Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the c... more Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. ''Nitrosopumilus koreensis'' AR1 and ''Nitrosopumilus sediminis'' AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer hemecontaining proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.
Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the m... more Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the mechanism of reducing the salinity stress on anammox granules is essential for the application of the anammox process for saline wastewater treatment. In this study, the effect of Ca2+ and Mg2+ augmentation on the recovery of the activity of freshwater anammox granules affected by salinity stress was evaluated. At the condition of a salinity stress of 5 g NaCl/L, the specific anammox activity (SAA) of the granule decreased to 50% of that of the SAA without NaCl treatment. Augmentation of Ca2+ at the optimum concentration of 200 mg/L increased the SAA up to 78% of the original activity, while the augmentation of Mg2+ at the optimum concentration of 70 mg/L increased the SAA up to 71%. EPS production in the granules was increased by the augmentation of divalent cations compared with the granules affected by salinity stress. In the soluble EPS, the ratio of protein to polysaccharides was hig...
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed... more Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate...
New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions... more New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions were isolated from industrial wastewater. The successful enrichment and isolation of these strains required selenite as a trace element. These isolates appeared to be closely related to Azoarcus species according to the results of 16S rRNA sequence analysis. An isolated strain, pF6, metabolized pyridine through the same pathway under both aerobic and anaerobic conditions. Since pyridine induced NAD-linked glutarate-dialdehyde dehydrogenase and isocitratase activities, it is likely that the mechanism of pyridine degradation in strain pF6 involves N-C-2 ring cleavage. Strain pF6 could degrade pyridine in the presence of nitrate, nitrite, and nitrous oxide as electron acceptors. In a batch culture with 6 mM nitrate, degradation of pyridine and denitrification were not sensitively affected by the redox potential, which gradually decreased from 150 to -200 mV. In a batch culture with the nit...
A dibenzothiophene (DBT)-desulfurizing bacterial strain was isolated and identified as Gordona st... more A dibenzothiophene (DBT)-desulfurizing bacterial strain was isolated and identified as Gordona strain CYKS1. Strain CYKS1 was found to transform DBT to 2-hydroxybiphenyl via the 4S pathway and to be able to also use organic sulfur compounds other than DBT as a sole sulfur source. Its desulfurization activity was susceptible to sulfate repression. Active resting cells for desulfurization could be prepared only in the early growth phase. When two types of diesel oils, middle distillate unit feed (MDUF) and light gas oil (LGO) containing various organic sulfur compounds including DBT, were treated with resting cells of strain CYKS1 for 12 h, the total sulfur content significantly decreased, from 0.15% (wt/wt) to 0.06% (wt/wt) for MDUF and from 0.3% (wt/wt) to 0.25% (wt/wt) for LGO. The newly isolated strain CYKS1 is considered to have good potential for application in the biodesulfurization of fossil fuels.
Soil acidification is accelerated by anthropogenic and agricultural activities, which could signi... more Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.
Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-redu... more Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H and Na ions, respectively. Strain IRF9 harbored two different ty...
Proceedings of the National Academy of Sciences of the United States of America, Jul 23, 2016
Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitousl... more Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dis...
The Cr(VI) concentrations at the shallow aquifer well (MPH-0-1) of the Moonpyung groundwater moni... more The Cr(VI) concentrations at the shallow aquifer well (MPH-0-1) of the Moonpyung groundwater monitoring station were in the range of 0.5 to 3.1 mg/L exceeding 10 to 62 times the guideline for drinking-water quality, indicating continuous contamination. However, Cr was not detected at the deep bedrock well and the other subsidiary monitoring wells except for MPH-1 and 6. Cross-correlation analyses were conducted for rainfall and groundwater level time series, resulting in the mean time of recharge after precipitation events to be 5.6 days. For rainy season, the water level was raised and the Cr(VI) concentration was several times lower than that during dry season at well MPH-0-1 well. Correlation of the Cr(VI) concentration with the groundwater-level showed that the Cr(VI) reduction was closely related with the groundwater-level rise in the well. However, the groundwater level rise during high water season induced the lateral migration of the Cr(VI)-contaminated groundwater at well M...
