Physiology and genetics of sulfur-oxidizing bacteria

Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs

Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.

Biochemical engineering for elemental sulfur from flue gases through multi-enzymatic based approaches - A review

Flue gases are the gases which are produced from industries related to chemical manufacturing, petrol refineries, power plants and ore processing plants. Along with other pollutants, sulfur present in the flue gas is detrimental to the environment. Therefore, environmentalists are concerned about its removal and recovery of resources from flue gases due to its activation ability in the atmosphere to transform into toxic substances. This review is aimed at a critical assessment of the techniques developed for resource recovery from flue gases. The manuscript discusses various bioreactors used in resource recovery such as hollow fibre membrane reactor, rotating biological contractor, sequential batch reactor, fluidized bed reactor, entrapped cell bioreactor and hybrid reactors. In conclusion, this manuscript provides a comprehensive analysis of the potential of thermotolerant and thermophilic microbes in sulfur removal. Additionally, it evaluates the efficacy of a multi-enzyme engineered bioreactor in this process. Furthermore, the study introduces a groundbreaking sustainable model for elemental sulfur recovery, offering promising prospects for environmentally-friendly and economically viable sulfur removal techniques in various industrial applications.

Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

Cultivar-specific response of rhizosphere bacterial community to uptake of cadmium and mineral elements in rice (Oryza sativa L.)

Toxic metal-contaminated farmland from Cadmium (Cd) can enhance the accumulation of Cd and impair the absorption of mineral elements in brown rice. Although several studies have been conducted on Cd exposure on rice, little has been reported on the relationship between Cd and mineral elements in brown rice and the regulatory mechanism of rhizosphere microorganisms during element uptake. Thus, a field study was undertaken to screen japonica rice cultivars with low Cd and high mineral elements levels, analyze the quantitative relationship between Cd and seven mineral elements, and investigate the cultivar-specific response of rice rhizosphere bacterial communities to differences in Cd and mineral uptake in japonica rice. Results showed that Huaidao-9 and Xudao-7 had low Cd absorption and high amounts of mineral nutrient elements (Fe, Zn, Mg, and Ca, LCHM group), whereas Zhongdao-1 and Xinkedao-31 showed opposite accumulation characteristics (HCLM group). Stepwise regression analysis showed that zinc, iron, and potassium are the key minerals that affect Cd accumulation in japonica rice and zinc was the most important factor, accounting for 68.99 %. The accumulation of Cd and mineral elements is potentially associated with rhizosphere soil bacteria. Taxa enriched in the LCHM rhizosphere (phyla Acidobacteriota and MBNT15) indicated the high nutrient characteristics of the soil and reduced activity of Cd in soil. The HCLM rhizosphere was highly colonized by metal-activating bacteria (Actinobacteria), lignin-degrading bacteria (Actinobacteria and Chlorofexi), and bacteria scavenging nutrients and trace elements (Anaerolinea and Ketobacter). Moreover, the differences in the uptake of Cd and mineral elements affected predicted functions of microbial communities, including sulfur oxidation and sulfur derivative formation, human or plant pathogen, and functions related to the iron oxidation and nitrate reduction. The results indicate a potential association of Cd and mineral elements uptake and accumulation with rhizosphere bacteria in rice, thus providing theoretical basis and a new perspective on the maintenance of rice security and high quality simultaneously.

Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field

The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1^T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 10⁵ cells/ml to 3.13 × 10⁸ cells/ml after 10 days, and that the δ¹³C_VPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO₃ as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.

A review on bacterial and archaeal thermostable sulfur oxidoreductases (SORS)-an insight into the biochemical, molecular and in-silico structural comparative analysis of a neglected thermostable enzyme of industrial significance

Diverse thermophilic microorganisms with the potential to withstand extreme physiological conditions have long been investigated and explored for human commercial benefit. Thermozymes with distinct functional and structural properties isolated from these thermophiles are known to have high thermostability without significant loss of specific enzyme activity. Thermophiles isolated and characterised from the thermophilic ecological niche of India are well documented. There is a plethora of work in the literature emphasising its industrial significance. However, in-depth knowledge of the thermophilic oxidoreductase group of enzymes (Oxizymes) is restricted. Sulfur Oxygenase Reductases or Sulfur Oxygen-Reductases (SORs) are a group of thermophilic oxizymes reported predominantly from thermophilic and mesophilic archaea and bacteria, which catalyse oxygen-dependent disproportionation reactions of elemental sulfur, producing sulfite, thiosulfate, and sulphide. There have been few reports on isolated and characterised SORs from the Indian geothermal niche. The review article will highlight the SORs reported till date with a concise overview of different archaeal and bacterial species producing the enzymes. Based on the literature available till date, characteristics including physico-chemical properties, amino acid sequence homology, conserved motifs and their 3D structure comparison have been discussed. In-silico sequence and structure level preliminary comparative analysis of various SORs has also been discussed. However, a few SORs whose structural information is not reported in the protein data bank have been modelled to enrich our analysis.

Metabolic arsenal of giant viruses: Host hijack or self-use?

Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.

Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences

Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.

