antarcticum sp. nov. is proposed with the type strain SPP2^T (= NBRC 111151^T = CECT 9460^T).

Interspecies microbial nexus facilitated methanation of polysaccharidic wastes

Compositional variations in organic wastes influence microbial abundancy and syntrophy during anaerobic digestion (AD), impacting the normal performance of digesters for methanation. Investigation of the microbial dynamics during AD following augmentation with polysaccharidic wastes (PW) revealed the association of effective digester performance and methane yields with the microbial nexus. Dominance of the acidogenic saccharolytic genera, Prevotella, Eubacterium, and Lachnoclostridium, enhanced the utilization of carbohydrates (54%) in PW-augmented digesters. Spearman's rs correlation showed dynamic interspecies interactions among acetogenic syntrophs, and that of iron oxidizers/reducers with acetoclastic and hydrogenotrophic methanogens. Propionate oxidizers in Chloroflexi (i.e., Bellilinea, Levilinea, and Longilinea) exhibited positive associations with acetoclastic methanogens. Increase in the population of acetoclastic methanogens (Methanosaeta, 77% and Methanosarcina, 9%) accelerated the methanogenic activity of PW-augmented digesters by 7 times during the exponential phase, increasing the methane yield (75%) compared to the control. Thus, microbial syntrophy facilitated the effective methanation of PW during AD process.

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.

Ancylomarina salipaludis sp. nov., isolated from a salt marsh

A Gram-stain-negative, aerobic, non-motile and rod-shaped or filamentous bacterial strain, designated SHSM-M15^T, was isolated from a salt marsh at Siheung in Republic of Korea and identified by polyphasic taxonomic study. Strain SHSM-M15^T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain SHSM-M15^T clusters with the type strain of Ancylomarina subtilis, showing 16S rRNA gene sequence similarity of 97.8 %. Strain SHSM-M15^T had 16S rRNA gene sequence similarities of less than 93.7 % with the type strains of other recognised species. Strain SHSM-M15^T contained MK-7 as the predominant menaquinone and iso-C_15 : 0, iso-C_15 : 0 3-OH and anteiso-C_15 : 0 as the major fatty acids. The major polar lipid detected in strain SHSM-M15^T was phosphatidylethanolamine. The DNA G+C content of strain SHSM-M15^T from genomic sequence was 36.6 %. Mean DNA-DNA relatedness value between strain SHSM-M15^T and the type strain of A. subtilis was 18 % and the average nucleotide identity value between strain SHSM-M15^T and the type strain of A. subtilis was 87.98 %. The phylogenetic and genetic data and differential phenotypic properties indicated that strain SHSM-M15^T is separated from A. subtilis. On the basis of the polyphasic data presented, strain SHSM-M15^T is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina salipaludis sp. nov. is proposed. The type strain is SHSM-M15^T (=KACC 19862^T=NBRC 113749^T).

Marinifilum breve sp. nov., a marine bacterium isolated from the Yongle Blue Hole in the South China Sea and emended description of the genus Marinifilum

A Gram-stain-negative, facultative anaerobic, non-motile, short-clavate and non-flagellated marine bacterium strain, designated JC075^T, was isolated from the Yongle Blue Hole in the South China Sea. Based on the 16S rRNA gene sequence, strain JC075^T was found to be closely related to Marinifilum albidiflavum FB208^T (97.10 %), Marinifilum flexuosum DSM 21950^T (96.43 %) and Marinifilum fragile JCM 15579^T (95.58 %), with less than 90.24 % sequence similarity to other genera of the family Marinifilaceae. The growth temperature was in the range of 10-37 °C, and the optimum temperature was 16 °C. Optimal growth occurred at pH 7.0 and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain JC075^T was identified as menaquinone-7 and the predominant fatty acids (>10 %) were iso-C15 : 0 (47.9 %), summed feature 9 (C17 : 1 or/and iso-C17 : 1ω9c; 18.7 %) and iso-C17 : 0 3-OH (14.9 %). The major polar lipids were one phosphatidylethanolamine, one phospholipid, one aminophospholipid, one glycolipid, one aminolipid and two unidentified lipids. The DNA G+C content of strain JC075^T was 35.8 mol%. On the basis of polyphasic analysis, strain JC075^T was considered to represent a novel species of the genus Marinifilum, for which the name Marinifilumbreve sp. nov. is proposed. The type strain is JC075^T (=KCTC 15646^T=MCCC 1K03477^T=JCM 32401^T).

