DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities

Optimization of fermentation conditions for the production of γ-aminobutyric acid by Lactobacillus hilgardii GZ2 from traditional Chinese fermented beverage system

γ-Aminobutyric acid (GABA) is a crucial neurotransmitter with wide application prospects. In this study, we focused on a GABA-producing strain from a traditional Chinese fermented beverage system. Among the six isolates, Lactobacillus hilgardii GZ2 exhibited the greatest ability to produce GABA in the traditional Chinese fermented beverage system. To increase GABA production, we optimized carbon sources, nitrogen sources, temperature, pH, and monosodium glutamate and glucose concentrations and conducted fed-batch fermentation. The best carbon and nitrogen sources for GABA production and cell growth were glucose, yeast extract and tryptone. Gradual increases in GABA were observed as the glucose and monosodium glutamate concentrations increased from 10 g/L to 50 g/L. During fed-batch fermentation, lactic acid was used to maintain the pH at 5.56, and after feeding with 0.03 g/mL glucose and 0.4 g/mL sodium glutamate for 72 h, the GABA yield reached 239 g/L. This novel high-GABA-producing strain holds great potential for the industrial production of GABA, as well as the development of health-promoting functional foods and medical fields.

The evolutionary mechanism and function analysis of two subgroups of histamine-producing and non-histamine-producing Tetragenococcus halophilus

Tetragenococcus halophilus is a halophilic bacterium that existed in the fermentation of soy sauce and miso for flavor production and probiotic benefits. However, it is composed of two subgroups, histamine-producing and non-histamine-producing, with the former causing histamine accumulation and offering risks to food safety. Exploring the evolutionary mechanisms and physiological function of histamine-biosynthesis is of significance for understanding the formative mechanism of T. halophilus's strain-specificity and is helpful for microbial control. Using systematic genomic analysis, we found that plasmid acquisition and loss is the evolutionary form resulting in the two subgroups of T. halophilus. Two plasmids, plasmid α with 30 kb and plasmid β with 4 kb existed in histamine-producing T. halophilus. We investigated the whole genetic information and proposed their genetic function in both two plasmids. The acquisition of histamine-producing plasmid enhanced the acid tolerance of histamine-producing T. halophilus but did not affect salt tolerance. More interestingly, we found that the existence of plasmid will promote the co-culture growth of T. halophilus. This study deepens our understanding of the formative mechanism of microbial species diversity, and provides our knowledge of the physiological function of histamine-producing plasmids.

Biocontrol of Geosmin Production by Inoculation of Native Microbiota during the Daqu-Making Process

Geosmin produced by Streptomyces can cause an earthy off-flavor at trace levels, seriously deteriorating the quality of Chinese liquor. Geosmin was detected during the Daqu (Chinese liquor fermentation starter)-making process, which is a multi-species fermentation process in an open system. Here, biocontrol, using the native microbiota present in Daqu making, was used to control the geosmin contamination. Six native strains were obtained according to their inhibitory effects on Streptomyces and then were inoculated into the Daqu fermentation. After inoculation, the content of geosmin decreased by 34.40% (from 7.18 ± 0.13 μg/kg to 4.71 ± 0.30 μg/kg) in the early stage and by 55.20% (from 8.86 ± 1.54 μg/kg to 3.97 ± 0.78 μg/kg) in the late stage. High-throughput sequencing combined with an interaction network revealed that the fungal community played an important role in the early stage and the correlation between Pichia and Streptomyces changed from the original indirect promotion to direct inhibition after inoculation. This study provides an effective strategy for controlling geosmin contamination in Daqu via precisely regulating microbial communities, as well as highlights the potential of biocontrol for controlling off-flavor chemicals at trace levels in complex fermentation systems.

In Situ Growth of Halophilic Bacteria in Saline Fracture Fluids from 2.4 km below Surface in the Deep Canadian Shield

Energy derived from water-rock interactions such as serpentinization and radiolysis, among others, can sustain microbial ecosystems deep within the continental crust, expanding the habitable biosphere kilometers below the earth's surface. Here, we describe a viable microbial community including sulfate-reducing microorganisms from one such subsurface lithoautotrophic ecosystem hosted in fracture waters in the Canadian Shield, 2.4 km below the surface in the Kidd Creek Observatory in Timmins, Ontario. The ancient groundwater housed in fractures in this system was previously shown to be rich in abiotically produced hydrogen, sulfate, methane, and short-chain hydrocarbons. We have further investigated this system by collecting filtered water samples and deploying sterile in situ biosampler units into boreholes to provide an attachment surface for the actively growing fraction of the microbial community. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and DNA sequencing analyses were undertaken to classify the recovered microorganisms. Moderately halophilic taxa (e.g., Marinobacter, Idiomarina, Chromohalobacter, Thiobacillus, Hyphomonas, Seohaeicola) were recovered from all sampled boreholes, and those boreholes that had previously been sealed to equilibrate with the fracture water contained taxa consistent with sulfate reduction (e.g., Desulfotomaculum) and hydrogen-driven homoacetogenesis (e.g., Fuchsiella). In contrast to this "corked" borehole that has been isolated from the mine environment for approximately 7 years at the time of sampling, we sampled additional open boreholes. The waters flowing freely from these open boreholes differ from those of the long-sealed borehole. This work complements ongoing efforts to describe the microbial diversity in fracture waters at Kidd Creek in order to better understand the processes shaping life in the deep terrestrial subsurface. In particular, this work demonstrates that anaerobic bacteria and known halophilic taxa are present and viable in the fracture waters presently outflowing from existing boreholes. Major cations and anions found in the fracture waters at the 2.4 km level of the mine are also reported.

