Degradation of Oil Shale by Sulfur-Oxidizing Bacteria

Approximately 40% of oil shale can be solubilized by the action of sulfur-oxidizing bacteria. Thiobacillus thiooxidans and Thiobacillus concretivorous are equally effective in solubilization. Continuous leaching experiments show that this process can be completed within 14 days. The growth of Thiobacillus and the production of acid were measured under several conditions. Almost all of the CaMg(CO(3))(2) was removed by this process, leaving a complex of silica and kerogen that could be burned as low-energy fuel. The silica-kerogen complex had not yet been biologically degraded.     

Chemolithotrophic Sulfur-Oxidizing Bacteria from the Galapagos Rift Hydrothermal Vents

Three distinct physiological types of sulfur-oxidizing bacteria were enriched and isolated from samples collected at several deep-sea hydrothermal vents (2,550 m) of the Galapagos Rift ocean floor spreading center. Twelve strains of the obligately chemolithotrophic genus Thiomicrospira were obtained from venting water and from microbial mats covering surfaces in the immediate vicinity of the vents. From these and other sources two types of obligately heterotrophic sulfur oxidizers were repeatedly isolated that presumably oxidized thiosulfate either to sulfate (acid producing; 9 strains) or to polythionates (base producing; 74 strains). The former were thiobacilli-like, exhibiting a thiosulfate-stimulated increase in growth and CO₂ incorporation, whereas the latter were similar to previously encountered pseudomonad-like heterotrophs. The presence of chemolithotrophic sulfur-oxidizing bacteria in the sulfide-containing hydrothermal water supports the hypothesis that chemosynthesis provides a substantial primary food source for the rich populations of invertebrates found in the immediate vicinity of the vents.     

Isolation, Characterization, and Ecology of Cold-Active, Chemolithotrophic, Sulfur-Oxidizing Bacteria from Perennially Ice-Covered Lake Fryxell, Antarctica

Novel strains of obligately chemolithoautotrophic, sulfur-oxidizing bacteria have been isolated from various depths of Lake Fryxell, Antarctica. Physiological, morphological, and phylogenetic analyses showed these strains to be related to mesophilic Thiobacillus species, such as T. thioparus. However, the psychrotolerant Antarctic isolates showed an adaptation to cold temperatures and thus should be active in the nearly freezing waters of the lake. Enumeration by most-probable-number analysis in an oxic, thiosulfate-containing medium revealed that the sulfur-oxidizing chemolithotroph population peaks precisely at the oxycline (9.5 m), although viable cells exist well into the anoxic, sulfidic waters of the lake. The sulfur-oxidizing bacteria described here likely play a key role in the biogeochemical cycling of carbon and sulfur in Lake Fryxell.     

Fractionation of Stable Carbon Isotopes during Chemoautotrophic Growth of Sulfur-Oxidizing Bacteria

Laboratory-grown strains of chemoautotrophic Thiomicrospira sp. strain L-12 and Thiobacillus neapolitanus produced cell carbon that was 24.6 to 25.1 ppt (24.6 to 25.1 mg/g) lower in ¹³C isotope abundance than the ambient source of carbon dioxide and bicarbonate. This degree of ¹³C isotope depletion was comparable to that found in organic material produced in deep-sea hydrothermal-vent communities.     

Autotrophic Nitrifying Bacteria in Acid Tea Soils from Bangladesh and Sri Lanka

Autotrophic ammonia-oxidizing bacteria were detected in some Bangladesh and Sri Lanka tea soils and in three other Bangladesh soils. Numbers ranged from 25 to 5500 organisms/g dry soil. Pure cultures were obtained from all the soils either by picking colonies from silica gel plates used for counts or by enrichment culture procedures. The isolates were identified as species of Nitrosolobus, Nitrosomonas and a new species of Nitrosospira .     

Limestone Corrosion by Neutrophilic Sulfur-Oxidizing Bacteria: A Coupled Microbe-Mineral System

