Bacillus thaonhiensis sp. nov., a new species, was isolated from the forest soil of Kyonggi University by using a modified culture method

Coconut Mesocarp-Based Lignocellulosic Waste as a Substrate for Cellulase Production from High Promising Multienzyme-Producing Bacillus amyloliquefaciens FW2 without Pretreatments

Facing the crucial issue of high cost in cellulase production from commercial celluloses, inexpensive lignocellulosic materials from agricultural wastes have been attractive. Therefore, several studies have focused on increasing the efficiency of cellulase production by potential microorganisms capable of secreting a high and diversified amount of enzymes using agricultural waste as valuable substrates. Especially, extremophilic bacteria play an important role in biorefinery due to their high value catalytic enzymes that are active even under harsh environmental conditions. Therefore, in this study, we aim to investigate the ability to produce cellulase from coconut-mesocarp of the potential bacterial strain FW2 that was isolated from kitchen food waste in South Korea. This strain was tolerant in a wide range of temperature (−6–75 °C, pH range (4.5–12)) and at high salt concentration up to 35% NaCl. The molecular weight of the purified cellulase produced from strain FW2 was estimated to be 55 kDa. Optimal conditions for the enzyme activity using commercial substrates were found to be 40–50 °C, pH 7.0–7.5, and 0–10% NaCl observed in 920 U/mL of CMCase, 1300 U/mL of Avicelase, and 150 U/mL of FPase. It was achieved in 650 U/mL, 720 U/mL, and 140 U/mL of CMCase, Avicelase, and FPase using coconut-mesocarp, respectively. The results revealed that enzyme production by strain FW2 may have significant commercial values for industry, argo-waste treatment, and other potential applications.

Purification and Characterization of Strong Simultaneous Enzyme Production of Protease and α-Amylase from an Extremophile-Bacillus sp. FW2 and Its Possibility in Food Waste Degradation

Microbial enzymes such as protease and amylase are valuable enzymes with various applications, widely investigated for their applications in degradation of organic waste, biofuel industries, agricultural, pharmaceuticals, chemistry, and biotechnology. In particular, extremophiles play an important role in biorefinery due to their novel metabolic products such as high value catalytic enzymes that are active even under harsh environmental conditions. Due to their potentials and very broad activities, this study isolated, investigated, and characterized the protease- and amylase-producing bacterial strain FW2 that was isolated from food waste. Strain FW2 belongs to the genus Bacillus and was found to be closest to Bacillus amyloliquefaciens DSM 7T with a similarity of 99.86%. This strain was able to degrade organic compounds at temperatures from −6 °C to 75 °C (but weak at 80 °C) under a wide pH range (4.5–12) and high-salinity conditions up to 35% NaCl. Maximum enzyme production was obtained at 1200 ± 23.4 U/mL for protease and 2400 ± 45.8 U/mL for amylase for 4 days at pH 7–7.5, 40–45 °C, and 0–10% NaCl. SDS-PAGE analysis showed that the molecular weights of purified protease were 28 kDa and 44 kDa, corresponding to alkaline protease (AprM) and neutral protease (NprM), respectively, and molecular weight of α-amylase was 55 kDa. Degradation food waste was determined after 15 days, observing a 69% of volume decrease. A potential commercial extremozyme-producing bacteria such as strain FW2 may be a promising contributor to waste degradation under extreme environmental conditions.

Improvement of Hydrogen Production during Anaerobic Fermentation of Food Waste Leachate by Enriched Bacterial Culture Using Biochar as an Additive

It has become urgent to develop cost-effective and clean technologies for the rapid and efficient treatment of food waste leachate, caused by the rapid accumulation of food waste volume. Moreover, to face the energy crisis, and to avoid dependence on non-renewable energy sources, the investigation of new sustainable and renewable energy sources from organic waste to energy conversion is an attractive option. Green energy biohydrogen production from food waste leachate, using a microbial pathway, is one of the most efficient technologies, due to its eco-friendly nature and high energy yield. Therefore, the present study aimed to evaluate the ability of an enriched bacterial mixture, isolated from forest soil, to enhance hydrogen production from food waste leachate using biochar. A lab-scale analysis was conducted at 35 °C and at different pH values (4, no adjustment, 6, 6.5, 7, and 7.5) over a period of 15 days. The sample with the enriched bacterial mixture supplemented with an optimum of 10 g/L of biochar showed the highest performance, with a maximum hydrogen yield of 1620 mL/day on day three. The total solid and volatile solid removal rates were 78.5% and 75% after 15 days, respectively. Acetic and butyrate acids were the dominant volatile fatty acids produced during the process, as favorable metabolic pathways for accelerating hydrogen production.