Mannitol and erythritol reduce the ethanol yield during Chinese Baijiu production

Chinese Baijiu is prepared using multiple microbial strains and complex metabolites by simultaneous saccharification and fermentation (SSF). Yeasts are challenged by various endogenous and exogenous factors, detrimentally affecting the ethanol yield. It is imperative to identify and control inhibitory factors. In the present study, microbial taxa and metabolites during Baijiu fermentation were evaluated to identify inhibitors of ethanol production. We found that filamentous fungi and Bacillus, contributing to saccharification, were negatively related to the ethanol content (Spearman's |ρ| > 0.5, P < 0.05). To explore how they affect ethanol production, ten filamentous fungi and three Bacillus strains were isolated. In addition to glucose and maltose, polyols were simultaneously generated by filamentous fungi and Bacillus via the hydrolysis of starch, among which mannitol and erythritol had the highest contents of up to 41.56 ± 2.01 g/kg and 16.16 ± 1.13 g/kg, respectively. The presence of mannitol and erythritol inhibited ethanol production by the functional yeasts Saccharomyces cerevisiae and Pichia kudriavzevii. The presence of 10.0 g/L mannitol significantly (P < 0.01) decreased the ethanol yield of S. cerevisiae by 12.67% (from 39.34 ± 0.02% to 32.71 ± 0.49%). These results revealed that polyols may inhibit the production of Baijiu and other fermented foods, suggesting that the origin and influence of polyols should be a focus of future research.

Effect of Pichia on shaping the fermentation microbial community of sauce-flavor Baijiu

In spontaneous food fermentation processes, environmental microbiota affects the yield and quality of the fermentation productions. Although the importance of environmental microbiota has been highlighted, the ecological processes that how the environmental microbiota affects the fermentation microbial community are poorly understood. To study the effect of the environmental microbiota on community assembly, the sources of microbiota and the ecological processes of the fermentation were characterized in sauce-flavor Baijiu. Results showed that the process of sauce-flavor Baijiu making could be divided into three phases according to fermentation parameters. Heap fermentation (phase I) was an important period for rapid temperature rise, substrate utilization and production accumulation. The microbial community of heap fermentation was characterized by decrease of diversity and rapid succession of community structure. Virgibacillus, Kroppenstedtia, Bacillus and Oceanobacillus were predominant in the initial heap fermentation, while Lactobacillus was predominant during the later stage. Pichia was the predominant fungal genus during the whole fermentation process. Then, SourceTracker results showed that Daqu provided 95.6% of the bacterial community and 28.10% of the fungal community to heap fermentation, whereas the environments (indoor ground and tools) provided 71.9% of the fungal communities (mainly Pichia) to heap fermentation. Next, the results revealed that the temperature, ethanol and microbial interaction of Pichia synergistically drove the dynamic of the microbial community during the heap fermentation process. Pichia was proved to be the heat-resistant fungi and strong competitor based on growth in different temperature and competition assays in vitro. Finally, the quick succession of heap fermentation microbiota increased the enrichment of volatile flavors such as acids and esters. Our comprehensive methods shows that Pichia, which mainly comes from the environment, can construct the microbial community of Baijiu fermentation, and highlights the importance of environmental microbiota in attempts to control and promote the formation of Baijiu fermentation microbial community. This systematic study of environmental microbiota is valuable for quality control and management during spontaneous fermentation.

Deciphering the crucial roles of transcriptional regulator GadR on gamma-aminobutyric acid production and acid resistance in Lactobacillus brevis

Background

In lactic acid bacteria (LAB), acid stress leads to decreases of cell vitality and fermentation yield. Glutamate decarboxylase (GAD) system is regarded as one of the essential acid-resistance mechanisms in LAB. However, the regulation of GAD system is not well identified in the genus Lactobacillus. Although potential transcriptional regulator gene located upstream of GAD system genes was found in several Lactobacillus species, such as Lactobacillus (L.) brevis, the contribution of the regulator to acid resistance of the genus Lactobacillus has not been experimentally determined.

Results

The potential transcriptional regulator gene gadR was disrupted by homologous recombination in L. brevis ATCC 367, leading to the decreased expression of gadC and gadB. The inactivation of GadR completely eliminated γ-aminobutyric acid (GABA) production and decreased the glutamate-dependent acid resistance. Moreover, expression of gadC and gadB in the presence of glutamate was increased and glutamate also stimulated the expression of gadR. In addition, L. brevis D17, a strain screened from acidic fermented grains of Chinese liquor production, had much higher expression level of gadR than the typical strain L. brevis ATCC 367. Under the pH-controlled and mixed-feed fermentation, L. brevis D17 achieved a titer of 177.74 g/L and a productivity of 4.94 g/L/h of GABA within 36 h. However, the L. brevis ATCC 367 only achieved a titer of 6.44 g/L and 0.18 g/L/h of GABA although the same fermentation control approach was employed.

Conclusions

GadR is a positive transcriptional regulator controlling GABA conversion and acid resistance in L. brevis. L. brevis strains with hyper-expressing of gadR are excellent candidates for GABA production in industrial scale.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1157-2) contains supplementary material, which is available to authorized users.