Subsurface karst aquifers receiving sulfidic water can host complex chemolithotrophic microbial communities that are capable of dissolving limestone, forming new karstic habitat. Neutrophilic sulfur-oxidizing bacteria use reduced sulfur compounds as energy rich substrate, potentially producing sulfuric acid as a geochemically reactive byproduct. The physicochemical relationship between a biofilm forming on a limestone surface and the extent of microbial influence on dissolution rate, however, are unknown. We investigated the rate of Madison limestone dissolution by sulfur-oxidizers both in the field at Lower Kane Cave, WY (LKC), and in the laboratory using continuous flow culture reactors and microbial mat collected from LKC. In the field, a microbial consortium rapidly colonized limestone chips forming a thick biofilm, with deep etching of mineral surfaces underneath. In the laboratory we found that a microbial biofilm oxidizing thiosulfate on the limestone surface accelerated dissolution rate up to 7 times faster than the abiotic baseline rate. In contrast, experiments done with H₂S or a mixture of H₂S and thiosulfate had no effect on dissolution rate. We hypothesize that the laboratory mat community dominated by Thiothrix sp. oxidizes thiosulfate to sulfate and H⁺, while H₂S is partially oxidized to S°. When all sulfur substrate is withheld, the community oxidizes stored intracellular sulfur, briefly accelerating limestone dissolution even in the absence of external supplied substrate. Accelerated corrosion occurs only in the reactive micro-environment under the biofilm, disconnected from the bulk reactor solution. When experiments are repeated where the microbial population is separated from the limestone by a dialysis membrane barrier, measured pH drop is greater, but there is only slight enhancement of rate. This work confirms our working hypothesis that neutrophilic sulfur-oxidizers colonize and rapidly dissolve limestone surfaces, possibly to buffer the production of excess acidity.     

Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria

The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [¹³C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.Archaea have long been known as extremophiles, since most cultivated archaeal strains were cultivated from extreme environments, such as acidic, hot, and high-salt environments. The view of archaea as extremophiles (i.e., acidophiles, thermophiles, and halophiles) has radically changed by the application of molecular technologies, including PCR in environmental microbiology. Using Archaea-specific PCR primers, novel archaeal 16S rRNA gene sequences were discovered in seawater (23, 27). Following these discoveries, an ever-increasing and unexpectedly high variety of archaeal 16S rRNA gene sequences has been reported from diverse “nonextreme” environments (67). This indicates that archaea are, like bacteria, ubiquitous in the biosphere rather than exclusively inhabiting specific extreme niches. Archaea are abundant in water columns of some oceanic provinces (33, 36) and deep-subsea floor sediments (11, 12, 48). Despite the increasing number of reports of the diversity and abundance of these nonextreme archaea by molecular ecological studies, their physiology and ecological roles have remained enigmatic.Oxidation of ammonia, a trait long thought to be exclusive to the domain Bacteria (13), was recently suggested to be a trait of archaea of the crenarchaeal groups I.1a and I.1b, based on a metagenome analysis (79) and supported by the discovery of archaeal amoA-like genes in environmental shotgun sequencing studies of Sargasso Sea water (80) and genomic analysis of “Candidatus Cenarchaeum symbiosum,” a symbiont of a marine sponge (30). Molecular ecological studies indicated that these ammonia-oxidizing archaea (AOA) are often predominant over ammonia-oxidizing bacteria (AOB) in ocean waters (9, 53, 87), soils (17, 47), and marine sediments (61). Critical evidence for autotrophic archaeal ammonia oxidation was obtained by the characterization of the first cultivated mesophilic crenarchaeon (group I.1a), “Candidatus Nitrosopumilus maritimus SCM1,” from an aquarium (38), and a related archaeon from North Sea water (87) and subsequently by enrichment of thermophilic AOA (22, 31). Whole-genome-based phylogenetic studies recently indicated that the nonthermophilic crenarchaea, including the AOA, likely form a phylum separate from the Crenarchaeota and Euryarchaeota phyla (15, 16, 72). This proposed new phylum was called Thaumarchaeota (15).Microorganisms in marine sediments contribute significantly to global biogeochemical cycles because of their abundance (85). Nitrification is essential to the nitrogen cycle in marine sediments and may be metabolically coupled with denitrification and anaerobic ammonium oxidation, resulting in the removal of nitrogen as molecular nitrogen and the generation of greenhouse gases, such as nitrous oxide (19, 75). Compared with studies on archaeal nitrification in the marine water column, only limited information on archaeal nitrification in marine sediments is available so far. Archaeal amoA genes have been retrieved from marine and coastal sediments (8, 26, 61), and the potentially important role of AOA in nitrification has been suggested based on the abundance of archaeal amoA genes relative to that of bacterial amoA genes in surface marine sediments from Donghae (South Korea) (61). Cultivation of AOA, although difficult (38), remains essential to estimating the metabolic potential of archaea in environments such as soils (47) and marine sediments (61). Here, we report the successful enrichment of AOA of crenarchaeal group I.1a from marine sediments by employing a coculture with sulfur-oxidizing bacteria (SOB) which was maintained for ca. 20 months with biweekly transfers. In this way, we were able to characterize AOA from marine sediments, providing a clue for the role of AOA in the nitrogen cycle of marine sediments.     