Recent advances in microbial capture of hydrogen sulfide from sour gas via sulfur-oxidizing bacteria

Biological desulfurization offers several remarkably environmental advantages of operation at ambient temperature and atmospheric pressure, no demand of toxic chemicals as well as the formation of biologically re-usable sulfur (S0), which has attracted increasing attention compared to conventionally physicochemical approaches in removing hydrogen sulfide from sour gas. However, the low biomass of SOB, the acidification of process solution, the recovery of SOB, and the selectivity of bio-S0 limit its industrial application. Therefore, more efforts should be made in the improvement of the BDS process for its industrial application via different research perspectives. This review summarized the recent research advances in the microbial capture of hydrogen sulfide from sour gas based on strain modification, absorption enhancement, and bioreactor modification. Several efficient solutions to limitations for the BDS process were proposed, which paved the way for the future development of BDS industrialization.

Effect on Chemical and Physical Properties of Soil Each Peat Moss, Elemental Sulfur, and Sulfur-Oxidizing Bacteria

Peat moss is an organic substance corroded by sphagnum moss and has a pH of 3.0-4.0. Elemental sulfur is sulfated and oxidized by the action of bacteria to become sulfuric acid. These biological factors can alter the soil environment. Blueberries require soil with a pH of 4.5-5.2 and high organic matter content. In this experiment, we investigated whether different treatment rates of peat moss, elemental sulfur, and sulfur-oxidizing bacteria affect changes in soil pH, physicochemical properties, and electrical conductivity. We detected strong changes in soil pH as a reaction to the supply of peat moss, elemental sulfur, and sulfur-oxidizing bacteria. The pH of the soil when peat moss and elemental sulfur each were supplied was reduced. In addition, the pH decreased faster when elemental sulfur and sulfur-oxidizing bacteria were supplied together than elemental sulfur alone, satisfying an acidic soil environment suitable for blueberry cultivation. In this experiment, it is shown that peat moss, elemental sulfur, and sulfur-oxidizing bacteria are suitable for lowering soil pH. It was demonstrated that when elemental sulfur and sulfur-oxidizing bacteria were treated together, the pH decreased faster than when treated with peat moss. It could be economically beneficial to farmers to use elemental sulfur and sulfur-oxidizing bacteria, which are cheaper than peat moss, to reduce the pH of the soil.

Hydrogen Sulfide Oxidation by Sulfide Quinone Oxidoreductase

Hydrogen sulfide (H2 S) is an environmental toxin and a heritage of ancient microbial metabolism that has stimulated new interest following its discovery as a neuromodulator. While many physiological responses have been attributed to low H2 S levels, higher levels inhibit complex IV in the electron transport chain. To prevent respiratory poisoning, a dedicated set of enzymes that make up the mitochondrial sulfide oxidation pathway exists to clear H2 S. The committed step in this pathway is catalyzed by sulfide quinone oxidoreductase (SQOR), which couples sulfide oxidation to coenzyme Q10 reduction in the electron transport chain. The SQOR reaction prevents H2 S accumulation and generates highly reactive persulfide species as products; these can be further oxidized or can modify cysteine residues in proteins by persulfidation. Here, we review the kinetic and structural characteristics of human SQOR, and how its unconventional redox cofactor configuration and substrate promiscuity lead to sulfide clearance and potentially expand the signaling potential of H2 S. This dual role of SQOR makes it a promising target for H2 S-based therapeutics.

Sirtuins-Mediated System-Level Regulation of Mammalian Tissues at the Interface between Metabolism and Cell Cycle: A Systematic Review

Sirtuins are a family of highly conserved NAD+-dependent proteins and this dependency links Sirtuins directly to metabolism. Sirtuins' activity has been shown to extend the lifespan of several organisms and mainly through the post-translational modification of their many target proteins, with deacetylation being the most common modification. The seven mammalian Sirtuins, SIRT1 through SIRT7, have been implicated in regulating physiological responses to metabolism and stress by acting as nutrient sensors, linking environmental and nutrient signals to mammalian metabolic homeostasis. Furthermore, mammalian Sirtuins have been implicated in playing major roles in mammalian pathophysiological conditions such as inflammation, obesity and cancer. Mammalian Sirtuins are expressed heterogeneously among different organs and tissues, and the same holds true for their substrates. Thus, the function of mammalian Sirtuins together with their substrates is expected to vary among tissues. Any therapy depending on Sirtuins could therefore have different local as well as systemic effects. Here, an introduction to processes relevant for the actions of Sirtuins, such as metabolism and cell cycle, will be followed by reasoning on the system-level function of Sirtuins and their substrates in different mammalian tissues. Their involvement in the healthy metabolism and metabolic disorders will be reviewed and critically discussed.

Diversity of Sulfur-oxidizing Bacteria at the Surface of Cattle Manure Composting Assessed by an Analysis of the Sulfur Oxidation Gene soxB

Sulfur-oxidizing bacterial diversity at the surface of cattle manure was characterized throughout the composting process using a sulfur oxidation gene (soxB) clone library approach. In the mesophilic phase, clones related to the genera Hydrogenophaga and Hydrogenophilus were characteristically detected. In the thermophilic phase, clones related to the genera Hydrogenophaga and Thiohalobacter were predominant. In the cooling phase, the predominant soxB sequences were related to the genus Pseudaminobacter and a new sulfur-oxidizing bacterium belonging to the class Alphaproteobacteria. The present study showed changes in the community composition of sulfur-oxidizing bacteria at the surface of compost throughout the composting process.