Inhibition of Wild Enterobacter cloacae Biofilm Formation by Nanostructured Graphene- and Hexagonal Boron Nitride-Coated Surfaces

Although biofilm formation is a very effective mechanism to sustain bacterial life, it is detrimental in medical and industrial sectors. Current strategies to control biofilm proliferation are typically based on biocides, which exhibit a negative environmental impact. In the search for environmentally friendly solutions, nanotechnology opens the possibility to control the interaction between biological systems and colonized surfaces by introducing nanostructured coatings that have the potential to affect bacterial adhesion by modifying surface properties at the same scale. In this work, we present a study on the performance of graphene and hexagonal boron nitride coatings (h-BN) to reduce biofilm formation. In contraposition to planktonic state, we focused on evaluating the efficiency of graphene and h-BN at the irreversible stage of biofilm formation, where most of the biocide solutions have a poor performance. A wild Enterobacter cloacae strain was isolated, from fouling found in a natural environment, and used in these experiments. According to our results, graphene and h-BN coatings modify surface energy and electrostatic interactions with biological systems. This nanoscale modification determines a significant reduction in biofilm formation at its irreversible stage. No bactericidal effects were found, suggesting both coatings offer a biocompatible solution for biofilm and fouling control in a wide range of applications.

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation

Many microorganisms in the environment participate in the fermentation process of Chinese liquor. However, it is unknown to what extent the environmental microbiota influences fermentation. In this study, high-throughput sequencing combined with multiphasic metabolite target analysis was applied to study the microbial succession and metabolism changes during Chinese liquor fermentation from two environments (old and new workshops). SourceTracker was applied to evaluate the contribution of environmental microbiota to fermentation. Results showed that Daqu contributed 9.10 to 27.39% of bacterial communities and 61.06 to 80.00% of fungal communities to fermentation, whereas environments (outdoor ground, indoor ground, tools, and other unknown environments) contributed 62.61 to 90.90% of bacterial communities and 20.00 to 38.94% of fungal communities to fermentation. In the old workshop, six bacterial genera (Lactobacillus [11.73% average relative abundance], Bacillus [20.78%], Pseudomonas [6.13%], Kroppenstedtia [10.99%], Weissella [16.64%], and Pantoea [3.40%]) and five fungal genera (Pichia [55.10%], Candida [1.47%], Aspergillus [10.66%], Saccharomycopsis [22.11%], and Wickerhamomyces [3.35%]) were abundant at the beginning of fermentation. However, in the new workshop, the change of environmental microbiota decreased the abundances of Bacillus (5.74%), Weissella (6.64%), Pichia (33.91%), Aspergillus (7.08%), and Wickerhamomyces (0.12%), and increased the abundances of Pseudomonas (17.04%), Kroppenstedtia (13.31%), Pantoea (11.41%), Acinetobacter (3.02%), Candida (16.47%), and Kazachstania (1.31%). Meanwhile, in the new workshop, the changes of microbial community resulted in the increase of acetic acid, lactic acid, malic acid, and ethyl acetate, and the decrease of ethyl lactate during fermentation. This study showed that the environmental microbiota was an important source of fermentation microbiota and could drive both microbial succession and metabolic profiles during liquor fermentation.IMPORTANCE Traditional solid-state fermentation of foods and beverages is mainly carried out by complex microbial communities from raw materials, starters, and the processing environments. However, it is still unclear how the environmental microbiota influences the quality of fermented foods and beverages, especially for Chinese liquors. In this study, we utilized high-throughput sequencing, microbial source tracking, and multiphasic metabolite target analysis to analyze the origins of microbiota and the metabolic profiles during liquor fermentation. This study contributes to a deeper understanding of the role of environmental microbiota during fermentation.

Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula

A novel coccus-shaped, Gram-stain-positive, non-motile and facultative aerobic bacterium, designated strain D7T301T, was isolated from the small intestine of a marten, Martes flavigula, which was killed on the road in Pocheon-si, Gyeonggi-do, Republic of Korea. Grown on a tryptic soy yeast agar plate, colonies had a creamy colour and irregular form. The new isolate formed a monophyletic clade with Vagococcus penaei CD276T on a phylogenetic consensus tree based on the 16S rRNA gene sequence. The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5 % (w/v) NaCl. The isolate was catalase- and oxidase-negative. The cell-wall peptidoglycan was type A4α l-Lys-d-Asp. The major cellular fatty acids were C16 : 0, C14 : 0, and C16 : 1ω9c. The predominant respiratory quinone was menaquinone MK-7 (85.1 %). The DNA G+C content based on genome sequencing was 33.8 mol%. The average nucleotide identity value obtained from comparative genomic analysis between strain D7T301T and V. penaei CIP 109914T was 72.6 %. On the basis of the phenotypic, phylogenetic, biochemical, chemotaxonomic, and genotypic analyses, Vagococcusmartis is proposed as a novel species of the genus Vagococcus. The type strain is D7T301T (=KCTC 21069T=JCM 31178T).

Simultaneous biodegradation of carbon tetrachloride and trichloroethylene in a coupled anaerobic/aerobic biobarrier

Simultaneous biodegradation of carbon tetrachloride (CT) and trichloroethylene (TCE) in a biobarrier with polyethylene glycol (PEG) carriers was studied. Toluene/methanol and hydrogen peroxide (H2O2) were used as electron donors and an electron acceptor source, respectively, in order to develop a biologically active zone. The average removal efficiencies for TCE and toluene were over 99.3%, leaving the respective residual concentrations of ∼12 and ∼57μg/L, which are below or close to the groundwater quality standards. The removal efficiency for CT was ∼98.1%, with its residual concentration (65.8μg/L) slightly over the standards. TCE was aerobically cometabolized with toluene as substrate while CT was anaerobically dechlorinated in the presence of electron donors, with the respective stoichiometric amount of chloride released. The oxygen supply at equivalent to 50% chemical oxygen demand of the injected electron donors supported successful toluene oxidation and also allowed local anaerobic environments for CT reduction. The originally augmented (immobilized in PEG carriers) aerobic microbes were gradually outcompeted in obtaining substrate and oxygen. Instead, newly developed biofilms originated from indigenous microbes in soil adapted to the coupled anaerobic/aerobic environment in the carrier for the simultaneous and almost complete removal of CT, TCE, and toluene. The declined removal rates when temperature fell from 28 to 18°C were recovered by doubling the retention time (7.2 days).

Flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, Nipponia nippon, and emended description of the genus Flexivirga

A novel Gram-staining-positive, aerobic, non-motile and coccus-shaped bacterium, designated strain TBS-100T, was isolated from the faeces of a crested ibis, Nipponia nippon. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the closest relative of TBS-100T was Flexivirga alba DSM 24460T with 97.11 % sequence similarity, and that strain TBS-100T belonged to the genus Flexivirga. The optimum growth conditions for strain TBS-100T were 30 °C, at a pH of 7 and in the presence of 0 % (w/v) NaCl. The primary cellular fatty acids of strain TBS-100T were anteiso-C17 : 0 and iso-C17 : 0. The predominant isoprenoid quinones were MK-8 (H4) (70.2 %) and MK-8 (H6) (29.7 %). The polar lipids were diphosphatidylglycerol, phosphatidylinositol, seven unidentified lipids and an unidentified phospholipid. The whole-cell sugars of strain TBS-100T were ribose, glucose, galactose, rhamnose and mannose. The peptidoglycan contained alanine, lysine, glutamic acid, glycine and aspartic acid. The DNA G+C content was 64.8 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain TBS-100T represents a novel species of the genus Flexivirga for which the name Flexivirga lutea sp. nov. is proposed. The type strain is TBS-100T (=KCTC 39625T=JCM 31200T). In addition, an emended description of the genus Flexivirga is proposed.

Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid

A novel Gram-stain-negative, motile, aerobic and rod-shaped alphaproteobacterium, designated strain KHS03T, was isolated from the intestinal tract of a Japanese flying squid, Todarodes pacificus, which was collected from the East Sea, Korea. The new isolate shared 97.4 % 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT. The isolate grew optimally at 25 °C and pH 7 in the presence of 1-2 % (w/v) NaCl, and had an absolute requirement of sodium ions for growth. The major cellular fatty acid was C18 : 1ω7c. The primary isoprenoid quinone was ubiquinone-10. Polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. Genotypic analyses indicated that the whole genomic DNA of the isolate had a G+C content of 59.9 mol%. DNA-DNA hybridization showed that the isolate shared 17.1±2.3 % (reciprocal 17.0±1.9 %) genomic relatedness with the closest related type strain, S. nanhaiensis NH52FT. Strain KHS03T is thus suggested to represent a novel species of the genus Sedimentitalea, for which the name Sedimentitalea todarodis sp. nov. is proposed. The type strain is KHS03T (=KCTC 42412T=JCM 31160T).

Biocontrol of geosmin-producing Streptomyces spp. by two Bacillus strains from Chinese liquor

Streptomyces spp. producing geosmin have been regarded as the most frequent and serious microbial contamination causing earthy off-flavor in Chinese liquor. It is therefore necessary to control the Streptomyces community during liquor fermentation. Biological control, using the native microbiota present in liquor making, appears to be a better solution than chemical methods. The objective of this study was to isolate native microbiota antagonistic toward Streptomyces spp. and then to evaluate the possible action mode of the antagonists. Fourteen Bacillus strains isolated from different Daqu (the fermentation starter) showed antagonistic activity against Streptomyces sampsonii, which is one of the dominant geosmin producers. Bacillus subtilis 2-16 and Bacillus amyloliquefaciens 1-45 from Maotai Daqu significantly inhibited the growth of S. sampsonii by 57.8% and 84.3% respectively, and effectively prevented the geosmin production in the simulated fermentation experiments (inoculation ratio 1:1). To probe the biocontrol mode, the ability of strain 2-16 and 1-45 to produce antimicrobial metabolites and to reduce geosmin in the fermentation system was investigated. Antimicrobial substances were identified as lipopeptides by ultra-performance liquid chromatography tandem electrospray ionization/quadrupole-time-of-flight mass spectrometry (UPLC-ESI/Q-TOF MS) and in vitro antibiotic assay. In addition, strains 2-16 and 1-45 were able to remove 45% and 15% of the geosmin respectively in the simulated solid-state fermentation. This study highlighted the potential of biocontrol, and how the use of native Bacillus species in Daqu could provide an eco-friendly method to prevent growth of Streptomyces spp. and geosmin contamination in Chinese liquor fermentation.

Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus

A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.

Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii

A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity-invasion resistance relationships in bacterial rhizosphere communities.

Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica

A novel Gram-staining-negative, non-spore-forming, non-flagellated, non-motile, aerobic, saffron-coloured, rod-shaped bacterium that did not produce flexirubin-type pigments was designated strain EM7T and was distinct from other members of the genus Bizionia by produce carotenoid-type pigments and being able to grow independently of NaCl. Strain EM7T was isolated from the intestinal tract of an egg cockle, Fulvia mutica, which had been collected from the West Sea in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EM7T belonged to the genus Bizionia, and showed sequence similarity to Bizionia paragorgiae KMM 6029T (97.9 %) and Bizionia saleffrena HFDT (97.73 %). Growth occurred on marine agar 2216 at 0–25 °C (optimum, 20 °C) and at pH 6–9 (optimum, pH 7). Growth occurred in the presence of 0–10 % (w/v) NaCl (optimum, 2 %, w/v, NaCl). The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major respiratory quinone was menaquinone MK-6. The polar lipids of strain EM7T comprised phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophospholipid and two unidentified lipids. The genomic DNA G+C content was 34.8 mol%. Bizionia paragorgiae KMM 6029T and Bizionia saleffrena HFDT to Bizionia paragorgiae KCTC 12304T and Bizionia saleffrena CIP 108534T, respectively. Thus, it is proposed that the isolate represents a novel species, Bizionia fulviae sp. nov., with strain EM7T ( = KACC 18255T = JCM 30417T) as the type strain.