Activated carbon enhanced anaerobic digestion of food waste - Laboratory-scale and Pilot-scale operation

Effects of activated carbon (AC) supplementation on anaerobic digestion (AD) of food waste were elucidated in lab- and pilot-scales. Lab-scale AD was performed in 1 L and 8 L digesters, while pilot-scale AD was conducted in a 1000 L digester. Based on the optimal dose of 15 g AC per working volume derived from the 1 L digester, for the same AC dosage in the 8 L digester, an improved operation stability coupled with a higher methane yield was achieved even when digesters without AC supplementation failed after 59 days due to accumulation of substantial organic intermediates. At the same time, color removal from the liquid phase of the digestate was dramatically enhanced and the particle size of the digestate solids was increased by 53% through AC supplementation after running for 59 days. Pyrosequencing of 16S rRNA gene showed the abundance of predominant phyla Firmicutes, Elusimicrobia and Proteobacteria selectively enhanced by 1.7-fold, 2.9-fold and 2.1-fold, respectively. Pilot-scale digester without AC gave an average methane yield of 0.466 L⋅(gVS)^-1⋅d^-1 at a composition of 53-61% v/v methane. With AC augmentation, an increase of 41% in methane yield was achieved in the 1000 L digester under optimal organic loading rate (1.6 g VS_FW·L^-1·d^-1).

Improved methanization and microbial diversity during batch mode cultivation with repetition of substrate addition using defined organic matter and marine sediment inoculum at seawater salinity

The activation of microbes, which are needed to initiate continuous methane production, can be accomplished by fed-batch methanization. In the present study, marine sediment inoculum was activated by batch mode methanization with repetition of substrate addition using defined organic matter from sugar, protein, or fat at seawater salinity to investigate the potential for application of the activation method to various types of saline waste and microbial community compositions. All substrates had methane potentials close to the theoretical value except for bovine serum albumin (BSA) whose methane potential was lower, but the maximum methane potential reached the value during repeated methanization. Beta diversity analysis revealed that substrate (especially BSA)-fed and non-fed cultures had distinct microbial community compositions. Bacterial members depended on substrate. Thus, marine sediment inocula activated via the methanization method can be used to effectively treat various types of saline waste.

Vertical distribution of microbial community and metabolic pathway in a methanogenic propionate degradation bioreactor

The methanogenic propionate degradation consortia were enriched in a propionate-fed semi-continuous bioreactor. The microbial community shift with depth, the microbial network and its correlation with metabolic pathway were also investigated. The results demonstrated that the maximum organic loading rate (OLR) of the reactor was 2.5g propionic acid (HPr) L^-1d^-1 with approximately 1.20LL^-1d^-1 of volumetric methane production (VMP). The organisms in the enrichment were spanning 36 bacterial phyla and 7 archaeal orders. Syntrophobacter, the main Hpr oxidizer in the digester, dominated bacteria with relative abundance changing from 63% to 37% with depth. The predominant methanogens shift from hydrogenotrophic Methanoculleus (∼60%) at the upper liquid layer to acetoclastic Methanothrix (∼51%) at the lower sediment layer in the bioreactor. These methanogens syntrophically support Syntrophobacter by degrading HPr catabolism by-products (H₂ and acetate). Other bacteria could scavenge anabolic products (carbohydrate and protein) presumably derived from detrital biomass produced by the HPr-degrading community.

Marinifilum albidiflavum sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, facultatively anaerobic, filamentous, and yellowish-white-pigmented marine bacterium, designated strain FB208T, was isolated from marine sediment obtained off the coastal area of Weihai, China. Cells of strain FB208T were filamentous during exponential growth, fragmented to rods in the stationary growth phase and became spherical in aged cultures. It grew optimally at 33 °C, at pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence, strain FB208T was found to be closely related to Marinifilum flexuosum DSM 21950T (96.9 % similarity) and Marinifilum fragile JCM 15579T (96.4 %), with less than 90.0 % sequence similarity to other genera of the class Bacteroidia. Phylogenetic analysis, also based on 16S rRNA gene sequences, placed strain FB208T in the genus Marinifilum, family Marinifilaceae. The predominant isoprenoid quinone of strain FB208T was identified as menaquinone MK-7. The main cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c, and the major polar lipids were an unidentified lipid and aminophospholipid. The G+C content of the genomic DNA was 43.8 mol%. Based on these phylogenetic and phenotypic data, strain FB208T represents a novel species of the genus Marinifilum, for which the name Marinifilum albidiflavum sp. nov. is proposed. The type strain is FB208T (=KCTC 42591T=MCCC 1H00113T).

Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales

A Gram-stain-negative, facultatively anaerobic, moderately halophilic, filamentous, non-motile bacterium, designated FA102T, was isolated from marine sediment from the coast of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FA102T formed a distinct evolutionary lineage within the family Marinifilaceae and its closest relative was Marinifilum fragile JCM 15579T (93.2 % sequence similarity). The DNA G+C content of the novel strain was 36.5 mol%. The predominant cellular fatty acids and respiratory quinone were iso-C15 : 0 and iso-C15 : 0 3-OH, and MK-7, respectively. On the basis of the phylogenetic, phenotypic and physiological data, strain FA102T represents a novel genus and species, for which the name Ancylomarina subtilis gen. nov., sp. nov. is proposed. The type strain of Ancylomarina subtilis is FA102T (=KCTC 42257T=DSM 28825T=CICC 10902T). Furthermore, a new order named Marinilabiliales is proposed to accommodate three families previously classified in the order Bacteroidales. Marinilabiliales ord. nov. encompasses the families Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae.

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

BACKGROUND

Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host.

RESULTS

Here, we provide the first whole genome exploration of this family, for which we propose the name "Candidatus Homeothermaceae," using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of "Ca. Homeothermaceae" to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates.

CONCLUSIONS

"Ca. Homeothermaceae" representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis.

Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov

Members of the phylum Bacteroidetes, which was originally defined as a monophyletic branch encompassing the genera Cytophaga, Flavobacterium and Bacteroides (CFB), are widely studied due to their importance in environmental and gut microbiology. As a consequence, the number of species names with standing in nomenclature has doubled in the past five years. In this study, a revision of an earlier phylogeny of Bacteroidetes has been performed using the 16S rRNA gene as a backbone in combination with the 23S rRNA gene, as well as multilocus sequence analysis (MLSA) of 29 orthologous protein sequences, and indels in the sequences of the beta subunit of the F-type ATPase and the alanyl-tRNA synthetase. In addition, taxonomic data for Bacteroidetes has been updated by considering the orphan species list, signature nucleotides in the 16S rRNA sequence, the list of outlier species, and discrepancies with the current taxonomy at the genus rank level. As a result, seven new taxa are proposed within Bacteroidetes (Chitinophagia classis nov., Chitinophagales ord. nov., Crocinitomicaceae fam. nov., Odoribacteraceae fam. nov., Hymenobacteraceae fam. nov., Thermonemataceae fam. nov. and Persicobacteraceae fam. nov.), as well as one new phylum Rhodothermaeota phyl. nov. that contains two classes, two orders, four families and a new genus with two new combinations.

Mariniphaga sediminis sp. nov., isolated from coastal sediment

A Gram-stain-negative and facultatively anaerobic bacterium, SY21T, was isolated from marine sediments of the coastal area in Weihai, China (122° 0′ 37″ E 37° 31′ 33″ N). Cells of strain SY21T were 0.3–0.5 μm wide and 1.5–2.5 μm long, catalase- and oxidase-positive. Colonies on 2216E agar were transparent, beige- to pale-brown-pigmented, and approximately 0.5 mm in diameter. Growth occurred optimally at 33–37 °C, pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene indicated that strain SY21T was a member of the genus Mariniphaga within the family Prolixibacteraceae. The closest described neighbour in terms of 16S rRNA gene sequences identity was Mariniphaga anaerophila Fu11-5T (94.7 %). The major respiratory quinone of strain SY21T was MK-7, and the dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0. The major polar lipids were phosphatidylethanolamine, aminolipid and an unidentified lipid, and the DNA G+C content was 37.9 mol%. The distinct phylogenetic position and phenotypic traits distinguished the novel isolate from M. anaerophila Fu11-5T. Phenotypic and genotypic analysis indicated that strain SY21T could be assigned to the genus Mariniphaga. The name Mariniphaga sediminis sp. nov. is proposed, with the type strain SY21T ( = KCTC 42260T = MCCC 1H00107T).

