The bacteria of the sulphur cycle

Environmental Homeopathy: Homeopathic Potencies Regulate the Toxicity and Growth of Raphidiopsis raciborskii (cyanobacteria) and can be Tracked Physico-Chemically. Part 1: Biological Results

INTRODUCTION

 Cyanobacteria are microorganisms found in many parts of the world and several genera, such as Raphidiopsis raciborskii, are producers of cyanotoxins. Homeopathic potencies have been found to modulate toxicity in different biological models, and the present study endeavors to discover whether this might also be the case with cyanobacteria.

OBJECTIVES

 Our objective was to investigate the possible effects of homeopathic potencies on the resilience of Artemia franciscana (brine shrimp) embryos to saxitoxin (STX; cyanotoxin) and on controlling the growth of R. raciborskii in vitro.

METHOD

 A. franciscana cysts were cultivated in seawater in 96-well plates to evaluate the hatching rate and vitality, plus the gene expression of heat shock proteins (HSPs), after being challenged with R. raciborskii extract containing 2.5 µg/L of STX and treated with different homeopathic potencies. Untreated wells were used as controls ("base-line"). Potencies were chosen from a screening process based on seven selected homeopathic preparations according to the similitude of STX symptoms (Sulphur, Zincum metallicum, Nitric acidum, Plumbum metallicum, Mercurius solubilis, Phosphoric acidum, Isotherapic from R. raciborskii extract; all at 6cH, 30cH and 200cH). Cultures of R. raciborskii maintained in an artificial seawater medium were equally treated with screened homeopathic potencies selected from the same list but specifically for their growth control as a function of time.

RESULTS

 A 15% lower rate of hatching of A. franciscana cysts was observed after treatment with Nitric acidum 6cH in comparison with baseline (p = 0.05). A complete toxicity reversal was seen after treatment with Isotherapic 200cH, with a 23-fold increase of Hsp 26 gene expression (p = 0.023) and a 24-fold increase of p26 gene expression (p ≤ 0.001) in relation to baseline. Nitric acidum 200cH and Mercurius solubilis 30cH limited the exponential growth of cyanobacteria up to 95% and 85% respectively (p ≤ 0.003) in relation to baseline. Succussed water presented only a transitory 50% inhibition effect.

CONCLUSION

 Isotherapic 200cH improved A. franciscana bioresilience to STX; Nitric acidum 200cH and Mercurius solubilis 30cH showed the optimal performance on limiting R. raciborskii growth. The results point to the potential of homeopathic potencies to mitigate environmental problems related to water quality.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Colonisation of the colonic mucus gel layer with butyrogenic and hydrogenotropic bacteria in health and ulcerative colitis

Butyrate is the primary energy source for colonocytes and is essential for mucosal integrity and repair. Butyrate deficiency as a result of colonic dysbiosis is a putative factor in ulcerative colitis (UC). Commensal microbes are butyrogenic, while others may inhibit butyrate, through hydrogenotropic activity. The aim of this study was to quantify butyrogenic and hydrogenotropic species and determine their relationship with inflammation within the colonic mucus gel layer (MGL). Mucosal brushings were obtained from 20 healthy controls (HC), 20 patients with active colitis (AC) and 14 with quiescent colitis (QUC). Abundance of each species was determined by RT-PCR. Inflammatory scores were available for each patient. Statistical analyses were performed using Mann-Whitney-U and Kruskall-Wallis tests. Butyrogenic R. hominis was more abundant in health than UC (p < 0.005), prior to normalisation against total bacteria. Hydrogenotropic B. wadsworthia was reduced in AC compared to HC and QUC (p < 0.005). An inverse correlation existed between inflammation and R. hominis (ρ - 0.460, p < 0.005) and B. wadsworthia (ρ - 0.646, p < 0.005). Other hydrogenotropic species did not widely colonise the MGL. These data support a role for butyrogenic bacteria in UC. Butyrate deficiency in UC may be related to reduced microbial production, rather than inhibition by microbial by-products.

H2S: A Novel Gasotransmitter that Signals by Sulfhydration

Hydrogen sulfide (H2S) is a member of the growing family of gasotransmitters. Once regarded as a noxious molecule predominantly present in the atmosphere, H2S is now known to be synthesized endogenously in mammals. H2S participates in a myriad of physiological processes ranging from regulation of blood pressure to neuroprotection. Its chemical nature precludes H2S from being stored in vesicles and acting on receptor proteins in the fashion of other chemical messengers. Thus, novel cellular mechanisms have evolved to mediate its effects. This review focuses on sulfhydration (or persulfidation), which appears to be the principal post-translational modification elicited by H2S.

Modes of physiologic H2S signaling in the brain and peripheral tissues

SIGNIFICANCE

Hydrogen sulfide (H2S), once associated with rotten eggs and sewers, is now recognized as a gasotransmitter that is synthesized in vivo in a regulated fashion. This ancient gaseous molecule has been retained throughout evolution to perform various roles in different life forms. H2S modulates important signaling functions in diverse cellular processes ranging from regulation of blood pressure to redox homeostasis.