Insights into the variability of microbial community composition and micropollutant degradation in diverse biological wastewater treatment systems

The biological potential of conventional wastewater treatment plants to remove micropollutants mainly depends on process conditions and the predominant microbial community. To explore this dependence and to connect the occurrence of genera with operating conditions, five pilot-scale reactors with different process conditions were combined into two reactor cascades and fed with the effluent of the primary clarifier of a municipal WWTP. All reactors and the WWTP were analyzed for the removal of 33 micropollutants by LC-MS/MS and the presence of the microbial community using 16S rRNA gene sequencing. The overall removal of the micropollutants was slightly improved (ca. 20%) by the reactor cascades in comparison to the WWTP while certain compounds such as diatrizoate, venlafaxine or diclofenac showed an enhanced removal (ca. 70% in one or both cascades). To explore the diverse bacteria in more detail, the general community was divided into a core and a specialized community. Despite their profoundly different operating parameters (especially redox conditions), the different treatments share a core community consisted of 143 genera (9% of the overall community). Furthermore, the alpha- and beta-biodiversity as well as the occurrence of several genera belonging to the specialized microbial community could be linked to the prevalent process conditions of the individual treatments. Members of the specialized community also correlated with the removal of certain groups of micropollutants. Hence, the comparison of the specialized community with micropollutant removal and operating conditions via correlation analysis is a valuable tool for an extended evaluation of prevalent process conditions. Based on an extended data set this approach could also be used to identify organisms as indicators for operating conditions which are beneficial for an improved removal of specific micropollutants.

The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes

Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na⁺/H⁺ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO₂ fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.

Lack of Microbial Diversity in an Extreme Mars Analog Setting: Poás Volcano, Costa Rica

The Poás volcano in Costa Rica has been studied as a Mars geochemical analog environment, since both the style of hydrothermal alteration present and the alteration mineralogy are consistent with Mars' relict hydrothermal systems. The site hosts an active volcano, with high-temperature fumaroles (up to 980°C) and an ultra-acidic lake. This lake, Laguna Caliente, is one of the most dynamic environments on Earth, with frequent phreatic eruptions, temperatures ranging from near-ambient to almost boiling, a pH range of -1 to 1.5, and a wide range of chemistries and redox potential. Martian acid-sulfate hydrothermal systems were likely similarly dynamic and equally challenging to life. The microbiology existing within Laguna Caliente was characterized for the first time, with sampling taking place in November, 2013. The diversity of the microbial community was surveyed via extraction of environmental DNA from fluid and sediment samples followed by Illumina sequencing of the 16S rRNA gene. The microbial diversity was limited to a single species of the bacterial genus Acidiphilium. This organism likely gets its energy from oxidation of reduced sulfur in the lake, including elemental sulfur. Given Mars' propensity for sulfur and acid-sulfate environments, this type of organism is of significant interest to the search for past or present life on the Red Planet. Key Words: Mars astrobiology-Acid-sulfate hydrothermal systems-Extremophiles-Acidic-High temperature-Acidiphilium bacteria. Astrobiology 18, 923-933.

Requirements for Efficient Thiosulfate Oxidation in Bradyrhizobium diazoefficiens

One of the many disparate lifestyles of Bradyrhizobium diazoefficiens is chemolithotrophic growth with thiosulfate as an electron donor for respiration. The employed carbon source may be CO₂ (autotrophy) or an organic compound such as succinate (mixotrophy). Here, we discovered three new facets of this capacity: (i) When thiosulfate and succinate were consumed concomitantly in conditions of mixotrophy, even a high molar excess of succinate did not exert efficient catabolite repression over the use of thiosulfate. (ii) Using appropriate cytochrome mutants, we found that electrons derived from thiosulfate during chemolithoautotrophic growth are preferentially channeled via cytochrome c₅₅₀ to the aa₃-type heme-copper cytochrome oxidase. (iii) Three genetic regulators were identified to act at least partially in the expression control of genes for chemolithoautotrophic thiosulfate oxidation: RegR and CbbR as activators, and SoxR as a repressor.