A Gram-positive and endospore-forming strain, JH8T, was isolated from deep-sea sediment and ident... more A Gram-positive and endospore-forming strain, JH8T, was isolated from deep-sea sediment and identified as a member of the genus Paenibacillus on the basis of 16S rRNA gene sequence and phenotypic analyses. According to a phylogenetic analysis, the most closely related species was Paenibacillus wynnii LMG 22176T (96.9%). Strain JH8T was also facultatively anaerobic and grew optimally at 20-25degreesC. The major cellular fatty acid was anteiso-C15:0, and the DNA G+C content was 53.1 mol%. The DNA-DNA relatedness between the isolate and Paenibacillus wynnii LMG 22176T was 7.6%, indicating that strain JH8T and P. wynnii belong to different species. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain JH8T would appear to belong to a novel species, for which the name Paenibacillus donghaensis sp. nov. is proposed (type strain =KCTC 13049T=LMG 23780T).
The effect of the presence of an alternate toxic compound (phenol) on the p-nitrophenol (PNP)-deg... more The effect of the presence of an alternate toxic compound (phenol) on the p-nitrophenol (PNP)-degrading activity of freely suspended and calcium alginate immobilized Nocardioides sp. NSP41 was investigated. In the single substrate experiments, when the concentration of phenol and PNP was increased to 1400 mg l −1 and 400 mg l −1 , respectively, the initial cell concentrations in the freely suspended cell culture should be higher than 1.5 g dry cell weight l −1 for complete degradation. In the simultaneous degradation experiment, when the initial concentration of phenol was increased from 100 to 400 mg l −1 , the specific PNP degradation rate at the concentration of 200 mg l −1 was decreased from 0.028 to 0.021 h −1. A freely suspended cell culture with a high initial cell concentration resulted in a high volumetric degradation rate, suggesting the potential use of immobilized cells for simultaneous degradation. In the immobilized cell cultures, although simultaneous degradation of PNP and phenol was maintained, the specific PNP and phenol degradation rate decreased. However, a high volumetric PNP and phenol degradation rate could be achieved by immobilization because of the high cell concentration. Furthermore, when the immobilized cells were reused in the simultaneous degradation of PNP and phenol, they did not lose their PNP-and phenol-degrading activity for 12 times in semi-continuous cultures. Taken together, the use of immobilized Nocardioides sp. NSP41 for the simultaneous degradation of PNP and phenol at high concentrations is quite feasible because of the high volumetric PNP and phenol degradation rate and the reusability of immobilized cells. Abbreviations: DCW-dry cell weight (mg l −1), 4-NC-4-nitrocatechol, PNPp-nitrophenol, q-specific degradation rate (h −1), r-volumetric degradation rate (mg l −1 h −1), Y-biomass yield (g g −1
Metal ions (Cd2+, Cu2+, Ni2+, Zn2+ and Cr3+) did not affect glucose degradation or the production... more Metal ions (Cd2+, Cu2+, Ni2+, Zn2+ and Cr3+) did not affect glucose degradation or the production of methane during anaerobic digestion with intact and disintegrated granules from a UASB (Upflow Anaerobic Sludge Blanket) reactor. However, when Cu2+ was at 500 mg g-1 VSS (volatile suspended solids) in the media, the glucose degradation rates and methane production rates decreased by 14% and
Indigenous bacteria isolated from contaminated sites play important roles to remediate contaminat... more Indigenous bacteria isolated from contaminated sites play important roles to remediate contaminated groundwater. Chromium has the most stable oxidation states. Cr(VI) is toxic, carcinogenic, and mobile, but Cr(III) is less toxic and immobile. In this study, indigenous microorganism (MMPH-0) was enriched from Cr(VI) contaminated groundwater, and identified by 16S rRNA gene analysis. Using MMPH-0, the effect of stimulating with e-donors (glucose, lactate, acetate, and no e-donor control), respiration conditions, biomass, tolerance, and geochemical changes on Cr(VI) reduction were investigated in batch experiments for 4 weeks. The changes of Cr(VI) concentration and geochemical conditions were monitored using UV-vis-spectrophotometer and Eh-pH meter. And the morphological and chemical characteristics of MMPH-0 and precipitates in the effluents were characterized by TEM-EDS and SEM-EDS analyses. MMPH-0 (Enterobacter aerogenes) was able to tolerate up to 2000 mg/L Cr(VI) and reduce Cr(VI) under aerobic and anaerobic conditions. MMPH-0 performed faster and higher efficiency of Cr(VI) reduction with electron donors (over 70% after 1 week with e-donor, 10-20% after 4 weeks without e-donor). The changes of Eh-pH in effluents showing the tendency from oxidizing to reducing condition and a bit of acidic change in pH due to microbial oxidation of organic matters donating electrons and protons suggested the roles of MMPH-0 on Cr(VI) in the contaminated water catalyzing to transit geochemical stable zone for more stable Cr(OH) 3 or Cr(III) precipitates. TEM/SEM-EDS analyses of MMPH-0 and precipitates indicate direct and indirect Cr(VI) reduction: extracellular polymers capturing Cr component outside cells. These results suggested diverse indigenous bacteria and their biogeochemical reactions might enhance more effective and feasible remediation technology of redox sensitive heavy metals in metal-contaminated in groundwater.