RECENT ADVANCES

One of the modes by which H2S signals is by post-translational modification of reactive cysteine residues in a process designated as sulfhydration, resulting in conversion of the -SH groups of target cysteine residues to -SSH. Using the modified biotin-switch assay and a fluorescent maleimide-based analysis, sulfhydration of several proteins has been detected in various cell types. Aberrant sulfhydration patterns occur in neurodegenerative conditions such as Parkinson's disease.

CRITICAL ISSUES

The exact concentration, source of H2S, and conditions under which various stores of H2S are utilized have not been fully elucidated. Currently, available inhibitors of the biosynthetic enzymes of H2S lack sufficient specificity to shed light on detailed mechanisms of H2S action. Probes with a higher sensitivity that can reliably detect cellular and tissue H2S levels are yet to be developed.

FUTURE DIRECTIONS

Availability of advanced probes and biosynthesis inhibitors would help in the measurement of real-time changes of endogenous H2S levels in an in vivo context. The study of the dynamics of sulfhydration and nitrosylation of critical cysteine residues of regulatory proteins involved in physiology and pathophysiology is an area of interest for the future.

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.

Sulphate-reducing bacteria and hydrogen sulphide in the aetiology of ulcerative colitis

BACKGROUND

The aetiology of ulcerative colitis is uncertain but may relate to environmental factors in genetically predisposed individuals. Sulphate-reducing bacteria (SRB) have been implicated through the harmful effects of hydrogen sulphide, a by-product of their respiration. Hydrogen sulphide is freely permeable to cell membranes and inhibits butyrate. This review examines the available evidence relating to SRB as a possible cause of ulcerative colitis.

METHODS

A literature search was conducted using the PubMed database and search terms 'sulphate reducing bacteria', 'hydrogen sulphide', 'ulcerative colitis', 'mucous gel layer' and 'trans-sulphuration'.

RESULTS

Search results were scrutinized and 113 pertinent full-text articles were selected for review. Collected data related to hydrogen sulphide metabolism, SRB respiration, mucous gel layer composition and their association with ulcerative colitis.

CONCLUSION

There is evidence to implicate SRB as an environmental factor in ulcerative colitis. More sophisticated mucosal dissection and molecular techniques using bacteria-directed probes are required to determine an association definitively.

Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor

High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n = 500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO3, SO4, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site.

Molecular properties of the dissimilatory sulfite reductase from Desulfovibrio desulfuricans (Essex) and comparison with the enzyme from Desulfovibrio vulgaris (Hildenborough)

The dissimilatory sulfite reductase desulfoviridin was purified from the membrane (mSiR) and the soluble fraction (sSiR) of the sulfate-reducing bacterium Desulfovibrio desulfuricans (Essex). Molecular and spectroscopic properties were determined and compared with the properties of the soluble desulfoviridin from Desulfovibrio vulgaris (Hildenborough). The enzymes were isolated as alpha 2 beta 2 gamma n (n = 1-3) multimers with a relative molecular mass of 200 +/- 10 (gel filtration). Both mSiR and sSiR from D. desulfuricans contained 24 +/- 3 Fe and 18 +/- 3 labile sulfide/200 kDa, respectively, and showed identical EPR spectra. Quantification of the high-spin Fe(III) heme resonances at g of approximately 6 indicated that close to 80% of the siroheme moiety in the enzyme from D. desulfuricans was demetallated. D. desulfuricans sulfite reductase showed S = 9/2 EPR signals with the highest apparent g value at g = 17 as reported for SiR from D. vulgaris. Antibodies raised against the alpha, beta and gamma subunit of the D. vulgaris enzyme exhibited cross-reactivity with the subunits of mSiR and sSiR from D. desulfuricans. N-terminal sequences of alpha, beta and gamma subunits of both mSiR and sSiR from D. desulfuricans were identical and showed a high degree of similarity with the sequences of the corresponding subunits obtained from the D. vulgaris enzyme. During gel filtration of sSiR from D. desulfuricans, under non-denaturing conditions, a small protein (molecular mass approximately 11 kDa) was separated. This 11-kDa protein exhibited cross-reactivity with the antibody raised against the gamma subunit of D. vulgaris sulfite reductase. In the case of D. desulfuricans sulfite reductase, the 11-kDa gamma subunit seems not to be an integral part of the protein and can be obtained from the soluble fraction and during purification of the soluble enzyme.

The bacterial degradation of benzoic acid and benzenoid compounds under anaerobic conditions: unifying trends and new perspectives