Molecular Interactions, Structural Transitions and Alterations in SoxB Protein Due to SoxYZ Interaction from Two Distinct β-Proteobacteria: An In silico Approach Towards the Thiosulfate Oxidation and Recycling of SoxY Protein

Microbial oxidation-reduction reactions utilizing the environmental thiosulfate ions and mediated mainly by the sox operon are very much essential to maintain the sulfur balance in the environment. Majority of the previously documented wet laboratory studies show genetics behind the functionality of Sox proteins encoded by the sox operon. However, the molecular details of the involvements of the essential SoxB, SoxY and SoxZ proteins in the beta-proteobacteria have not yet been elucidated. In this work, an attempt was made to analyze the interaction profiles of the aforementioned SoxB, SoxY and SoxZ proteins to predict their roles in biological sulfur oxidation process. In order to establish the possible roles of these Sox proteins, we built the homology models of these proteins from the two different beta-proteobacteria Dechloromonas aromatica and Thiobacillus denitrificans. We then used molecular docking and simulation studies to further analyze the interaction profiles of these sox proteins. Our analyses revealed that SoxB protein from T. denitrificans exhibited steadier and stronger interactions with SoxYZ protein complex. On the other hand, SoxB protein from D. aromatica was found to exhibit a spontaneous interaction with greater ΔG values and therefore was well documented to exhibit a dual role. This is the first research article to discern the molecular level of interaction profiles of SoxB with SoxYZ protein complex in the beta-proteobacteria D. aromatica and T. denitrificans during the oxidations of thiosulfate. It would further prompt the future investigation into the mutational impact on the sequential interaction pattern in sox operon.

The Two-Component System RsrS-RsrR Regulates the Tetrathionate Intermediate Pathway for Thiosulfate Oxidation in Acidithiobacillus caldus

Acidithiobacillus caldus (A. caldus) is a common bioleaching bacterium that possesses a sophisticated and highly efficient inorganic sulfur compound metabolism network. Thiosulfate, a central intermediate in the sulfur metabolism network of A. caldus and other sulfur-oxidizing microorganisms, can be metabolized via the tetrathionate intermediate (S₄I) pathway catalyzed by thiosulfate:quinol oxidoreductase (Tqo or DoxDA) and tetrathionate hydrolase (TetH). In A. caldus, there is an additional two-component system called RsrS-RsrR. Since rsrS and rsrR are arranged as an operon with doxDA and tetH in the genome, we suggest that the regulation of the S₄I pathway may occur via the RsrS-RsrR system. To examine the regulatory role of the two-component system RsrS-RsrR on the S₄I pathway, ΔrsrR and ΔrsrS strains were constructed in A. caldus using a newly developed markerless gene knockout method. Transcriptional analysis of the tetH cluster in the wild type and mutant strains revealed positive regulation of the S₄I pathway by the RsrS-RsrR system. A 19 bp inverted repeat sequence (IRS, AACACCTGTTACACCTGTT) located upstream of the tetH promoter was identified as the binding site for RsrR by using electrophoretic mobility shift assays (EMSAs) in vitro and promoter-probe vectors in vivo. In addition, ΔrsrR, and ΔrsrS strains cultivated in K₂S₄O₆-medium exhibited significant growth differences when compared with the wild type. Transcriptional analysis indicated that the absence of rsrS or rsrR had different effects on the expression of genes involved in sulfur metabolism and signaling systems. Finally, a model of tetrathionate sensing by RsrS, signal transduction via RsrR, and transcriptional activation of tetH-doxDA was proposed to provide insights toward the understanding of sulfur metabolism in A. caldus. This study also provided a powerful genetic tool for studies in A. caldus.

Insight into the Conformational Variations in SoxYZ Protein Complex from Two Different Members of the β-Proteobacterial Family Involved in Sulfur Oxidation

Sulfur anions serve as the important environmental pollutants. Microbes use hydrogen sulfide in different redox reactions and thus make the environment pollution-free. The sulfur redox processes are performed by a gene cluster called the sox operon, possessed by a diverse set of microorganisms. However, most of the previous studies were confined to α-proteobacteria. In this work, we tried to elucidate the mechanistic details of sulfur oxidation in β-proteobacteria. We compared the molecular mechanism of sulfur oxidation process using Dechloromonas aromatica and Thiobacillus denitrificans. Dechloromonas aromatica possesses the entire sox operon, whereas T. denitrificans lacks SoxCD. In both the organisms, SoxYZ complex formation is essential for thiosulfate oxidation. This SoxYZ protein complex interacts with SoxCD and SoxAX, respectively, for recycling the thiosulfate-bound SoxY protein. For this purpose, individual proteins were modeled via manifold modeling techniques. Protein-protein docking studies were executed to generate duo- and quadro-protein complexes. Different stability parameters such as free energy of folding, solvent accessibility area (for final complexes), and electrostatic surface potential (for SoxYZ complexes) were calculated and analyzed. Fifteen strengthening ionic interactions were accomplished in the SoxYZAX complex, whereas eight such interactions were observed in SoxYZCD complex. From the result, SoxYZAX complex was found to be more stable and interactive one. This study is the first of its kind that analyzes the comparative aspects of the binding interactions of the proteins involved in redox reactions of sulfur anions. This study may, therefore, be helpful in tailoring the microorganisms to function in a better way to remove the environmental sulfur pollutants.