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica

Bacteria belonging to the newly classified candidate phylum “Atribacteria” (formerly referred to as “OP9” and “JS1”) are common in anoxic methane-rich sediments. However, the metabolic functions and biogeochemical role of these microorganisms in the subsurface remains unrealized due to the lack of pure culture representatives. In this study of deep sediment from Antarctica’s Adélie Basin, collected during Expedition 318 of the Integrated Ocean Drilling Program (IODP), Atribacteria-related sequences of the 16S rRNA gene were abundant (up to 51% of the sequences) and steadily increased in relative abundance with depth throughout the methane-rich zones. To better understand the metabolic potential of Atribacteria within this environment, and to compare with phylogenetically distinct Atribacteria from non-deep-sea environments, individual cells were sorted for single cell genomics from sediment collected from 97.41 m below the seafloor from IODP Hole U1357C. As observed for non-marine Atribacteria, a partial single cell genome suggests a heterotrophic metabolism, with Atribacteria potentially producing fermentation products such as acetate, ethanol, and CO₂. These products may in turn support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacteria in anoxic methane-rich sediments. This first report of a single cell genome from deep sediment broadens the known diversity within the Atribacteria phylum and highlights the potential role of Atribacteria in carbon cycling in deep sediment.

Corynebacterium atrinae sp. nov., isolated from the gastrointestinal tract of a pen shell, Atrina pectinata

A novel Gram-stain-positive, non-motile, facultatively anaerobic and rod-shaped bacterium, strain PSPT56T, was isolated from the gastrointestinal tract of a pen shell (Atrina pectinata). Optimal growth of strain PSPT56T was ascertained to occur at 30 °C, pH 8.0 and in the presence of 1–2 % (w/v) NaCl. The strain was catalase-positive and oxidase-negative. The major cellular fatty acids were C18 : 1ω9c, C16 : 0, C17 : 1ω8c and C17 : 0. Tuberculostearic acid was not present. The major cell-wall sugars were ribose, galactose, glucose and arabinose. Peptidoglycan amino acids were meso-diaminopimelic acid, alanine and glutamic acid. The predominant isoprenoid quinone was MK-8(H2). Strain PSPT56T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified lipids and two unidentified amino-lipids. Mycolic acids were detected as constitutive components of the cell wall. A phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain PSPT56T was most closely related to Corynebacterium testudinoris M935/96/4T and Corynebacterium felinum M714/95/5T with 98.69 % and 97.01 % similarity, respectively. DNA–DNA hybridization experiments indicated less than 29.9 % relatedness to the phylogenetically closest species. The G+C content of genomic DNA was 67.6 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain PSPT56T represents a novel species within the genus Corynebacterium , for which the name Corynebacterium atrinae is proposed. The type strain is PSPT56T ( = KACC 17525T = JCM 19266T).

Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter

A novel strain, designated strain W113T, was isolated from the gut of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Actibacter in the family Flavobacteriaceae and it shared the highest sequence similarity with the type strain of Actibacter sediminis (98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C15 : 1 G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113T represents a novel species in the genus Actibacter , for which the name Actibacter haliotis sp. nov. is proposed. The type strain is W113T ( = KACC 17209T = JCM 18868T).

Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata

A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus Polaribacter in the family Flavobacteriaceae and the highest sequence similarity was shared with the type strain of Polaribacter sejongensis (98.5 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C15 : 1ω6c and iso-C15 : 0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus Polaribacter , for which the name Polaribacter atrinae sp. nov. is proposed, with the type strain WP25T ( = KACC 17473T = JCM 19202T).

Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata

A novel bacterium, designated strain WP70(T), was isolated from the gut of a comb pen shell (Atrina pectinata) collected from the southern sea of Yeosu in Korea. The isolate was Gram-stain-negative, aerobic, non-motile and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WP70(T) belonged to the genus Endozoicomonas. The highest level of sequence similarity (98.4%) was shared with Endozoicomonas elysicola MKT110(T). Optimal growth occurred in 2% (w/v) NaCl at 30 °C and at pH 7. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The main respiratory quinone was Q-9. The polar lipids comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid. The genomic DNA G+C content was 50.5 mol% and DNA-DNA hybridization values indicated <11% genomic relatedness to the closest species. Physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WP70(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas atrinae sp. nov. is proposed. The type strain is WP70(T) ( = KACC 17474(T)  = JCM 19190(T)).

Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

A novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80T, was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7–8 and with 1 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80T fell within the cluster of the genus Actinomyces , with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8 % similarity) and Actinomyces urogenitalis (97.0 % similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA–DNA hybridization values with closely related strains indicated less than 7.6 % genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80T represents a novel species of the genus Actinomyces , for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80T ( = KACC 17211T = JCM 18848T).

Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain WM35T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The cells of the isolate grew optimally at 30 °C, pH 7, and with 3 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity comparisons, strain WM35T was grouped in the genus Shimia and was closely related to the type strains of Shimia isoporae (98.7 % similarity) and Shimia marina (97.8 % similarity). The major cellular fatty acids were summed feature 8 and C16 : 0 2-OH. Ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids of strain WM35T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of the isolate was 53.8 mol%. DNA–DNA hybridization values indicated <16 % genomic relatedness with members of the genus Shimia . The physiological, chemical and genotypic analyses indicated that strain WM35T represents a novel species of the genus Shimia , for which the name Shimia haliotis sp. nov. is proposed. The type strain is WM35T ( = KACC 17212T = JCM 18870T).