Volatile Fatty Acid Production from Food Waste Leachate Using Enriched Bacterial Culture and Soil Bacteria as Co-Digester

The production of volatile fatty acids (VFAs) from waste stream has been recently getting attention as a cost-effective and environmentally friendly approach in mechanical–biological treatment plants. This is the first study to explore the use of a functional bacterium, AM5 isolated from forest soil, which is capable of enhancing the production of VFAs in the presence of soil bacteria as a co-digester in non-strict anaerobic fermentation processes of food waste leachates. Batch laboratory-scale trials were conducted under thermophilic conditions at 55 °C and different pH values ranging from approximately 5 to 11, as well as under uncontrolled pH for 15 days. Total solid content (TS) and volatile solid content (VS) were observed with 58.42% and 65.17% removal, respectively. An effluent with a VFA concentration of up to 33,849 mg/L (2365.57 mg/g VS; 2244.45 mg/g chemical oxygen demand (COD)-VFA VS; 1249 mg/g VSremoved) was obtained at pH 10.5 on the second day of the batch culture. The pH resulted in a significant effect on VFA concentration and composition at various values. Additionally, all types of VFAs were produced under pH no-adjustment (approximately 5) and at pH 10.5. This research might lead to interesting questions and ideas for further studies on the complex metabolic pathways of microbial communities in the mixture of a soil solution and food waste leachate.

Bacillus spongiae sp. nov., isolated from sponge of Jeju Island

A Gram-reaction-positive, strictly aerobic, motile, endospore- forming, and rod-shaped bacterial strain designated 135PIL107-10^T was isolated from a sponge on Jeju Island, and its taxonomic position was investigated using a polyphasic approach. Strain 135PIL107-10^T grew at 20-37°C (optimum temperature, 25°C) and pH 6.0-10.0 (optimum pH, 6.0) on marine and R2A agars. Based on 16S rRNA gene phylogeny analysis, the novel strain formed a new branch within the genus Bacillus of the family Bacillaceae, and formed clusters with Bacillus thaohiensis NHI-38^T (96.8%), Bacillus fengqiuensis NPK15^T (96.7%), and Bacillus songklensis CAU 1033^T (96.7%). Lower sequence similarities (97.0%) were found with the type strains of all other recognized members of the genus Bacillus (95.6-96.8% similarity). The G + C content of the genomic DNA was 43.6 mol%. The predominant respiratory quinone was menaquinone-7 and the major fatty acids were iso-C_15:0 and iso-C_17:1ω10c. The overall polar lipid patterns were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The isolate therefore represents a novel species, for which the name Bacillus spongiae sp. nov. is proposed, with the type strain 135PIL107-10^T (= KACC 19275^T = LMG 30080^T).

Bacillus zanthoxyli sp. nov., a novel nematicidal bacterium isolated from Chinese red pepper (Zanthoxylum bungeanum Maxim) leaves in China

A novel strain, 1433^T, was isolated from leaves of Chinese red pepper (Huajiao, Zanthoxylum bungeanum Maxim) collected from Gansu province in northwestern China, and was characterised by a polyphasic approach. Cells of strain 1433^T were observed to be Gram-stain positive, aerobic, asporogenous, rod shaped, motile and to have peritrichous flagella. The strain was observed to grow at a range of temperatures and pH, 4-45 °C (optimum 28-32 °C) and 6.0-10.0 (optimum pH 6.0-7.0), respectively. Growth was found to occur in the presence of 0-7% (w/v) NaCl [optimum 0-3% (w/v)]. The G+C content of the genomic DNA was determined to be 41.9 mol% and the cell wall peptidoglycan found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as MK-7 and the major polar lipids as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified polar lipid and three unidentified phospholipids. The major cellular fatty acids were identified as iso-C_15:0 (31.6%), anteiso-C_15:0 (26.9%) and iso-C_14:0 (17.1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1433^T is a member of the genus Bacillus and is closely related to Bacillus aryabhattai DSM 21047^T (99.4% sequence similarity) and Bacillus megaterium DSM 32^T (99.2%). DNA-DNA relatedness of the novel strain 1433^T with B. aryabhattai DSM 21047^T and B. megaterium DSM 32^T was 33.8 ± 2.8% and 28.9 ± 3.4%, respectively. On the basis of the polyphasic evidence presented, strain 1433^T is considered to represent a novel species of the genus Bacillus, for which we propose the name Bacillus zanthoxyli sp. nov. The type strain is 1433^T (= CCTCC AB 2016326^T = KCTC33730^T).