Microbially mediated dehalogenation processes contribute to the global cycling of both biogenic a... more Microbially mediated dehalogenation processes contribute to the global cycling of both biogenic and anthropogenic halogenated organic compounds. Detailed information on biodegradation mechanisms for a variety of organohalides and on the microorganisms mediating these processes has greatly increased our understanding of the cycling and fate of these unique and widespread compounds in our environment. The marine environment appears to be a particularly rich source of dehalogenating microorganisms. It is well established by laboratory and field studies that anaerobic dehalogenation of sediment contaminants, such as PCBs, pesticides, and dioxins, occurs intrinsically and can be enhanced via various methods. Specific dehalogenating bacterial populations can be enriched on various organohalides. Biodehalogenation processes are likely to be significantly affected by the prevailing terminal electron-accepting condition, and thus, biotransformation of organohalide contaminants in marine and estuarine environments will vary as a function of the redox conditions within the sediment profile. Fundamental knowledge of the activities and interactions of dehalogenating microorganisms is providing a strong basis for development of new bioremediation technologies for removal of harmful halogenated compounds from our environment.
A chlorophenol-contaminated soil was tested for the biodegradability in a semi-pilot scale microc... more A chlorophenol-contaminated soil was tested for the biodegradability in a semi-pilot scale microcosm using indigenous microorganisms. More than 90% of 4-chlorophenol and 2,4,6-trichlorophenol, initially at 30 mg kg-1, were removed within 60 days and 30 mg pentachlorophenol kg-1 was completely degraded within 140 days. The chlorophenols were degraded more effectively under aerobic condition than under anaerobic condition. Soil moisture had a significant effect with the slowest degradation rate of chlorophenols at 25% in the range of 10–40% moisture content. At 25–40%, the rate of chlorophenol degradation was directly related to the soil moisture content, whereas at 10–25%, it was inversely related. Limited oxygen availability through soil agglomeration at 25% moisture content might decrease the degradation rate of chlorophenols.
The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it repres... more The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39-42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta-and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria (some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly detected by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.
The fatty acid composition of Pimelobacter sp. is of the complex type. When pyridine was used as ... more The fatty acid composition of Pimelobacter sp. is of the complex type. When pyridine was used as a sole inhibitory substrate, the fatty acid composition of Pimelobacter sp. was quite different from that within other readily available substrates. When compared with the fatty acid composition in a complex medium, the proportion of isopalmitic acid (iso-CIs,.) drastically decreased from 68.4% to 7.7%, while the proportion of anteisoheptadecanoic acid (anteiso-CIT:o) remained almost constant at ca. 7%. Concomitantly, this decrease of the branched-chain fatty acid was accompanied by the increase of the straight-chain, especially long-chain, fatty acid such as heptadecanoic (CITLO), octadecenoic (Clszl), IO-methylheptadecanoic (lo-me-18) and lo-methyloctadecanoic (lo-me-19) acids. Consequently, in response to membrane active organic solvents, Pimelobacter sp. was found to regulate its membrane fatty acid composition in a fashion different from Gram-negative bacteria.
Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the c... more Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. ''Nitrosopumilus koreensis'' AR1 and ''Nitrosopumilus sediminis'' AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer hemecontaining proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.
Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the m... more Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the mechanism of reducing the salinity stress on anammox granules is essential for the application of the anammox process for saline wastewater treatment. In this study, the effect of Ca2+ and Mg2+ augmentation on the recovery of the activity of freshwater anammox granules affected by salinity stress was evaluated. At the condition of a salinity stress of 5 g NaCl/L, the specific anammox activity (SAA) of the granule decreased to 50% of that of the SAA without NaCl treatment. Augmentation of Ca2+ at the optimum concentration of 200 mg/L increased the SAA up to 78% of the original activity, while the augmentation of Mg2+ at the optimum concentration of 70 mg/L increased the SAA up to 71%. EPS production in the granules was increased by the augmentation of divalent cations compared with the granules affected by salinity stress. In the soluble EPS, the ratio of protein to polysaccharides was hig...
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed... more Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate...
New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions... more New denitrifying bacteria that could degrade pyridine under both aerobic and anaerobic conditions were isolated from industrial wastewater. The successful enrichment and isolation of these strains required selenite as a trace element. These isolates appeared to be closely related to Azoarcus species according to the results of 16S rRNA sequence analysis. An isolated strain, pF6, metabolized pyridine through the same pathway under both aerobic and anaerobic conditions. Since pyridine induced NAD-linked glutarate-dialdehyde dehydrogenase and isocitratase activities, it is likely that the mechanism of pyridine degradation in strain pF6 involves N-C-2 ring cleavage. Strain pF6 could degrade pyridine in the presence of nitrate, nitrite, and nitrous oxide as electron acceptors. In a batch culture with 6 mM nitrate, degradation of pyridine and denitrification were not sensitively affected by the redox potential, which gradually decreased from 150 to -200 mV. In a batch culture with the nit...
A dibenzothiophene (DBT)-desulfurizing bacterial strain was isolated and identified as Gordona st... more A dibenzothiophene (DBT)-desulfurizing bacterial strain was isolated and identified as Gordona strain CYKS1. Strain CYKS1 was found to transform DBT to 2-hydroxybiphenyl via the 4S pathway and to be able to also use organic sulfur compounds other than DBT as a sole sulfur source. Its desulfurization activity was susceptible to sulfate repression. Active resting cells for desulfurization could be prepared only in the early growth phase. When two types of diesel oils, middle distillate unit feed (MDUF) and light gas oil (LGO) containing various organic sulfur compounds including DBT, were treated with resting cells of strain CYKS1 for 12 h, the total sulfur content significantly decreased, from 0.15% (wt/wt) to 0.06% (wt/wt) for MDUF and from 0.3% (wt/wt) to 0.25% (wt/wt) for LGO. The newly isolated strain CYKS1 is considered to have good potential for application in the biodesulfurization of fossil fuels.
Soil acidification is accelerated by anthropogenic and agricultural activities, which could signi... more Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.
Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-redu... more Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H and Na ions, respectively. Strain IRF9 harbored two different ty...
Proceedings of the National Academy of Sciences of the United States of America, Jul 23, 2016
Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitousl... more Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dis...
The Cr(VI) concentrations at the shallow aquifer well (MPH-0-1) of the Moonpyung groundwater moni... more The Cr(VI) concentrations at the shallow aquifer well (MPH-0-1) of the Moonpyung groundwater monitoring station were in the range of 0.5 to 3.1 mg/L exceeding 10 to 62 times the guideline for drinking-water quality, indicating continuous contamination. However, Cr was not detected at the deep bedrock well and the other subsidiary monitoring wells except for MPH-1 and 6. Cross-correlation analyses were conducted for rainfall and groundwater level time series, resulting in the mean time of recharge after precipitation events to be 5.6 days. For rainy season, the water level was raised and the Cr(VI) concentration was several times lower than that during dry season at well MPH-0-1 well. Correlation of the Cr(VI) concentration with the groundwater-level showed that the Cr(VI) reduction was closely related with the groundwater-level rise in the well. However, the groundwater level rise during high water season induced the lateral migration of the Cr(VI)-contaminated groundwater at well M...