Paenalcaligenes hermetiae sp. nov., isolated from the larval gut of Hermetia illucens (Diptera: Stratiomyidae), and emended description of the genus Paenalcaligenes

A novel Gram-stain-negative, facultatively anaerobic, non-motile and short rod-shaped bacterium, strain KBL009T, was isolated from the larval gut of Hermetia illucens. Strain KBL009T grew optimally at 37 °C, at pH 6.0 and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence of strain KBL009T showed 97.6 % similarity to that of Paenalcaligenes hominis CCUG 53761AT indicating its classification with the genus Paenalcaligenes . The major fatty acids were cyclo-C17 : 0, C16 : 0 and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The respiratory quinones were ubiquinone-8 (Q-8), predominating, and a minor amount of Q-7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unknown aminolipid and five unknown polar lipids. The polyamine pattern contained predominantly putrescine and relatively high amounts of spermidine. The betaproteobacterial-specific 2-hydroxyputrescine could only be detected in trace amounts. The G+C content of genomic DNA was 56.1 mol%. Results from DNA–DNA hybridization with P. hominis KCTC 23583T unambiguously demonstrated that strain KBL009T represents a novel species in the genus Paenalcaligenes . Based on phenotypic, genotypic and phylogenetic characterization, the novel species Paenalcaligenes hermetiae sp. nov. is proposed. The type strain is KBL009T ( = KACC 16840T = JCM 18423T). An emended description of the genus Paenalcaligenes is also provided.

Cloacibacterium haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai

A novel Gram-stain-negative, aerobic, non-motile, yellow-pigmented and rod-shaped bacterium, designated strain WB5(T), was isolated from the intestinal tract of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. The isolate grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WB5(T) was clustered in the genus Cloacibacterium and shared the highest sequence similarity with C. normanense (98.2 % similarity). The predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Menaquinone-6 was the major respiratory quinone. The genomic DNA G+C content was 29.6 mol%. The DNA-DNA hybridization values indicated <22 % genomic relatedness with other members of the genus Cloacibacterium. The results of physiological, biochemical, chemotaxonomic and genotypic analyses showed that strain WB5(T) represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium haliotis sp. nov. is proposed. The type strain is WB5(T) ( = KACC 17210(T) = JCM 18869(T)).

Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai

A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium, designated strain WM67(T), was isolated from the gut of an abalone (Haliotis discus hannai) collected from the northern coast of Jeju Island in Korea. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain WM67(T) clustered in the genus Pseudoruegeria, and the highest sequence similarity was shared with Pseudoruegeria lutimaris (98.0 % similarity to the type strain). Optimal growth of the isolate occurred at 30 °C, pH 7-8 and with 1 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Ubiquinone Q-10 was the major respiratory quinone. The polar lipids of strain WM67(T) comprised phosphatidylserine, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and three unidentified lipids. The genomic DNA G+C content was 66.5 mol%. DNA-DNA hybridization indicated <17 % genomic relatedness to other members of the genus Pseudoruegeria. The physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WM67(T) represents a novel species of Pseudoruegeria, for which the name Pseudoruegeria haliotis sp. nov. is proposed. The type strain is WM67(T) ( = KACC 17214(T) = JCM 18872(T)).

Enterococcus diestrammenae sp. nov., isolated from the gut of Diestrammena coreana

A novel Gram-stain-positive, facultatively anaerobic, non-motile and lactic-acid-producing bacterium, designated strain ORL-24(T), was isolated from the gut of the camel cricket, Diestrammena coreana. Optimal growth occurred at 37 °C, pH 8 and with 0 % (w/v) NaCl. The ratio of l-lactate to d-lactate in strain ORL-24(T) was 96 : 4. Lancefield antigen D was not detected. The strain was negative for oxidase activity and catalase activity. According to a phylogenetic analysis based on 16S rRNA gene sequences, strain ORL-24(T) was most closely related to the type strain of Enterococcus asini (96.9 % similarity). Comparative pheS and rpoA sequence analyses of strain ORL-24(T) indicated that the strain belonged to the genus Enterococcus. The major fatty acids were C16 : 0 and C18 : 1ω9c. The DNA G+C content was 41.3 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain ORL-24(T) represents a novel species of the genus Enterococcus, for which the name Enterococcus diestrammenae is proposed. The type strain is ORL-24(T) ( = KACC 16708(T) = JCM 18359(T)).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33(T), was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33(T) grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33(T) contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33(T) was most closely related to Gibbsiella quercinecans FRB 97(T) and Gibbsiella dentisursi NUM 1720(T), with 98.7 % similarities. DNA-DNA hybridization experiments indicated less than 40.7 ± 2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97(T). The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33(T) represents a novel species within the genus Gibbsiella, for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33(T) ( = KACC 16707(T) = JCM 18389(T)). An emended description of the genus Gibbsiella is also proposed.

Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii

A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to Ruegeria lacuscaerulensis DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus Ruegeria , for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T  = JCM 17315T).

Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas

A Gram-negative, motile, facultatively anaerobic rod, designated A36T, was isolated from a dead ark clam found on the south coast of Korea. The isolate was catalase- and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain A36T was most closely related to Kistimonas asteriae KMD 001T, with which it shared 98.2 % 16S rRNA gene sequence similarity. Strain A36T grew optimally at 30–37 °C, with 1 % (w/v) NaCl and at pH 8.0. The major respiratory quinone was ubiquinone-9 (Q-9). The major polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 2-OH) and C16 : 0. The genomic DNA G+C content was 47.3 mol%. DNA–DNA relatedness between the isolate and K. asteriae JCM 15607T was <25±3 %. Strain A36T represents a novel species of the genus Kistimonas , for which the name Kistimonas scapharcae sp. nov. is proposed. The type strain is A36T ( = KACC 16204T  = JCM 17805T). An emended description of the genus Kistimonas is also provided.