Cold and Hot Extremozymes: Industrial Relevance and Current Trends

The development of enzymes for industrial applications relies heavily on the use of microorganisms. The intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. Extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. These microorganisms have developed unique mechanisms and molecular means to cope with extreme temperatures, acidic and basic pH, high salinity, high radiation, low water activity, and high metal concentrations among other environmental conditions. Extremophile-derived enzymes, or extremozymes, are able to catalyze chemical reactions under harsh conditions, like those found in industrial processes, which were previously not thought to be conducive for enzymatic activity. Due to their optimal activity and stability under extreme conditions, extremozymes offer new catalytic alternatives for current industrial applications. These extremozymes also represent the cornerstone for the development of environmentally friendly, efficient, and sustainable industrial technologies. Many advances in industrial biocatalysis have been achieved in recent years; however, the potential of biocatalysis through the use of extremozymes is far from being fully realized. In this article, the adaptations and significance of psychrophilic, thermophilic, and hyperthermophilic enzymes, and their applications in selected industrial markets will be reviewed. Also, the current challenges in the development and mass production of extremozymes as well as future prospects and trends for their biotechnological application will be discussed.

Patterns of Macroinvertebrate and Fish Diversity in Freshwater Sulphide Springs

Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates) and cyprinodontiforms (among fishes) appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

Involvement of Sulfide:Quinone Oxidoreductase in Sulfur Oxidation of an Acidophilic Iron-Oxidizing Bacterium,Acidithiobacillus ferrooxidansNASF-1

The effects of cyanide, azide, and 2-n-Heptyl-4-hydroxy-quinoline-N-oxide (HQNO) on the oxidation of ferrous ion or elemental sulfur with Acidithiobacillus ferrooxidans NASF-1 cells grown in iron- or sulfur-medium were examined. The iron oxidation of both iron- and sulfur-grown cells was strongly inhibited by cyanide and azide, but not by HQNO. Sulfur oxidation was relatively resistant to cyanide and azide, and inhibited by HQNO. Higher sulfide oxidation, ubiquinol dehydrogenase activity, and sulfide:quinone oxidoreductase (SQR) activity were observed in sulfur-grown cells more than in iron-grown cells. Sulfide oxidation in the presence of ubiquinone with the membrane fraction was inhibited by HQNO, but not by cyanide, azide, antimycin A, and myxothiazol. The transcription of three genes, encoding an aa(3)-type cytochrome c oxidase (coxB), a bd-type ubiquinol oxidase (cydA), and an sqr, were measured by real-time reverse transcription polymerase chain reaction. The transcriptional levels of coxB and cydA genes were similar in sulfur- and iron-grown cells, but that of sqr was 3-fold higher in sulfur-grown cells than in iron-grown cells. A model is proposed for the oxidation of reduced inorganic sulfur compounds in A. ferrooxidans NASF-1 cells.

Determination of vitamin B6 (pyridoxine hydrochloride) based on a novel BZ oscillating reaction system catalyzed by a macrocyclic complex

This paper reports a new method for determination of VB6 (pyridoxine hydrochloride) by its perturbation effects on a novel Belousov-Zhabotinskii (BZ) oscillating system. This novel BZ system, in which malic acid serves as the substrate, contains an enzyme-like complex, macrocyclic complex {[CuL](ClO4)2}, as catalyst. The ligand L in the complex is 5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene. Results show that the addition of pyridoxine hydrochloride can perturb the oscillation amplitude and period, and the change of the oscillation amplitude is linearly proportional to the concentration of pyridoxine hydrochloride in the range of 5×10−7−2.5×10−4 M. The obtained RSD with seven samples is 3.073%. An assay of pharmaceutical tablets of vitamin B6 was evaluated. Some foreign ions were studied with respect to their possible influence on the determination of pyridoxine hydrochloride. The factors which influence this reaction include the concentration of reactant, the temperature of the reaction, property of catalyst, etc. Furthermore, the possible reaction mechanism has been proposed using the Field-Körös-Noyes (FKN) model.

Structural, biochemical and genetic characterization of dissimilatory ATP sulfurylase from Allochromatium vinosum

ATP sulfurylase (ATPS) catalyzes a key reaction in the global sulfur cycle by reversibly converting inorganic sulfate (SO4 (2-)) with ATP to adenosine 5'-phosphosulfate (APS) and pyrophosphate (PPi). In this work we report on the sat encoded dissimilatory ATP sulfurylase from the sulfur-oxidizing purple sulfur bacterium Allochromatium vinosum. In this organism, the sat gene is located in one operon and co-transcribed with the aprMBA genes for membrane-bound APS reductase. Like APS reductase, Sat is dispensible for growth on reduced sulfur compounds due to the presence of an alternate, so far unidentified sulfite-oxidizing pathway in A. vinosum. Sulfate assimilation also proceeds independently of Sat by a separate pathway involving a cysDN-encoded assimilatory ATP sulfurylase. We produced the purple bacterial sat-encoded ATP sulfurylase as a recombinant protein in E. coli, determined crucial kinetic parameters and obtained a crystal structure in an open state with a ligand-free active site. By comparison with several known structures of the ATPS-APS complex in the closed state a scenario about substrate-induced conformational changes was worked out. Despite different kinetic properties ATPS involved in sulfur-oxidizing and sulfate-reducing processes are not distinguishable on a structural level presumably due to the interference between functional and evolutionary processes.

Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans

The prokaryotic oxidation of reduced inorganic sulfur compounds (RISCs) is a topic of utmost importance from a biogeochemical and industrial perspective. Despite sulfur oxidizing bacterial activity is largely known, no quantitative approaches to biological RISCs oxidation have been made, gathering all the complex abiotic and enzymatic stoichiometry involved. Even though in the case of neutrophilic bacteria such as Paracoccus and Beggiatoa species the RISCs oxidation systems are well described, there is a lack of knowledge for acidophilic microorganisms. Here, we present the first experimentally validated stoichiometric model able to assess RISCs oxidation quantitatively in Acidithiobacillus thiooxidans (strain DSM 17318), the archetype of the sulfur oxidizing acidophilic chemolithoautotrophs. This model was built based on literature and genomic analysis, considering a widespread mix of formerly proposed RISCs oxidation models combined and evaluated experimentally. Thiosulfate partial oxidation by the Sox system (SoxABXYZ) was placed as central step of sulfur oxidation model, along with abiotic reactions. This model was coupled with a detailed stoichiometry of biomass production, providing accurate bacterial growth predictions. In silico deletion/inactivation highlights the role of sulfur dioxygenase as the main catalyzer and a moderate function of tetrathionate hydrolase in elemental sulfur catabolism, demonstrating that this model constitutes an advanced instrument for the optimization of At. thiooxidans biomass production with potential use in biohydrometallurgical and environmental applications.

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves

Mangroves are unique and highly productive ecosystems and harbor very special microbial communities. Although the phylogenetic diversity of sediment microbial communities of mangrove habitats has been examined extensively, little is known regarding their functional gene diversity and metabolic potential. In this study, a high-throughput functional gene array (GeoChip 4.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of microbial communities in mangrove habitats from mangrove national nature reserves in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 4.0 were detected in the mangrove microbial communities, including carbon (C) fixation, C degradation, methane generation, nitrogen (N) fixation, nitrification, denitrification, ammonification, N reduction, sulfur (S) metabolism, metal resistance, antibiotic resistance, and organic contaminant degradation. Detrended correspondence analysis (DCA) of all detected genes showed that Spartina alterniflora (HH), an invasive species, did not harbor significantly different microbial communities from Aegiceras corniculatum (THY), a native species, but did differ from other species, Kenaelia candel (QQ), Aricennia marina (BGR), and mangrove-free mud flat (GT). Canonical correspondence analysis (CCA) results indicated the microbial community structure was largely shaped by surrounding environmental variables, such as total nitrogen (TN), total carbon (TC), pH, C/N ratio, and especially salinity. This study presents a comprehensive survey of functional gene diversity of soil microbial communities from different mangrove habitats/species and provides new insights into our understanding of the functional potential of microbial communities in mangrove ecosystems.

Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

Background

Concrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.

Results

Taxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.

Conclusions

The function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.

The sulfur oxidation operon repressor function is influenced by the product of its adjacent upstream ORF in Pseudaminobacter salicylatoxidans KCT001

The repressor of sulfur-oxidizing (sox) operon regulates expression of genes encoding a multienzyme complex that governs the chemolithotrophic sulfur oxidation in Pseudaminobacter salycylatoxidans KCT001. The inducer of sox operon viz., thiosulfate and other sulfur anions had no impact on in vitro repressor-operator interaction which indicates an atypical derepression mechanism. The reduced repressor has higher affinity for its operator DNA. The sulfur oxidation repressor binds with operator regions and led to efficient repression in trans, however, increased repressor concentration resulted in higher gene expression. Using a reporter system in E. coli, the present study established that the thioredoxin-like protein, encoded in immediate upstream ORF, could nullify the observed reversal of the repression at higher repressor concentration. In this context, the involvement of the upstream gene product in the regulation of the sulfur oxidation gene expression has been reported.

Sulfur metabolisms in epsilon- and gamma-proteobacteria in deep-sea hydrothermal fields

In deep-sea hydrothermal systems, super hot and reduced vent fluids from the subseafloor blend with cold and oxidized seawater. Very unique and dense ecosystems are formed within these environments. Many molecular ecological studies showed that chemoautotrophic epsilon- and gamma-Proteobacteria are predominant primary producers in both free-living and symbiotic microbial communities in global deep-sea hydrothermal fields. Inorganic sulfur compounds are important substrates for the energy conservative metabolic pathways in these microorganisms. Recent genomic and metagenomic analyses and biochemical studies have contributed to the understanding of potential sulfur metabolic pathways for these chemoautotrophs. Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, gamma-Proteobacteria utilize two different sulfur-oxidizing pathways. It is hypothesized that differences between the metabolic pathways used by these two predominant proteobacterial phyla are associated with different ecophysiological strategies; extending the energetically feasible habitats with versatile energy metabolisms in the epsilon-Proteobacteria and optimizing energy production rate and yield for relatively narrow habitable zones in the gamma-Proteobacteria.