Prolixibacter denitrificans sp. nov., an iron-corroding, facultatively aerobic, nitrate-reducing bacterium isolated from crude oil, and emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans

The facultatively aerobic, non-hydrogenotrophic, iron (Fe0)-corroding, nitrate-reducing Prolixibacter sp. strain MIC1-1T was characterized for representation of a novel species of the genus Prolixibacter. Strain MIC1-1T grew optimally at 35–37 °C, at pH 6.5 and with 2  % (w/v) NaCl. Strain MIC1-1T also grew fermentatively on some pentoses, hexoses, disaccharides and soluble starch. Succinic acid was the major end-product from d-glucose fermentation. Strain MIC1-1T was differentiated from the type strain of Prolixibacter bellariivorans by cell size, optimum growth temperature, range of temperature and NaCl for growth, and nitrate reduction. On the basis of phenotypic features and the phylogenetic position, a novel species of the genus Prolixibacter is proposed for strain MIC1-1T, to be named Prolixibacter denitrificans sp. nov. The type strain is MIC1-1T ( = JCM 18694T = NBRC 102688T = DSM 27267T). Emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans are also provided.

Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment

A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08T, was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5–8.0 and with 2–3 % (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88–90 % sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08T ( = KCTC 42261T = CICC 10901T).

Draconibacterium sediminis sp. nov., isolated from river sediment

A Gram-reaction-negative, facultatively anaerobic and rod-shaped bacterium, designated strain JN14CK-3T, was isolated from surface sediment of the Jiulong River of China and was characterized phenotypically and phylogenetically. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain JN14CK-3T belonged to the genus Draconibacterium, with the highest sequence similarity (98.3 %) to Draconibacterium orientale FH5T. By contrast, strain JN14CK-3T shared low 16S rRNA gene sequence similarities ( < 91.0 %) with other type strains. The sole respiratory quinone was MK-7.The polar lipids were phosphatidylethanolamine and several unidentified phospholipids and lipids. The major fatty acids were iso-C15:0, iso-C16:0, anteiso-C15:0, C17:0 2-OH, iso-C16:0 3-OH and iso-C17:0 3-OH. The G+C content of the genomic DNA was 40.9 mol%. The digital DNA–DNA hybridization value and average nucleotide identity (ANI) between strain JN14CK-3T and D. orientale FH5T were 34.2 ± 2.5 % and 87.1 %, respectively. The combined genotypic and phenotypic data showed that strain JN14CK-3T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium sediminis sp. nov. is proposed, with the type strain JN14CK-3T ( = MCCC 1A00734T = KCTC 42152T).

Draconibacterium filum sp. nov., a new species of the genus of Draconibacterium from sediment of the east coast of the Korean Peninsula

A Gram-stain negative, long rod shaped, facultatively anaerobic bacterium, designated strain F2(T), was isolated from coastal sediment of the Korean Peninsula. Strain F2(T) was found to grow at 10-40 °C (optimum 30 °C), at pH 6.0-8.5 (optimum pH 7.5) and at 0.0-8.0 % (w/v) NaCl (optimum 3.0 %). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain F2(T) is closely related to Draconibacterium orientale FH5(T) (with 97.9 % 16S rRNA gene similarity) of the family Prolixibacteraceae of the phylum Bacteroidetes. The major isoprenoid quinone was identified as MK-7 and the main fatty acids as iso-C15:0 (24.1 %), anteiso-C15:0 (15.4 %), C16:0 (10.7 %), iso-C17:0 3-OH (7.6 %) and iso-C16:0 3-OH (5.9 %). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylinositol and four unidentified polar lipids. The genomic DNA G+C content of strain F2(T) was determined to be 44.7 mol% and the DNA-DNA relatedness of strain F2(T) with D. orientale DSM 25947(T) was 34.6 ± 4.3 %. Nitrate reduction capability and cell morphology of strain F2(T) are distinct from those of the closest relative, D. orientale DSM 25947(T). Based on these properties, we propose strain F2(T) represents a novel species within the genus Draconibacterium, with the name Draconibacterium filum sp. nov. The type strain of D. filum is F2(T) (=KCTC 32486(T) = JCM 19986(T)).

Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes

Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093(T) and Geofilum rubicundum JCM 15548(T). In addition to these and previously reported 'Candidatus Azobacteroides pseudotrichonymphae' and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.