A Gram-positive and endospore-forming strain, JH8T, was isolated from deep-sea sediment and ident... more A Gram-positive and endospore-forming strain, JH8T, was isolated from deep-sea sediment and identified as a member of the genus Paenibacillus on the basis of 16S rRNA gene sequence and phenotypic analyses. According to a phylogenetic analysis, the most closely related species was Paenibacillus wynnii LMG 22176T (96.9%). Strain JH8T was also facultatively anaerobic and grew optimally at 20-25degreesC. The major cellular fatty acid was anteiso-C15:0, and the DNA G+C content was 53.1 mol%. The DNA-DNA relatedness between the isolate and Paenibacillus wynnii LMG 22176T was 7.6%, indicating that strain JH8T and P. wynnii belong to different species. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain JH8T would appear to belong to a novel species, for which the name Paenibacillus donghaensis sp. nov. is proposed (type strain =KCTC 13049T=LMG 23780T).
The effect of the presence of an alternate toxic compound (phenol) on the p-nitrophenol (PNP)-deg... more The effect of the presence of an alternate toxic compound (phenol) on the p-nitrophenol (PNP)-degrading activity of freely suspended and calcium alginate immobilized Nocardioides sp. NSP41 was investigated. In the single substrate experiments, when the concentration of phenol and PNP was increased to 1400 mg l −1 and 400 mg l −1 , respectively, the initial cell concentrations in the freely suspended cell culture should be higher than 1.5 g dry cell weight l −1 for complete degradation. In the simultaneous degradation experiment, when the initial concentration of phenol was increased from 100 to 400 mg l −1 , the specific PNP degradation rate at the concentration of 200 mg l −1 was decreased from 0.028 to 0.021 h −1. A freely suspended cell culture with a high initial cell concentration resulted in a high volumetric degradation rate, suggesting the potential use of immobilized cells for simultaneous degradation. In the immobilized cell cultures, although simultaneous degradation of PNP and phenol was maintained, the specific PNP and phenol degradation rate decreased. However, a high volumetric PNP and phenol degradation rate could be achieved by immobilization because of the high cell concentration. Furthermore, when the immobilized cells were reused in the simultaneous degradation of PNP and phenol, they did not lose their PNP-and phenol-degrading activity for 12 times in semi-continuous cultures. Taken together, the use of immobilized Nocardioides sp. NSP41 for the simultaneous degradation of PNP and phenol at high concentrations is quite feasible because of the high volumetric PNP and phenol degradation rate and the reusability of immobilized cells. Abbreviations: DCW-dry cell weight (mg l −1), 4-NC-4-nitrocatechol, PNPp-nitrophenol, q-specific degradation rate (h −1), r-volumetric degradation rate (mg l −1 h −1), Y-biomass yield (g g −1
Metal ions (Cd2+, Cu2+, Ni2+, Zn2+ and Cr3+) did not affect glucose degradation or the production... more Metal ions (Cd2+, Cu2+, Ni2+, Zn2+ and Cr3+) did not affect glucose degradation or the production of methane during anaerobic digestion with intact and disintegrated granules from a UASB (Upflow Anaerobic Sludge Blanket) reactor. However, when Cu2+ was at 500 mg g-1 VSS (volatile suspended solids) in the media, the glucose degradation rates and methane production rates decreased by 14% and
Indigenous bacteria isolated from contaminated sites play important roles to remediate contaminat... more Indigenous bacteria isolated from contaminated sites play important roles to remediate contaminated groundwater. Chromium has the most stable oxidation states. Cr(VI) is toxic, carcinogenic, and mobile, but Cr(III) is less toxic and immobile. In this study, indigenous microorganism (MMPH-0) was enriched from Cr(VI) contaminated groundwater, and identified by 16S rRNA gene analysis. Using MMPH-0, the effect of stimulating with e-donors (glucose, lactate, acetate, and no e-donor control), respiration conditions, biomass, tolerance, and geochemical changes on Cr(VI) reduction were investigated in batch experiments for 4 weeks. The changes of Cr(VI) concentration and geochemical conditions were monitored using UV-vis-spectrophotometer and Eh-pH meter. And the morphological and chemical characteristics of MMPH-0 and precipitates in the effluents were characterized by TEM-EDS and SEM-EDS analyses. MMPH-0 (Enterobacter aerogenes) was able to tolerate up to 2000 mg/L Cr(VI) and reduce Cr(VI) under aerobic and anaerobic conditions. MMPH-0 performed faster and higher efficiency of Cr(VI) reduction with electron donors (over 70% after 1 week with e-donor, 10-20% after 4 weeks without e-donor). The changes of Eh-pH in effluents showing the tendency from oxidizing to reducing condition and a bit of acidic change in pH due to microbial oxidation of organic matters donating electrons and protons suggested the roles of MMPH-0 on Cr(VI) in the contaminated water catalyzing to transit geochemical stable zone for more stable Cr(OH) 3 or Cr(III) precipitates. TEM/SEM-EDS analyses of MMPH-0 and precipitates indicate direct and indirect Cr(VI) reduction: extracellular polymers capturing Cr component outside cells. These results suggested diverse indigenous bacteria and their biogeochemical reactions might enhance more effective and feasible remediation technology of redox sensitive heavy metals in metal-contaminated in groundwater.
