Oxygen defense in sulfate-reducing bacteria

Differential associations of five riverine organism groups with multiple stressors

The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

A neutral polysaccharide from Persicaria hydropiper (L.) Spach ameliorates lipopolysaccharide-induced intestinal barrier injury via regulating the gut microbiota and modulating AKT/PI3K/mTOR and MAPK signaling pathways

ETHNOPHARMACOLOGICAL RELEVANCE

Persicaria hydropiper (L.) Spach, a herb that is prevalent across Asia and Europe, finds utility as both a culinary ingredient and medicinal herb. In China, P. hydropiper decoction is commonly employed to alleviate dysentery, gastroenteritis, and diarrhea symptoms.

AIM OF THE STUDY

To assess the effects of a neutral polysaccharide from P. hydropiper (PHP) on the intestinal barrier (IB) injury induced by lipopolysaccharide (LPS) in mice, and elucidate the molecular mechanisms involved.

MATERIALS AND METHODS

PHP was extracted from dried P. hydropiper herb using hot water extraction, followed by ethanol precipitation. The extract underwent successive isolation and purification steps involving anion-exchange and gel filtration chromatography. The primary structure of PHP was determined using Fourier-transformed infrared spectroscopy, ion chromatography, gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) spectroscopy. Male BALB/c mice were randomly assigned to control (CON), model (MOD), berberine hydrochloride (BBR), and PHP (20, 40 and 80 mg/kg) groups. Histopathological changes in jejunal tissues were assessed through hematoxylin and eosin (HE) staining. The expression levels of proteins and genes involved in AKT/PI3K/mTOR and MAPK signaling pathways were evaluated using qRT-PCR and Western blotting, respectively. The composition and abundance of the gut microbiota in mice were analyzed using high-throughput 16S rRNA gene sequencing. Additionally, the concentrations of short-chain fatty acids (SCFAs) were determined using GC-MS.

RESULTS

The main components of PHP included arabinose, galactose, and glucose (molar ratio = 1.00:5.52:11.39). The backbone of PHP consisted of →4)-Glcp-(1→, →4,6)-Glcp-(1→, →4)-Galp-(1→, →4,6)-Galp-(1→. The branched chains primarily consisted of 5)-Araf-(1→ residues, which were attached to the backbone through →6)-Glcp-(1→ and →6)-Galp-(1→ at the 6-position. Histological analysis demonstrated that PHP exhibited a mitigating effect on intestinal damage induced by LPS. PHP could markedly reduce the mRNA levels of PI3K, AKT, mTOR, p70 S6K, Ras, Raf1, MEK1/2, p38, ERK1/2, and JNK, while downregulating the protein levels of p-mTOR, p-PI3K, p-AKT, p-p38, p-ERK, and p-JNK. PHP also modulated the diversities and abundances of the gut microbiota, resulting in an increase in the abundances of Lactobacillaceae, Anaerovoracaceae, Lachnospiraceae, Eggerthellaceae, and Desulfovibrionaceae and a decrease in the abundances of Muribaculaceae, Prevotellaceae, and Rikenellaceae. Additionally, PHP significantly increased the content of various SCFAs.

CONCLUSION

PHP emerges as a pivotal factor in the repair of IB injury by virtue of its ability to regulate the gut microbiota, elevate SCFA levels, and inhibit the MAPK and AKT/PI3K/mTOR pathways. It is worth noting that the therapeutic effect of high-dose PHP was remarkably significant, surpassing even the positive control of berberine hydrochloride.

An allosteric redox switch involved in oxygen protection in a CO2 reductase

Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.

Contribution of holothuroids to the bioremediation and stimulation of the benthic microbial metabolism in aquaculture

The implementation of sustainable system designs in aquaculture comprises the biological treatment of pollutants. In order to test the potential of Holothuria (Roweothuria) poli as a candidate for bioremediation of aquaculture wastes, the effect of this species on the benthic microbial activity was studied. Two experimental treatments, with and without holothuroids, were allocated in two benthocosms, each one containing four replicate tanks with undisturbed sediment and a volume of water above it. It was anticipated that H. poli could affect the overall assimilative capacity of the aquaculture effluent system either through the consumption of particulate organic matter or through the stimulation of benthic microbial metabolism. Indeed, the results indicated that the microbial activity related to the mineralization of the N and C was significantly different between the treatments verifying our hypothesis that deposit-feeders that move above or inside the sediment matrix can accelerate the depletion of organic matter through bioturbation.

Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System

The search for extant microbial life will be a major focus of future astrobiology missions; however, no direct extant life detection instrumentation is included in current missions to Mars. In this study, we developed the semiautomated MicroLife detection platform that collects and processes environmental samples, detects biosignatures, and characterizes microbial activity. This platform is composed of a drill for sample collection, a redox dye colorimetric system for microbial metabolic activity detection and assessment (μMAMA [microfluidics Microbial Activity MicroAssay]), and a MinION sequencer for biosignature detection and characterization of microbial communities. The MicroLife platform was field-tested on White Glacier on Axel Heiberg Island in the Canadian high Arctic, with two extracted ice cores. The μMAMA successfully detected microbial metabolism from the ice cores within 1 day of incubation. The MinION sequencing of the ice cores and the positive μMAMA card identified a microbial community consistent with cold and oligotrophic environments. Furthermore, isolation and identification of microbial isolates from the μMAMA card corroborated the MinION sequencing. Together, these analyses support the MicroLife platform's efficacy in identifying microbes natively present in cryoenvironments and detecting their metabolic activity. Given our MicroLife platform's size and low energy requirements, it could be incorporated into a future landed platform or rovers for life detection.

A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells

The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.

Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling

BACKGROUND

Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO₂ or to a stoichiometric mix of CO₂ and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen.

RESULTS

Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO₂. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited.

CONCLUSIONS

Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.

Genomic insight into iron acquisition by sulfate-reducing bacteria in microaerophilic environments

Historically, sulfate-reducing bacteria (SRB) have been considered to be strict anaerobes, but reports in the past couple of decades indicate that SRB tolerate exposure to O2 and can even grow in aerophilic environments. With the transition from anaerobic to microaerophilic conditions, the uptake of Fe(III) from the environment by SRB would become important. In evaluating the metabolic capability for the uptake of iron, the genomes of 26 SRB, representing eight families, were examined. All SRB reviewed carry genes (feoA and feoB) for the ferrous uptake system to transport Fe(II) across the plasma membrane into the cytoplasm. In addition, all of the SRB genomes examined have putative genes for a canonical ABC transporter that may transport ferric siderophore or ferric chelated species from the environment. Gram-negative SRB have additional machinery to import ferric siderophores and ferric chelated species since they have the TonB system that can work alongside any of the outer membrane porins annotated in the genome. Included in this review is the discussion that SRB may use the putative siderophore uptake system to import metals other than iron.

Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps

Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.

Effects of Yucca schidigera extract on serum biochemical parameters, humoral immune response, and intestinal health in young pigeons

Introduction

It is of great importance to find antibiotic alternatives that can improve poultry performance and enhance immunity. Plant-derived extracts and their concentrates are natural bioactive compounds that are widely and effectively applied as the antibiotic alternatives in animal industries. This study was conducted to investigate the effects of Yucca schidigera extract (YSE) on growth performance, serum biochemical parameters, immune function, intestinal morphology, and microbiota diversity of young pigeons.

Methods

A total of 120 healthy White King pigeons (28 days old) with similar weight were randomly assigned to 4 treatments with six replicate cages. Each of the pigeons from 4 treatments was orally administrated with 0 (control), 5, 10, and 15 mg YSE per day, respectively.

Results

The results showed that orally supplemental YSE had no significant effects (P > 0.05) on the growth performance and immune organ index of pigeons. The serum total protein and IgM contents in the 10 mg YSE group were significantly higher (P < 0.05) than those in the control group. Supplemental 10 and 15 mg YSE significantly lowered the level of serum total cholesterol (P < 0.05) and increased (P < 0.05) the villi height in the jejunum compared with the control group. Supplemental 5 and 10 mg YSE significantly decreased (P < 0.05) the level of serum alanine aminotransferase and the crypt depth in the ileum compared with the control group. The beta diversity showed a distinct difference in the ileum microbial composition between the control and the 10 mg YES group. YSE supplementation enriched the bacterial genera Sulfurospirillum, Solobacterium, Desulfovibrio, Desulfobulbus, Lactococcus, Parabacteroides, Acidaminococcus, Acetobacter, and Streptococcus. Additionally, Enterococcus genus showed a significantly negative correlation with serum alanine aminotransferase (R = -0.618, P = 0.043). Actinomyces genus showed a significantly negative correlation with cholesterol (R = -0.633, P = 0.036). Turicibacter genus showed a significantly positive correlation with villi height in the jejunum (R = 0.751, P = 0.008).

Discussion

In conclusion, orally supplemental YSE could improve serum biochemistry, immunoglobulin contents, and intestinal morphology by regulating the composition of microbial community in the ileum of young pigeons.

Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.

Evaluation of a Microbial Consortium and Selection of a Support in an Anaerobic Reactor Directed to the Bio-Treatment of Wastewater of the Textile Industry

The dyeing processes of the textile industry generate waste products such as unfixed dyes, phenolic surfactants and heavy metals. These constitute an environmental problem for the bodies receiving their wastewater due to the interruption of the lighting in the aquatic environment and the release of toxic molecules by the decomposition of the dyes. There are several treatment methods, of which biological methods are the most feasible. In the current study, the I5-ESPE microbial consortium was obtained and evaluated on the components of textile wastewater, in addition to the selection of a support for an anaerobic reactor that is directed to the treatment of effluents from the textile industry. Two microbial consortia were achieved by exposure to air in Pseudomonas culture medium modified with direct dyes Red 23 and Blue 106, evaluating their removal capacity of the reactive dyes Navy 171, Red 141 and Yellow 84. The consortium I5-ESPE was selected for its greatest action, yielding approximately 95% removal. Its tolerance to phenol was also determined; we reached 98% removal of chromium(VI) and 67% of total chromium under anaerobic conditions and some 25% zinc in aerobiosis. The reduction in the chemical oxygen demand (COD) was evaluated with (57.03%) and without (31.47%) aeration. The species Staphylococcus xylosus, Saccharomyces cerevisiae and Candida tropicalis were identified prior to treatment of textile wastewater, as well as Enterobacter cloacae and Bacillus megaterium after treatment. Bacillus subtilis was present throughout the process. We evaluated coconut shell as a support for an anaerobic reactor, and it demonstrated better physical characteristics than plastic and common rock, in addition to similar results in the reduction in COD of 50%, volatile suspended solids of 2545.46 mg/L and total suspended solids of 282.82 mg/L.

The Diverse Indigenous Bacterial Community in the Rudna Mine Does Not Cause Dissolution of Copper from Kupferschiefer in Oxic Conditions

Blasting and fracking of rock in mines exposes fresh rock surfaces to the local water and microbial communities. This may lead to leaching of metals from the rock by chemical or biological means and can cause acidification of the water system in the mine, i.e., acid rock drainage (ARD). Failure to prevent leakage of metal contaminated mine water may be harmful for the environment, especially to the local groundwater. In the Rudna mine, Poland, an in situ bioleaching pilot test at approximately 1 km depth was performed in the H2020 BIOMOre project (Grant Agreement #642456). After the leaching stage, different methods for irreversible inhibition of acidophilic iron oxidizing microorganisms used for reoxidation of reduced iron in the leaching solution were tested and were shown to be effective. However, the potential of the natural mine water microbial communities to cause leaching of copper or acidification of the mine waters has not been tested. In this study, we set up a microcosm experiment simulating the exposure of freshly fractionated Kupferschiefer sandstone or black schist to two different chloride-rich water types in the Rudna mine. The pH of the microcosms water was measured over time. At the end of an 18-week incubation, the bacterial community was examined by high throughput sequencing and qPCR, and the presence of copper tolerant heterotrophic bacteria was tested by cultivation. The dissolution of copper into the chloride rich microcosm water was measured. The pH in the microcosms did not decrease over the time of incubation. The sandstone increased the number of bacteria in the microcosms with one or over two orders of magnitude compared to the original water. The bacterial communities in the two tested mine waters were diverse and similar despite the difference in salinity. The bacterial diversity was high but changed in the less saline water during the incubation. There was a high content of sulphate reducing bacteria in the original mine waters and in the microcosms, and their number increased during the incubation. No acidophilic iron oxidizers were detected, but in the microcosms containing the less saline water low numbers of Cu tolerant bacteria were detected. Copper to a concentration of up to 939 mg L−1 was leached from the rock also in the microbe-free negative controls, which was up to 2.4 times that leached in the biotic microcosms, indicating that the leaching was also abiotic, not only caused by bacteria.