A sulfite respiration pathway from Thermus thermophilus and the key role of newly identified cytochrome c₅₅₀

Sulfite, produced for instance during amino acid metabolism, is a very reactive and toxic compound. Various detoxification mechanisms exist, but sulfite oxidoreductases (SORs) are one of the major actors in sulfite remediation in bacteria and animals. Here we describe the existence of an operon in the extreme thermophilic bacterium Thermus thermophilus HB8 encoding both a SOR and a diheme c-type cytochrome. The in vitro analysis clearly showed that the newly identified cytochrome c₅₅₀ acts as an acceptor of the electrons generated by the SOR enzyme during the oxidation of sulfite. The electrons are then rapidly shuttled via cytochrome c₅₅₂ to the terminal ba₃- and caa₃-type oxidases, thereby unveiling a novel electron transfer pathway, linking sulfite oxidation to oxygen reduction in T. thermophilus: sulfite → SOR(HB8) → cytochrome c₅₅₀ → cytochrome c₅₅₂ → ba₃ oxidase/caa₃ oxidase → O₂. The description of the complete pathway reveals that electrons generated during sulfite oxidation by the SOR are funneled into the respiratory chain, participating in the energy production of T. thermophilus.

Evidence from the structure and function of cytochromes c(2) that nonsulfur purple bacterial photosynthesis followed the evolution of oxygen respiration

Cytochromes c(2) are the nearest bacterial homologs of mitochondrial cytochrome c. The sequences of the known cytochromes c(2) can be placed in two subfamilies based upon insertions and deletions, one subfamily is most like mitochondrial cytochrome c (the small C2s, without significant insertions and deletions), and the other, designated large C2, shares 3- and 8-residue insertions as well as a single-residue deletion. C2s generally function between cytochrome bc(1) and cytochrome oxidase in respiration (ca 80 examples known to date) and between cytochrome bc(1) and the reaction center in nonsulfur purple bacterial photosynthesis (ca 21 examples). However, members of the large C2 subfamily are almost always involved in photosynthesis (12 of 14 examples). In addition, the gene for the large C2 (cycA) is associated with those for the photosynthetic reaction center (pufBALM). We hypothesize that the insertions in the large C2s, which were already functioning in photosynthesis, allowed them to replace the membrane-bound tetraheme cytochrome, PufC, that otherwise mediates between the small C2 or other redox proteins and photosynthetic reaction centers. Based upon our analysis, we propose that the involvement of C2 in nonsulfur purple bacterial photosynthesis was a metabolic feature subsequent to the evolution of oxygen respiration.

Endogenous production of H2S in the gastrointestinal tract: still in search of a physiologic function

Hydrogen sulfide (H(2)S) has long been associated with the gastrointestinal tract, especially the bacteria-derived H(2)S present in flatus. Along with evidence from other organ systems, the finding that gastrointestinal tissues are capable of endogenous production of H(2)S has led to the hypothesis that H(2)S is an endogenous gaseous signaling molecule. In this review, the criteria of gasotransmitters are reexamined, and evidence from the literature regarding H(2)S as a gaseous signaling molecule is discussed. H(2)S is produced enzymatically by gastrointestinal tissues, but evidence is lacking on whether H(2)S production is regulated. H(2)S causes well-defined physiologic effects in gastrointestinal tissues, but evidence for a receptor for H(2)S is lacking. H(2)S is inactivated through enzymatic oxidation, but evidence is lacking on whether manipulating H(2)S oxidation alters endogenous cell signaling. Remaining questions regarding the role of H(2)S as a gaseous signaling molecule in the gastrointestinal tract suggest that H(2)S currently remains a molecule in search of a physiologic function.

Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans

Background

Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus.

Results

Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa₃ oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool.

Conclusion

Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea

Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.

Phylogenomic dating--the relative antiquity of archaeal metabolic and physiological traits

Ancestral trait reconstruction was used to identify the relative ancestry of metabolic and physiological traits in the archaeal domain of life. First, well-resolved phylogenetic trees were inferred with multiple gene sequences obtained from whole genome sequences. Next, metabolic and physiological traits were coded into characters, and ancestral state reconstruction was used to identify ancient and derived traits. Traits inferred to be ancient included sulfur reduction, methanogenesis, and hydrogen oxidation. By using the articulation of the "oxygen age constraint," several other traits were inferred to have arisen at or after 2.32 Ga: aerobic respiration, nitrate reduction, sulfate reduction, thiosulfate reduction, sulfur oxidation, and sulfide oxidation. Complex organic metabolism appeared to be nearly as ancient as autotrophy. Hyperthermophily was ancestral, while hyperacidophily and extreme halophily likely arose after 2.32 Ga. The ancestral euryarchaeote was inferred to have been a hyperthermophilic marine methanogen that lived in a deep-sea hydrothermal vent. In contrast, the ancestral crenarchaeote was most likely a hyperthermophilic sulfur reducer that lived in a slightly acidic terrestrial environment, perhaps a fumarole. Cross-colonization of these habitats may not have occurred until after 2.32 Ga, which suggests that both archaeal lineages exhibited niche specialization on early Earth for a protracted period of time.

Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring

A bacterial isolate S23 capable of oxidizing thiosulfate was isolated from a sulfur spring. Strain S23 is gram-negative, aerobic, and motile. The G + C content of DNA is 61.4 mol%. The fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence of strain S23 showed that it is related to the members of the genus Comamonas, and most closely related to Comamonas testosteroni (99.9% sequence similarity). The isolate S23 exhibited thiosulfate oxidation under a mixotrophic growth condition. Polymerase chain reaction (PCR) using soxB-specific primers and DNA sequencing showed the presence of the soxB gene. This is the first report in Comamonas sp. showing thiosulfate oxidation under a mixotrophic growth condition.

Genetic polymorphism at the candidate gene in Iranian Sistani cattle (Bos indicus)

The genotypes for Leptin, Kappa-Casein, Calpastatin and BoLA-DRB3 loci were determined by polymerase chain reaction and restriction enzyme digestion method in native Iranian breed cattle, Sistani. Blood samples were collected from Sistani Breeding Station located in Zehak, Zabol in Iran. The extraction of genomic DNA was based on Guanidin Thiocyanate-Silica gel method. After PCR reaction, amplicons were digested with appropriate restriction enzymes. The Calpastatin locus had 3 genotypes with frequencies of 0.62, 0.29 and 0.09 for MM, MN and NN, respectively; kappa-Casein and Leptin had 3 genotypes with frequencies of 0.27, 0.57 and 0.16 for kappa-Casein, 0.77, 0.22 and 0.01 for Leptin for AA, AB and BB genotypes, respectively. For BoLA-DRB3 we identified 19 alleles, that DRB3. 2*8 had the highest allelic frequency (22.4%) and DRB3. 2*3, *29, *37 and *51 had the lowest allelic frequency (1%). One of the 19 alleles had a new pattern. Average heterozygosity values for all loci were low. Chi2-test did not confirm the Hardy-Weinberg equilibrium for Leptin and Calpastatin in this population. These data provide evidence that Iranian's Sistani breed have a good genetic variability, which opens interesting prospects for future selection programs, especially marker-assistant selection.

16S rDNA and 16S-23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Acidithiobacillus phylogeny

In order to contribute to our understanding of Acidithiobacillus taxonomy, we determined 16S rDNA sequences and the 16S-23S internally transcribed spacer (ITS) sequence of 35 Chinese Acidithiobacillus isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and Acidithiobacillus strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polymorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter- and intraspecific genealogical relationships of the genus Acidithiobacillus. Similarity values of the ITSs varied from 60.5 % to 84.7 % between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13 %. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three Acidithiobacillus ferrooxidans phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese Acidithiobacillus-like isolates represent one or two new species of the genus Acidithiobacillus. The ITS may be a potential target for the development of fluorescent in situ hybridization probes for more accurately detecting distinct ecotypes of Acidithiobacillus strains and other closely related sulfur-oxidizing bacteria.

Computational identification of significantly regulated metabolic reactions by integration of data on enzyme activity and gene expression

The concentrations and catalytic activities of enzymes control metabolic rates. Previous studies have focused on enzyme concentrations because there are no genome-wide techniques used for the measurement of enzyme activity. We propose a method for evaluating the significance of enzyme activity by integrating metabolic network topologies and genome-wide microarray gene expression profiles. We quantified the enzymatic activity of reactions and report the 388 significant reactions in five perturbation datasets. For the 388 enzymatic reactions, we identified 70 that were significantly regulated (P-value < 0.001). Thirty-one of these reactions were part of anaerobic metabolism, 23 were part of low-pH aerobic metabolism, 8 were part of high-pH anaerobic metabolism, 3 were part of low-pH aerobic reactions, and 5 were part of high-pH anaerobic metabolism.

Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis

Denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA, aprA, and amoA genes demonstrated that a phylogenetically diverse and complex microbial community was associated with the Caribbean deep-water sponge Polymastia cf. corticata Ridley and Dendy, 1887. From the 38 archaeal and bacterial 16S rRNA phylotypes identified, 53% branched into the sponge-specific, monophyletic sequence clusters determined by previous studies (considering predominantly shallow-water sponge species), whereas 26% appeared to be P. cf. corticata specifically associated microorganisms ("specialists"); 21% of the phylotypes were confirmed to represent seawater- and sediment-derived proteobacterial species ("contaminants") acquired by filtration processes from the host environment. Consistently, the aprA and amoA gene-based analyses indicated the presence of environmentally derived sulfur- and ammonia-oxidizers besides putative sponge-specific sulfur-oxidizing Gammaproteobacteria and Alphaproteobacteria and a sulfate-reducing archaeon. A sponge-specific, endosymbiotic sulfur cycle as described for marine oligochaetes is proposed to be also present in P. cf. corticata. Overall, the results of this work support the recent studies that demonstrated the sponge species specificity of the associated microbial community while the biogeography of the host collection site has only a minor influence on the composition. In P. cf. corticata, the specificity of the sponge-microbe associations is even extended to the spatial distribution of the microorganisms within the sponge body; distinct bacterial populations were associated with the different tissue sections, papillae, outer and inner cortex, and choanosome. The local distribution of a phylotype within P. cf. corticata correlated with its (1) phylogenetic affiliation, (2) classification as sponge-specific or nonspecifically associated microorganism, and (3) potential ecological role in the host sponge.