Simple homocyclic aromatic compounds are extremely abundant in the environment and are derived largely from lignin. Such compounds may enter anaerobic environments and several groups of bacteria, exhibiting diverse energy-yielding mechanisms, have evolved the capacity to overcome the thermodynamic stability of the benzene nucleus and degrade aromatic compounds under these conditions. Over the last few years considerable advances have been made in our understanding of the biochemical strategies underlying the bacterial degradation of aromatic compounds in anoxic environments. The study of the biochemistry, and more recently the molecular genetics of the photosynthetic bacterium Rhodopseudomonas palustris and several strains of denitrifying pseudomonads, has provided the greatest insight into the mechanism and regulation of aromatic degradation under anaerobic conditions. Research has centred around the anaerobic degradation of benzoic acid. This involves the initial activation to form benzoyl-Coenzyme A, reduction of the aromatic nucleus--a reaction that has only recently been demonstrated in vitro--and the subsequent degradation of the alicyclic intermediates. Recently, much information regarding the exact nature of these intermediates has been obtained. Also through recent studies, it has become increasingly clear that benzoyl-CoA is a central metabolic intermediate during the anaerobic degradation of structurally diverse aromatic compounds. The initial metabolism of these compounds involves the formation of a carboxyl group on the aromatic nucleus (if necessary) and the synthesis of the respective Coenzyme A thioester; this results in the direct formation of benzoyl-Coenzyme A rather than benzoate. In many cases of anaerobic aromatic degradation studied in batch culture, aromatic intermediates are transiently excreted into the medium. It is argued that the study of this phenomenon may facilitate the understanding of the regulation and kinetics of the aromatic degradative pathways.

An investigation of Chromatium vinosum high-potential iron-sulfur protein by EPR and Mossbauer spectroscopy; evidence for a freezing-induced dimerization in NaCl solutions

The high-potential iron-sulfur protein (HiPIP) from Chromatium vinosum contains a cubane prosthetic group that shuttles between the [4Fe-4S]3+,2+ states. We find that the EPR spectra from this protein can be explained as a sum of two components, a major one with g = 2.02; 2.04; 2.12, and a minor one with g = 2.04; 2.07; approximately 2.13. In the presence of 0.1-2.0 M NaCl, freezing induces polymerization of the protein (presumably dimers), which is detected as intercluster spin-spin interaction in the EPR. The observed spin-spin interactions are interpreted as being due to two very similar dimeric structures in an approx. 1:2 ratio. Computer simulation of the X- and Q-band EPR spectra shows that the z-components of the g-tensors in each dimer pair must be co-linear, with center-to-center distances between the clusters of approximately 13 A and approximately 16 A. Inspection of possible dimeric structures of C. vinosum HiPIP by standard molecular graphics procedures revealed that the Fe/S cluster is exposed toward a flattened surface and is accessible to solvent. Moreover, the Fe/S clusters in two HiPIP molecules can easily achieve a center-to-center distance of approximately 14 A when approaching along a common 3-fold axis that extends through the S4 sulfur atom of the cubane; the z-component of the EPR g-tensor is co-linear with this symmetry axis.

Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world

Among sulfur compounds, thiosulfate and polythionates are present at least transiently in many environments. These compounds have a similar chemical structure and their metabolism appears closely related. They are commonly used as energy sources for photoautotrophic or chemolithotrophic microorganisms, but their assimilation has been seldom studied and their importance in bacterial physiology is not well understood. Almost all bacterial strains are able to cleave these compounds since they possess thiosulfate sulfur transferase, thiosulfate reductase or S-sulfocysteine synthase activities. However, the role of these enzymes in the assimilation of thiosulfate or polythionates has not always been clearly established. Elemental sulfur is, on the contrary, very common in the environment. It is an energy source for sulfur-reducing eubacteria and archaebacteria and many sulfur-oxidizing archaebacteria. A phenomenon still not well understood is the 'excessive assimilatory sulfur metabolism' as observed in methanogens which perform a sulfur reduction which exceeds their anabolic needs without any apparent benefit. In heterotrophs, assimilation of elemental sulfur is seldom described and it is uncertain whether this process actually has a physiological significance. Thus, reduction of thiosulfate and elemental sulfur is a common but incompletely understood feature among bacteria. These activities could give bacteria a selective advantage, but further investigations are needed to clarify this possibility. Presence of thiosulfate, polythionates and sulfur reductase activities does not imply obligatorily that these activities play a role in thiosulfate, polythionates or sulfur assimilation as these compounds could be merely intermediates in bacterial metabolism. The possibility also exists that the assimilation of these sulfur compounds is just a side effect of an enzymatic activity with a completely different function. As long as these questions remain unanswered, our understanding of sulfur and thiosulfate metabolism will remain incomplete.

Kinetics of Sulfate and Acetate Uptake by Desulfobacter postgatei

The kinetics of sulfate and acetate uptake was studied in the sulfate-reducing bacterium Desulfobacter postgatei (DSM 2034). Kinetic parameters ( K m and V max ) were estimated from substrate consumption curves by resting cell suspensions with [ 35 S]sulfate and [ 14 C]acetate. Both sulfate and acetate consumption followed Michaelis-Menten saturation kinetics. The half-saturation constant ( K m ) for acetate uptake was 70 μM with cells from either long-term sulfate- or long-term acetate-limited chemostat cultures. The average K m value for sulfate uptake by D. postgatei was about 200 μM. K m values for sulfate uptake did not differ significantly when determined with cells derived either from batch cultures or sulfate- or acetate-limited chemostat cultures. Acetate consumption was observed at acetate concentrations of ≤1 μM, whereas sulfate uptake usually ceased at 5 to 20 μM. The results show that D. postgatei is not freely permeable to sulfate ions and further indicate that sulfate uptake is an energy-requiring process.