Succession of Sulfur-Oxidizing Bacteria in the Microbial Community on Corroding Concrete in Sewer Systems

Microbially induced concrete corrosion (MICC) in sewer systems has been a serious problem for a long time. A better understanding of the succession of microbial community members responsible for the production of sulfuric acid is essential for the efficient control of MICC. In this study, the succession of sulfur-oxidizing bacteria (SOB) in the bacterial community on corroding concrete in a sewer system in situ was investigated over 1 year by culture-independent 16S rRNA gene-based molecular techniques. Results revealed that at least six phylotypes of SOB species were involved in the MICC process, and the predominant SOB species shifted in the following order: Thiothrix sp., Thiobacillus plumbophilus, Thiomonas intermedia, Halothiobacillus neapolitanus, Acidiphilium acidophilum, and Acidithiobacillus thiooxidans. A. thiooxidans, a hyperacidophilic SOB, was the most dominant (accounting for 70% of EUB338-mixed probe-hybridized cells) in the heavily corroded concrete after 1 year. This succession of SOB species could be dependent on the pH of the concrete surface as well as on trophic properties (e.g., autotrophic or mixotrophic) and on the ability of the SOB to utilize different sulfur compounds (e.g., H₂S, S⁰, and S₂O₃²⁻). In addition, diverse heterotrophic bacterial species (e.g., halo-tolerant, neutrophilic, and acidophilic bacteria) were associated with these SOB. The microbial succession of these microorganisms was involved in the colonization of the concrete and the production of sulfuric acid. Furthermore, the vertical distribution of microbial community members revealed that A. thiooxidans was the most dominant throughout the heavily corroded concrete (gypsum) layer and that A. thiooxidans was most abundant at the highest surface (1.5-mm) layer and decreased logarithmically with depth because of oxygen and H₂S transport limitations. This suggested that the production of sulfuric acid by A. thiooxidans occurred mainly on the concrete surface and the sulfuric acid produced penetrated through the corroded concrete layer and reacted with the sound concrete below.     

The Ecology of the Acetic Acid Bacteria with Particular Reference to Cider Manufacture

The ecology of the acetic acid bacteria has been studied at various stages of their association with cider manufacture. Of the 278 strains of bacteria isolated during the survey, 255 proved to be representative of 6 species of acetic acid bacteria. The remaining 23 strains included one example of the spoilage organism, Zymomonas anaerobia , but they were mostly ubiquitous soil bacteria which could not survive the low pH of apple juice and were only found associated with the early stages of cider making. The acetic acid bacteria were isolated in a sequential type of pattern. Those species which preferentially oxidize sugars were found at the early stages of processing when sugars abound, but these were replaced by the relatively more acid-tolerant species, which are better equipped to oxidize alcohols, after the yeast fermentation had converted most of the sugar to ethanol.     

Repeatedly Evolved Host-Specific Ectosymbioses between Sulfur-Oxidizing Bacteria and Amphipods Living in a Cave Ecosystem

Ectosymbioses between invertebrates and sulfur-oxidizing bacteria are widespread in sulfidic marine environments and have evolved independently in several invertebrate phyla. The first example from a freshwater habitat, involving Niphargus ictus amphipods and filamentous Thiothrix ectosymbionts, was recently reported from the sulfide-rich Frasassi caves in Italy. Subsequently, two new Niphargus species, N. frasassianus and N. montanarius, were discovered within Frasassi and found to co-occur with N. ictus. Using a variety of microscopic and molecular techniques, we found that all three Frasassi-dwelling Niphargus species harbor Thiothrix ectosymbionts, which belong to three distinct phylogenetic clades (named T1, T2, and T3). T1 and T3 Thiothrix dominate the N. frasassianus ectosymbiont community, whereas T2 and T3 are prevalent on N. ictus and N. montanarius. Relative distribution patterns of the three ectosymbionts are host species-specific and consistent over different sampling locations and collection years. Free-living counterparts of T1–T3 are rare or absent in Frasassi cave microbial mats, suggesting that ectosymbiont transmission among Niphargus occurs primarily through inter- or intraspecific inoculations. Phylogenetic analyses indicate that the Niphargus-Thiothrix association has evolved independently at least two times. While ectosymbioses with T1 and T2 may have been established within Frasassi, T3 ectosymbionts seem to have been introduced to the cave system by Niphargus.     