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria- and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.

Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176)

Abstract The prokaryotic community inhabiting the deep subsurface sediments in the Forearc Basin of the Nankai Trough southeast of Japan (ODP Site 1176) was analyzed by 16S rDNA sequencing. Sediment samples from 1.15, 51.05, 98.50 and 193.96 m below sea floor (mbsf) harbored highly diverse bacterial communities. The most frequently retrieved clones included members of the Green non-sulfur bacteria whose closest relatives come from deep subsurface environments, a new epsilon-proteobacterial phylotype, and representatives of a cluster of closely related bacterial sequences from hydrocarbon- and methane-rich sediments around the world. Archaeal clones were limited to members of the genus Thermococcus, and were only obtained from the two deepest samples.

Tropicimonas sediminicola sp. nov., isolated from marine sediment

A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97T, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97T was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1–2 % (w/v) NaCl and at pH 7–8. The main cellular fatty acids were C16 : 0, C18 : 1ω7c, C12 : 0 3-OH and cyclo-C19 : 0ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97T belongs to the genus Tropicimonas , with highest sequence similarity to Tropicimonas aquimaris DPG-21T (99.0 %). The DNA G+C content of strain M97T was 68.5 mol%. Mean DNA–DNA relatedness between strain M97T and T. aquimaris DPG-21T was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97T is considered to represent a novel species of the genus Tropicimonas , for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97T ( = KACC 15544T = JCM 17731T).

Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus

A novel Gram-stain-negative, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain C7(T), was isolated from the gut of the butterfly Sasakia charonda. Strain C7(T) grew optimally at 20-25 °C, at pH 7-8 and with 1 % (w/v) NaCl. The strain was negative for oxidase activity but positive for catalase activity. The 16S rRNA gene sequences of strain C7(T) and Orbus hercynius CN3(T) shared 96.8 % similarity. The major fatty acids identified were C14 : 0, C16 : 0, C18 : 1ω7c and summed feature 2 (comprising C14 : 0 3-OH/iso-C16 : 1). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C7(T) were phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid and two unidentified aminophospholipids. The G+C content of the genomic DNA extracted from strain C7(T) was 32.1 mol%. Taken together, the phenotypic, genotypic and phylogenetic analyses indicate that strain C7(T) represents a novel species of the genus Orbus, for which the name Orbus sasakiae sp. nov. is proposed. The type strain is C7(T) ( = KACC 16544(T) = JCM 18050(T)). An emended description of the genus Orbus is provided.

Paenibacillus oceanisediminis sp. nov. isolated from marine sediment

A Gram-stain-negative, non-motile, aerobic, endospore forming and rod-shaped bacterium, designated strain L10(T), was isolated from marine sediment collected from the South Korean coast. The organism grew optimally under conditions of 30 °C, 1 % (w/v) NaCl and pH 6.0. It was oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L10(T) was associated with the genus Paenibacillus and most closely related to Paenibacillus barcinonensis BP-23(T) (98.2 % similarity). The major fatty acids of strain L10(T) were iso-C(14 : 0), anteiso-C(15 : 0) and iso-C(16 : 0). The cell-wall peptidoglycan was the A1γ type, and the predominant isoprenoid quinone was menaquinone-7. Strain L10(T) contained two unidentified lipids, an unidentified amino-phospholipid, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The G+C content of the genomic DNA was 44 mol% and the DNA-DNA hybridization values with closely related strains were below 14±2 %. Based on phenotypic, genotypic, and phylogenetic data, strain L10(T) should be classified as a novel species within the genus Paenibacillus. The name Paenibacillus oceanisediminis sp. nov. is proposed. The type strain is L10(T) ( = KACC 16203(T) = JCM 17814(T)).

Leucobacter celer sp. nov., isolated from Korean fermented seafood

A novel, Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterial strain, designated NAL101T, was isolated from gajami-sikhae, a traditional Korean fermented seafood made of flatfish. Growth occurred at 4–45 °C, at pH 5–10 and in 0–12 % (w/v) NaCl. Optimum growth occurred at 30–37 °C, at pH 8 and in 0–1 % (w/v) NaCl. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, threonine and glutamic acid and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-11. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The 16S rRNA gene sequence of strain NAL101T showed 97.7 % similarity to that of Leucobacter chironomi MM2LBT, its closest relative. The DNA G+C content was 68.8 mol% and DNA–DNA hybridization values with closely related strains were <22 %. Phylogenetic analyses based on 16S rRNA gene sequences as well as differences in its physiological and biochemical characteristics indicated that strain NAL101T represents a novel species of the genus Leucobacter in the family Microbacteriaceae, for which the name Leucobacter celer sp. nov. is proposed. The type strain is NAL101T ( = KACC 14220T  = JCM 16465T).

Oceanisphaera sediminis sp. nov., isolated from marine sediment

Two strains, designated TW92(T) and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92(T) grew optimally in the presence of 2 % (w/v) NaCl (range 1-5%) while strain TW93 grew optimally in the presence of 1% (w/v) NaCl (range 0-12%), and both strains had an optimal growth temperature of 30 °C (range 4-37 °C). Strains TW92(T) and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92(T) and TW93 were most closely related to Oceanisphaera donghaensis BL1(T), with 98.8% and 98.7% similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92(T) and TW93 was 99.9%. The major fatty acids of both strains were summed features 3 (comprising C(16:1)ω7c/iso-C(15) 2-OH), C(16:0) and C(18:1)ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92(T) and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA-DNA hybridization of strains TW92(T) and TW93 with related species were below 47% and 31%, respectively. DNA-DNA hybridization values between strains TW92(T) and TW93 were above 85%. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, Oceanisphaera sediminis sp. nov., with strain TW92(T) (=KACC 15117(T)=JCM 17329(T)) as the type strain and strain TW93 (=KACC 15118=JCM 17330) as an additional strain.