Cultivation strategies for growth of uncultivated bacteria

BACKGROUND

The majority of environmental bacteria and around a third of oral bacteria remain uncultivated. Furthermore, several bacterial phyla have no cultivable members and are recognised only by detection of their DNA by molecular methods. Possible explanations for the resistance of certain bacteria to cultivation in purity in vitro include: unmet fastidious growth requirements; inhibition by environmental conditions or chemical factors produced by neighbouring bacteria in mixed cultures; or conversely, dependence on interactions with other bacteria in the natural environment, without which they cannot survive in isolation. Auxotrophic bacteria, with small genomes lacking in the necessary genetic material to encode for essential nutrients, frequently rely on close symbiotic relationships with other bacteria for survival, and may therefore be recalcitrant to cultivation in purity.

HIGHLIGHT

Since in-vitro culture is essential for the comprehensive characterisation of bacteria, particularly with regard to virulence and antimicrobial resistance, the cultivation of uncultivated organisms has been a primary focus of several research laboratories. Many targeted and open-ended strategies have been devised and successfully used. Examples include: the targeted detection of specific bacteria in mixed plate cultures using colony hybridisation; growth in simulated natural environments or in co-culture with 'helper' strains; and modified media preparation techniques or development of customised media eg. supplementation of media with potential growth-stimulatory factors such as siderophores.

CONCLUSION

Despite significant advances in recent years in methodologies for the cultivation of previously uncultivated bacteria, a substantial proportion remain to be cultured and efforts to devise high-throughput strategies should be a high priority.

Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil

Strain NHI-1T is a Gram-negative, motile, non-spore-forming bacterium isolated from oil-contaminated soil in South Korea. The strain was able to grow by using gasoline, diesel and kerosene as energy and carbon sources. After incubation for 14 days, cells (1 g l− 1) degraded approximately 58 % of oil present at concentration of 1500 p.p.m. at pH 8 and 28 °C. Strain NHI-1T grew well under aerobic conditions, with optimal growth at pH 7–9 and 28 °C–37 °C but grew poorly in the presence of ≥ 0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest relatives of strain NHI-1T were Aquabacterium fontiphilum CS-6T (97.96 % sequence similarity), Aquabacterium parvum B6T (96.39 %), Aquabacterium commune B8T (95.76 %), Aquabacterium limnoticum ABP-4T (95.72 %) and Aquabacterium citratiphilum B4T (95.25 %). DNA–DNA relatedness was 41–53 % between strain NHI-1T and its closest type strains. The major fatty acids present in strain NHI-1T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 44.5 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c, 21.5 %) and C16 : 0 (16.2 %), and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol and uncharacterized aminophospholipids. Strain NHI-1T was distinguishable from other members of genus Aquabacterium based on phenotypic, chemotaxonomic and genotypic characteristics. Therefore, strain NHI-1T represents a novel species of the genus Aquabacterium for which the name Aquabacterium olei sp. nov. is proposed. The type strain is NHI-1T ( = KEMB 9005-082T =  KACC 18244T = NBRC 110486T).

Streptomyces bambusae sp. nov., Showing Antifungal and Antibacterial Activities, Isolated from Bamboo (Bambuseae) Rhizosphere Soil Using a Modified Culture Method