Abundance and Diversity of Sulfur-Oxidizing Bacteria along a Salinity Gradient in Four Qinghai-Tibetan Lakes,China

Sulfur-oxidizing bacteria (SOB) play important roles in the sulfur cycle and are widespread in a number of environments, but their occurrence and relationship to geochemical conditions in (hyper)saline lakes are still poorly understood. In this study, the abundance and diversity of SOB populations were investigated in four Qinghai-Tibetan lakes (Erhai Lake, Gahai Lake 1, Gahai Lake 2 and Xiaochaidan Lake) by using quantitative polymerase chain reaction (qPCR) and soxB gene- (encoding sulfate thiohydrolase) based phylogenectic analyses. qPCR analyses showed that in the studied lakes, the total bacterial 16S rRNA and soxB gene abundances in the sediments were distinctly higher than in the overlying waters. The 16S rRNA gene abundance in the waters ranged 5.27 × 10⁶–6.09 × 10⁸ copies per mL and 7.39 × 10¹⁰–2.9 × 10¹¹ copies per gram sediment. The soxB gene abundance in the waters ranged from 1.88 × 10⁴ to 5.21 × 10⁵ per mL and 4.73 × 10⁶–2.65 × 10⁷ copies per gram sediment. The soxB gene in the waters of the two hypersaline lakes (Gahai Lake 2 and Xiaochaidan Lake) was more abundant (2.97 × 10⁵ and 5.21 × 10⁵ copies per mL) than that in the two low-salinity lakes (1.88 × 10⁴ and 3.36 × 10⁴ copies per mL). Phylogenetic analysis showed that Alpha- and Betaproteobacteria were dominant SOB in the investigated lakes, and the composition of proteobacterial subgroups varied with salinity: in freshwater Erhai Lake and low-salinity Gahai Lake 1, the SOB populations were dominated by the Betaproteobacteria, whereas in hypersaline Lake Gahai 2 and Xiaochaidan Lake, the SOB populations were dominated by Alphaproteobacteria. Overall, salinity played a key role in controlling the diversity and distribution of SOB populations in the investigated Qinghai-Tibetan lakes.     

Ecology of Hymexazol-Insensitive Pythium Species in Field Soils

Soils from 100 irrigated fields (95 under vegetables, 5 under citrus) in different geographical locations in the West Bank (Palestinian Autonomous Territory) were surveyed for hymexazol-insensitive (HIS) Pythium species using the surface soil dilution plate (SSDP) method with the VP3 medium amended with 50 mg/L hymexazol (HMI) (VP3H50), over a period of 12 months. HIS Pythium species were isolated from 37% of the soils surveyed, with mean population levels ranging from 4.3-1422 CFU g(-1) dry weight. Eight HIS Pythium taxa were recovered on the VP3H50 medium, the most abundant of which was P. vexans (found in 29% of field soils surveyed). Seasonal variations in population levels of HIS Pythium species were studied in four fields over a period of 12 months. Significant seasonal variations in HIS population levels were detected in the four fields, with the highest population levels of HIS Pythium spp. encountered in spring and the lowest population levels in winter in three of the fields surveyed. Effects of HMI on linear growth and colony morphology of 149 Pythium ssp. isolates were examined on CMA amended with HMI at five concentrations. Pythium vexans isolates responded differently from those of the other Pythium species. Isolates of this important pathogen were more insensitive to HMI at high concentrations than the other main species tested. A large proportion of the P. ultimum isolates was either insensitive or weakly sensitive to HMI. Furthermore, a few isolates of other Pythium species were insensitive to the fungicide at various concentrations. The colony morphology of P. vexans isolates was not affected by HMI, whereas colonies of the other species showed sparse growth on the HMI amended medium relative to the control. The pathogenicity of P. vexans and P. ultimum isolates to cucumber seedlings was examined in growth chambers. Insensitive isolates of both species were found to be more virulent damping-off pathogens than the sensitive isolates. The present study demonstrates that HMI can not be used effectively in controlling Pythium spp. in soil inhabited with high densities of HIS Pythium spp. pathogens.     