Knoellia locipacati sp. nov., from soil of the Demilitarized Zone in South Korea

A gram-positive, aerobic, rod- or coccus-shaped, non-motile bacterium, designated DMZ1(T), was isolated from soil of the Demilitarized Zone, South Korea. Strain DMZ1(T) grew optimally at 30 °C, at pH 7-8 and with 1 % (w/v) NaCl. The isolate showed high 16S rRNA gene sequence similarity with Knoellia aerolata 5317S-21(T) (98.2 %). The cell-wall sugars were glucose and ribose. The peptidoglycan amino acids were meso-diaminopimelic acid, glutamic acid and glycine. The major cellular fatty acids were iso-C(16 : 0), iso-C(15 : 0) and iso-C(14 : 0). The polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and five unknown phospholipids. The isolate did not contain mycolic acids. The DNA G+C content was 72.6 mol%. The isolate showed <28 % DNA-DNA relatedness with members of the genus Knoellia. Phylogenetic, phenotypic and genotypic analysis indicated that strain DMZ1(T) represents a novel species of the genus Knoellia, for which the name Knoellia locipacati sp. nov. is proposed. The type strain is DMZ1(T) ( = KACC 15114(T)  = JCM 17313(T)).

Corynebacterium nuruki sp. nov., isolated from an alcohol fermentation starter

A novel Gram-positive, strictly aerobic and non-motile bacterial strain, S6-4(T), was isolated from a Korean alcohol fermentation starter. Optimal growth occurred at 37 °C, at pH 8 and in 1 % (w/v) NaCl. The isolate was positive for oxidase and catalase. It assimilated various sugars and acids were produced from several carbohydrates. The major cell-wall sugars were galactose and arabinose. The major fatty acids of strain S6-4(T) were C(16 : 0), C(17 : 1)ω9c, C(18 : 1)ω9c and 10-methyl C(18 : 0) (tuberculostearic acid). The predominant isoprenoid quinone was menaquinone MK-9(H(2)) and peptidoglycan amino acids were meso-diaminopimelic acid, alanine, glycine and glutamic acid. The strain contained mycolic acids. According to phylogenetic analysis based on 16S rRNA gene sequences, strain S6-4(T) was most closely related to Corynebacterium variabile DSM 20132(T) (98.1 % similarity). The genomic DNA G+C content of strain S6-4(T) was 73.6 mol% and DNA-DNA hybridization values with related strains were below 33±4 %. On the basis of phenotypic, genotypic and phylogenetic data, strain S6-4(T) represents a novel species in the genus Corynebacterium, for which the name Corynebacterium nuruki sp. nov. is proposed; the type strain is S6-4(T) ( = KACC 15032(T)  = JCM 17162(T)).

Evaluation of DNA extraction methods from complex phototrophic biofilms

Phototrophic biofilms are used in a variety of biotechnological and industrial processes. Understanding their structure, ie microbial composition, is a necessary step for understanding their function and, ultimately, for the success of their application. DNA analysis methods can be used to obtain information on the taxonomic composition and relative abundance of the biofilm members. The potential bias introduced by DNA extraction methods in the study of the diversity of a complex phototrophic sulfide-oxidizing biofilm was examined. The efficiency of eight different DNA extraction methods combining physical, mechanical and chemical procedures was assessed. Methods were compared in terms of extraction efficiency, measured by DNA quantification, and detectable diversity (16S rRNA genes recovered), evaluated by denaturing gradient gel electrophoresis (DGGE). Significant differences were found in DNA yields ranging from 116 +/- 12 to 1893 +/- 96 ng of DNA. The different DGGE fingerprints ranged from 7 to 12 bands. Methods including phenol-chloroform extraction after enzymatic lysis resulted in the greatest DNA yields and detectable diversity. Additionally, two methods showing similar yields and retrieved diversity were compared by cloning and sequencing. Clones belonging to members of the Alpha-, Beta- and Gamma- proteobacteria, Bacteroidetes, Cyanobacteria and to the Firmicutes were recovered from both libraries. However, when bead-beating was applied, clones belonging to the Deltaproteobacteria were also recovered, as well as plastid signatures. Phenol-chloroform extraction after bead-beating and enzymatic lysis was therefore considered to be the most suitable method for DNA extraction from such highly diverse phototrophic biofilms.

A method for obtaining DNA from compost

An effective cell lysis method for extraction of bacterial genomic DNA from compost was developed in this study. Enzymatic disruption method, physical-chemical combination method, and commercial kit method were used to extract DNA from compost samples and were compared by analyzing DNA yield and efficient cell lysis. The results showed that all the three methods can be used to extract high-quality DNA from compost, but the enzymatic method had better cell lysis efficiency and DNA yields than others without the use of special equipment and expensive spending. Comparison of different methods for lysing gram-positive bacteria Bacillus subtilis indicated that the enzymatic cell lysis is superior for destroying the gram-positive cell wall. Spin-bind DNA column was used for DNA purification, and the purity of the purified sample was checked by polymerase chain reaction to amplify a region of the 16S rRNA. Results indicated that the part of 16S rRNA were amplified from all the purified DNA samples, and all the amplification products could be digested by the restriction enzyme HhaI.

Endophytic colonization of potato (Solanum tuberosum L.) by a novel competent bacterial endophyte, Pseudomonas putida strain P9, and its effect on associated bacterial communities

Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.