Microbially mediated dehalogenation processes contribute to the global cycling of both biogenic a... more Microbially mediated dehalogenation processes contribute to the global cycling of both biogenic and anthropogenic halogenated organic compounds. Detailed information on biodegradation mechanisms for a variety of organohalides and on the microorganisms mediating these processes has greatly increased our understanding of the cycling and fate of these unique and widespread compounds in our environment. The marine environment appears to be a particularly rich source of dehalogenating microorganisms. It is well established by laboratory and field studies that anaerobic dehalogenation of sediment contaminants, such as PCBs, pesticides, and dioxins, occurs intrinsically and can be enhanced via various methods. Specific dehalogenating bacterial populations can be enriched on various organohalides. Biodehalogenation processes are likely to be significantly affected by the prevailing terminal electron-accepting condition, and thus, biotransformation of organohalide contaminants in marine and estuarine environments will vary as a function of the redox conditions within the sediment profile. Fundamental knowledge of the activities and interactions of dehalogenating microorganisms is providing a strong basis for development of new bioremediation technologies for removal of harmful halogenated compounds from our environment.
A chlorophenol-contaminated soil was tested for the biodegradability in a semi-pilot scale microc... more A chlorophenol-contaminated soil was tested for the biodegradability in a semi-pilot scale microcosm using indigenous microorganisms. More than 90% of 4-chlorophenol and 2,4,6-trichlorophenol, initially at 30 mg kg-1, were removed within 60 days and 30 mg pentachlorophenol kg-1 was completely degraded within 140 days. The chlorophenols were degraded more effectively under aerobic condition than under anaerobic condition. Soil moisture had a significant effect with the slowest degradation rate of chlorophenols at 25% in the range of 10–40% moisture content. At 25–40%, the rate of chlorophenol degradation was directly related to the soil moisture content, whereas at 10–25%, it was inversely related. Limited oxygen availability through soil agglomeration at 25% moisture content might decrease the degradation rate of chlorophenols.
The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it repres... more The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39-42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta-and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria (some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly detected by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.
The fatty acid composition of Pimelobacter sp. is of the complex type. When pyridine was used as ... more The fatty acid composition of Pimelobacter sp. is of the complex type. When pyridine was used as a sole inhibitory substrate, the fatty acid composition of Pimelobacter sp. was quite different from that within other readily available substrates. When compared with the fatty acid composition in a complex medium, the proportion of isopalmitic acid (iso-CIs,.) drastically decreased from 68.4% to 7.7%, while the proportion of anteisoheptadecanoic acid (anteiso-CIT:o) remained almost constant at ca. 7%. Concomitantly, this decrease of the branched-chain fatty acid was accompanied by the increase of the straight-chain, especially long-chain, fatty acid such as heptadecanoic (CITLO), octadecenoic (Clszl), IO-methylheptadecanoic (lo-me-18) and lo-methyloctadecanoic (lo-me-19) acids. Consequently, in response to membrane active organic solvents, Pimelobacter sp. was found to regulate its membrane fatty acid composition in a fashion different from Gram-negative bacteria.
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Papers by Sung-Keun Rhee