Immunological Detection of Nitrospira-like Bacteria in Various Soils

Chemolithotrophic nitrite oxidizers were enriched from five different soils including freshwater marsh, permafrost, garden, agricultural, and desert soils and monitored during the cultivation procedure. Immunoblot analysis was used to identify the nitrite oxidizing organisms with monoclonal antibodies, which recognize the key enzyme of nitrite oxidation in a genus-specific reaction [Bartosch et al. (1999) Appl Environ Microbiol 65:4126-4133]. The morphological characteristics of the enriched nitrite oxidizers were additionally studied using transmission electron microscopy (TEM) and fluorescence microscopy. By means of the antibodies and TEM analysis Nitrospira could be clearly identified in enrichment cultures derived from freshwater marsh and from permafrost soil. Nitrospira cells were enriched simultaneously with cells of the genus Nitrobacter when nitrite concentrations of 0.2 g of NaNO2 L(-1) were used. However, in enrichment cultures containing 2 g of NaNO2 L(-1) Nitrobacter was exclusively detected. During fluorescence microscopic observations of DAPI stained samples microcolonies were found in enrichment cultures from freshwater marsh, permafrost, garden, and agricultural soil. They had a similar morphology to Nitrospira-like microcolonies from activated sludge. In conclusion, Nitrospira seems to be not only a common aquatic but also a usual soil bacterium.     

Diversity and Ecology of Viruses in Hyperarid Desert Soils

In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.     

酸性硫酸盐土中铝的形态

采用连续分级提取方法 ,把酸性硫酸盐土中可提取的非晶体态铝区分为交换态铝 (ExAl)、吸附态无机羟基铝 (HyAl)、有机配合铝 (OrAl)、氧化铁结合铝 (DCBAl)、层间铝 (InAl)和非晶体态铝硅酸盐 (NcAl) ,其平均值分别为 1.79、2 .5 1、4.17、4.14、4.31和 18.6 6g·kg-1Al2 O3.实际酸性硫酸盐土中NcAl>OrAl >InAl >DCBAl>ExAl>HyAl,潜在酸性硫酸盐土NcAl >InAl >DCBAl >HyAl >OrAl >ExAl.可提取Al总量平均为 35 .5 7Al2 O3g·kg-1,占全Al 2 5 .0 4% .其显著特征是活性铝ExAl、HyAl和OrAl的含量较高 .每一种Al形态的结构组成与酸性硫酸盐土相应性质和生态特性密切相关 .酸化的ASS的强酸环境导致Al的过量游离 ,并转化为活度较大的活性Al,从而产生Al毒     

Pyruvate-Associated Acid Resistance in Bacteria

Glucose confers acid resistance on exponentially growing bacteria by repressing formation of the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex and consequently activating acid resistance genes. Therefore, in a glucose-rich growth environment, bacteria are capable of resisting acidic stresses due to low levels of cAMP-CRP. Here we reveal a second mechanism for glucose-conferred acid resistance. We show that glucose induces acid resistance in exponentially growing bacteria through pyruvate, the glycolysis product. Pyruvate and/or the downstream metabolites induce expression of the small noncoding RNA (sncRNA) Spot42, and the sncRNA, in turn, activates expression of the master regulator of acid resistance, RpoS. In contrast to glucose, pyruvate has little effect on levels of the cAMP-CRP complex and does not require the complex for its effects on acid resistance. Another important difference between glucose and pyruvate is that pyruvate can be produced by bacteria. This means that bacteria have the potential to protect themselves from acidic stresses by controlling glucose-derived generation of pyruvate, pyruvate-acetate efflux, or reversion from acetate to pyruvate. We tested this possibility by shutting down pyruvate-acetate efflux and found that the resulting accumulation of pyruvate elevated acid resistance. Many sugars can be broken into glucose, and the subsequent glycolysis generates pyruvate. Therefore, pyruvate-associated acid resistance is not confined to glucose-grown bacteria but is functional in bacteria grown on various sugars.     

Association of Bacteria and Yeasts in Hot Springs

The thermophilic bacterium Bacillus sp. strain TB-1 was isolated in association with the yeast Debaryomyces vanriji from hot springs at 46°C. It was shown that TB-1 excreted thiamine into the culture broth, which not only promoted D. vanriji growth in mixed culture but also increased the maximal temperature for yeast growth.     

乳酸菌酸胁迫反应机制研究进展

乳酸菌可发酵糖类产生乳酸,并广泛应用于食品、药物和饲料等工业。由于有机酸的积累,乳酸菌大部分的生长代谢都在低pH的酸性环境中进行,具有酸胁迫反应。pH的自我平衡、ATR反应机制、对大分子的保护和修复作用及细胞膜的变化等是乳酸菌酸胁迫反应的主要机制,其中,pH自我平衡包括F0F1-ATPase质子泵、精氨酸脱氨酶途径(ADI)和谷氨酸脱羧酶途径(GAD)等。由此可见,乳酸菌酸胁迫反应机制涉及到基因和蛋白的表达调控等,是非常复杂的网络调控体系。