Strain T110(T) was isolated from a bamboo rhizosphere soil sample in the Republic of Korea and was found to produce antibiotics and secondary metabolites against a broad range of bacterial and fungal pathogens. It is a gram-positive actinobacterium with a straight and smooth, spore chain morphology. Morphological, physiological, and biochemical characterization suggest that T110(T) belongs to the genus Streptomyces. The predominant menaquinones of strain T110(T) were MK-9 (H6), MK-9 (H8), and MK-10 (H4). The cell wall peptidoglycan contained L L-diaminopimelic acid, glutamic acid, alanine, and glycine. Ribose and glucose were detected as whole-cell hydrolysates. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol. The main fatty acids were anteiso-C(15:0), anteiso-C(17:0), C(16:0), and iso-C(16:0). Sequence analysis of the 16S rRNA gene (GenBank accession no. KM229361) combined with multiple alignment tools revealed that T110(T) shared the highest degree of similarity with Streptomyces albosporeus subsp. labilomyceticus NBRC 15387(T) (97.9%). However, DNA-DNA hybridization and phylogenetic analysis indicate that strain T110(T) is distinct from its most closely related species. Therefore, we conclude that strain T110(T) is a novel species of the genus Streptomyces and propose naming it Streptomyces bambusae. The type strain is T110(T) (=KEMB 9005-214(T) = KACC 18225(T) = NBRC 110903(T)).

Role of fatty acids in Bacillus environmental adaptation

The large bacterial genus Bacillus is widely distributed in the environment and is able to colonize highly diverse niches. Some Bacillus species harbor pathogenic characteristics. The fatty acid (FA) composition is among the essential criteria used to define Bacillus species. Some elements of the FA pattern composition are common to Bacillus species, whereas others are specific and can be categorized in relation to the ecological niches of the species. Bacillus species are able to modify their FA patterns to adapt to a wide range of environmental changes, including changes in the growth medium, temperature, food processing conditions, and pH. Like many other Gram-positive bacteria, Bacillus strains display a well-defined FA synthesis II system that is equilibrated with a FA degradation pathway and regulated to efficiently respond to the needs of the cell. Like endogenous FAs, exogenous FAs may positively or negatively affect the survival of Bacillus vegetative cells and the spore germination ability in a given environment. Some of these exogenous FAs may provide a powerful strategy for preserving food against contamination by the Bacillus pathogenic strains responsible for foodborne illness.

Psychrobacillus soli sp. nov., capable of degrading oil, isolated from oil-contaminated soil

A novel, aerobic, psychrotolerant, Gram-stain-positive, endospore-forming strain, NHI-2(T), was isolated from oil-contaminated soil near a gas station in Mongolia. This strain was characterized by motile rods and grew over a wide range of temperatures ( -2 to 40 °C) with optimal growth at 28-30 °C. It tolerated salt concentrations of up to 7% over a five-day incubation period. Analysis of 16S rRNA gene sequence indicated that strain NHI-2(T) belongs to the genus Psychrobacillus. Sequence similarity between NHI-2(T) and members of the genus Psychrobacillus with validly published names ranged from 97.83 to 98.18%. DNA-DNA hybridization indicated less than 70% relatedness to reference strains within the genus. The G+C content of the genomic DNA was 36 mol%. This strain contained MK-8 as a predominant isoprenoid menaquinone. NHI-2(T) had ornithine in the cell wall similar to reference strains of the genus Psychrobacillus. The major fatty acids present in NHI-2(T )were anteiso-C15 : 0 (51.0%), iso-C15 : 0 (9.1%) and anteiso-C17 : 0 (8.0%). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. These data highlight that the phenotype of strain NHI-2(T) differs from that of related species in terms of chemotaxonomic properties and genotype characteristics. Therefore, this strain is proposed as a representative of a novel species, named Psychrobacillus soli. The type strain is NHI-2(T) ( = KEMB 9005-135(T) = KACC 18243(T) = NBRC 110600(T)).

Simple surface foam application enhances bioremediation of oil-contaminated soil in cold conditions

Landfarming of oil-contaminated soil is ineffective at low temperatures, because the number and activity of micro-organisms declines. This study presents a simple and versatile technique for bioremediation of diesel-contaminated soil, which involves spraying foam on the soil surface without additional works such as tilling, or supply of water and air. Surfactant foam containing psychrophilic oil-degrading microbes and nutrients was sprayed twice daily over diesel-contaminated soil at 6 °C. Removal efficiencies in total petroleum hydrocarbon (TPH) at 30 days were 46.3% for landfarming and 73.7% for foam-spraying. The first-order kinetic biodegradation rates for landfarming and foam-spraying were calculated as 0.019 d(-1) and 0.044 d(-1), respectively. Foam acted as an insulating medium, keeping the soil 2 °C warmer than ambient air. Sprayed foam was slowly converted to aqueous solution within 10-12h and infiltrated the soil, providing microbes, nutrients, water, and air for bioaugmentation. Furthermore, surfactant present in the aqueous solution accelerated the dissolution of oil from the soil, resulting in readily biodegradable aqueous form. Significant reductions in hydrocarbon concentration were simultaneously observed in both semi-volatile and non-volatile fractions. As the initial soil TPH concentration increased, the TPH removal rate of the foam-spraying method also increased.

Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method

A new, modified culture method that utilizes a transwell plate with a 0.4 µm pore-size microporous membrane was developed. This system allows only trace nutrients from the soil into the liquid culture through the microporous membrane. The method is a more powerful tool for the discovery of novel species from soils than are traditional methods. Such newly identified species could potentially produce useful metabolites. A bacterial strain, T515(T), was isolated using this modified culture method. Growth of strain T515(T) occurred at pH 4-9 in a temperature range between 20 °C and 40 °C and in the presence of 0-2 % (w/v) NaCl on R2A agar. Colonies on the agar plates were tiny, white, and convex after 5 days incubation at 28 °C. Comparative analysis of the nearly full-length 16S rRNA gene sequence of strain T515(T) revealed close pairwise similarity with species of the genus Bacillus, and strain T515(T) was most closely related to Bacillus panaciterrae Gsoil 1517(T) (96.7 %) and Bacillus funiculus NAF001(T) (96.0 %). The major quinone of strain T515(T) was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0 (45.5 %), anteiso-C15 : 0 (23.2 %) and C16 : 0 (10.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain T515(T) was sensitive to streptomycin and tetracycline, but resistant to rifampicin (0.125 µg ml(-1)), ampicillin (0.5 µg ml(-1)) and chloramphenicol (1 µg ml(-1)). The strain showed antimicrobial activities against the six strains tested: Bacillus subtilis KEMB 51201-001, Staphylococcus aureus KEMB 4659, Pseudomonas aeruginosa KACC 10185, Staphylococcus epidermidis KACC 13234, Paenibacillus larvae KACC 14031 and Escherichia coli KEMB 212-234. Based on these results, strain T515(T) represents a novel species of the genus Bacillus with the proposed name, Bacillus polymachus sp. nov. The type strain is T515(T) ( = KEMB 9005-168(T) = KACC 18242(T) = NBRC 110614(T)).

Bacillus fengqiuensis sp. nov., isolated from a typical sandy loam soil under long-term fertilization

A Gram-staining-positive, endospore-forming, moderately alkaliphilic bacterium, strain NPK15(T), was isolated from a typical sandy loam soil under long-term NPK fertilization in northern China and was subjected to a polyphasic taxonomic study. The diamino acid of the cell-wall peptidoglycan of strain NPK15(T) was found to be meso-diaminopimelic acid and the cell-wall sugars were xylose, glucose and traces of mannose. The only respiratory quinone found in strain NPK15(T) was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), C(16 : 0) and C(16 : 1)ω6c/C(16 : 1)ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis of the strain based on its 16S rRNA gene sequence showed that it was related most closely to 'Bacillus thaonhiensis' KACC 17216 (99.59%), B. songklensis KCTC 13881(T) (99.52%) and B. abyssalis CCTCC AB 2012074(T) (99.00%). DNA-DNA hybridization results indicated that the strain was distinct from other species of the genus Bacillus, the degree of relatedness being 35.4% with B. abyssalis CCTCC AB 2012074(T), 39.7% with B. songklensis KCTC 13881(T) and 51.2% with 'B. thaonhiensis' KACC 17216. The DNA G+C content of strain NPK15(T) was 45.5 mol%. Phenotypic, chemotaxonomic and molecular analyses identified strain NPK15(T) as a member of a novel species of the genus Bacillus, for which the name Bacillus fengqiuensis sp. nov. is proposed. The type strain is NPK15(T) ( = DSM 26745(T) = CCTCC AB 2013156(T)).

Isolation of Paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-Do, Korea

Using a new culture method for unculturable soil bacteria, strain NB5(T) was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0-9.5 (optimum, 6.5-9.5) and at temperatures between 15°C and 45°C (optimum, 25-40°C). Growth was possible at 0-5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3(T) and P. agaridevorans DSM 1355(T), respectively. The predominant menaquinone in NB5(T) was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472(T)=KEMB 9005-025(T)=JCM 19203(T)).