Evolution of urban black and odorous water: The characteristics of microbial community and driving-factors

Urban black blooms that are primarily caused by organic carbon are deleterious environmental problems. However, detailed studies on the microbial characteristics that form urban black blooms are lacking. In this study, we observed the composition, diversity, and function of bacterial community in the overlying water and sediments during the occurrence and remediation of urban black blooms using high-throughput 16S rRNA gene amplicon sequencing analysis. First, we found that pivotal consortia in the overlying water increased significantly during the formation of black blooms, including the genera Acidovorax, Brevundimonas, Pusillimonas, and Burkholderiales involved in the degradation of refractory organics, as well as the genera Desulfovibrio, Dechloromonas, and Rhizobium related to the production of black and odorous substances. An RDA analysis revealed that chemical oxygen demand, dissolved oxygen, and oxidation reduction potential were related to the changes in microbial community composition. Furthermore, aeration was found to accelerate the removal of ammonia nitrogen and enhance the function of microbial community by stimulating the growth of order Planktomycetes during the remediation of black blooms, but aeration substantially damaged the microbial diversity and richness. Therefore, the health of the aquatic ecosystem should be comprehensively considered when aeration is applied to restore polluted waterbodies. Notably, we observed a large number of pathogenic bacteria in urban black blooms, which emphasizes the importance of treating domestic sewage so that it is harmless. Together, these findings provide new insights and a basis to prevent and manage urban black blooms.

Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli

Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

L-Cysteine Synthase Enhanced Sulfide Biotransformation in Subtropical Marine Mangrove Sediments as Revealed by Metagenomics Analysis

High sulfides concentrations can be poisonous to environment because of anthropogenic waste production or natural occurrences. How to elucidate the biological transformation mechanisms of sulfide pollutants in the subtropical marine mangrove ecosystem has gained increased interest. Thus, in the present study, the sulfide biotransformation in subtropical mangroves ecosystem was accurately evaluated using metagenomic sequencing and quantitative polymerase chain reaction analysis. Most abundant genes were related to the organic sulfur transformation. Furthermore, an ecological model of sulfide conversion was constructed. Total phosphorus was the dominant environmental factor that drove the sulfur cycle and microbial communities. We compared mangrove and non-mangrove soils and found that the former enhanced metabolism that was related to sulfate reduction when compared to the latter. Total organic carbon, total organic nitrogen, iron, and available sulfur were the key environmental factors that effectively influenced the dissimilatory sulfate reduction. The taxonomic assignment of dissimilatory sulfate-reducing genes revealed that Desulfobacterales and Chromatiales were mainly responsible for sulfate reduction. Chromatiales were most sensitive to environmental factors. The high abundance of cysE and cysK could contribute to the coping of the microbial community with the toxic sulfide produced by Desulfobacterales. Collectively, these findings provided a theoretical basis for the mechanism of the sulfur cycle in subtropical mangrove ecosystems.

Microbiology of barrier component analogues of a deep geological repository

Canada is currently implementing a site selection process to identify a location for a deep geological repository (DGR) for the long-term storage of Canada's used nuclear fuel, wherein used nuclear fuel bundles will be sealed inside copper-coated carbon steel containers, encased in highly compacted bentonite clay buffer boxes, and sealed deep underground in a stable geosphere. Because a DGR must remain functional for a million years, it is important to examine ancient natural systems that serve as analogues for planned DGR components. Specifically, studying the microbiology of natural analogue components of a DGR is important for developing an understanding of the types of microorganisms that may be able to grow and influence the long-term stability of a DGR. This study explored the abundance, viability, and composition of microorganisms in several ancient natural analogues using a combination of cultivation and cultivation-independent approaches. Samples were obtained from the Tsukinuno bentonite deposit (Japan) that formed ∼10 mya, the Opalinus Clay formation (Switzerland) that formed ∼174 mya, and Canadian shield crystalline rock from Northern Ontario that formed ∼2.7 bya. Analysis of 16S rRNA gene amplicons revealed that three of the ten Tsukinuno bentonite samples analyzed were dominated by putative aerobic heterotrophs and fermenting bacteria from the phylum Actinobacteria, whereas five of the Tsukinuno bentonite samples were dominated by sequences associated with putative acidophilic chemolithoautotrophs capable of sulfur reduction. The remaining Tsukinuno bentonite samples, the Northern Ontario rock samples, and the Opalinus Clay samples generated inconsistent replicate 16S rRNA gene profiles and were associated primarily with contaminant sequences, suggesting that the microbial profiles detected were not sample-specific but spurious. Culturable aerobic heterotroph abundances were relatively low for all Tsukinuno bentonite samples, culturable anaerobic heterotrophs were only detected in half of the Tsukinuno samples, and sulfate-reducing bacteria (SRB) were only detected in one Tsukinuno sample by cultivation. Culture-specific 16S rRNA gene profiles from Tsukinuno clay samples demonstrated the presence of phyla Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes among aerobic heterotroph cultures and additional bacteria from the phyla Actinobacteria and Firmicutes from anaerobic heterotroph plate incubations. Only one nucleic acid sequence detected from a culture was also associated with its corresponding clay sample profile, suggesting that nucleic acids from culturable bacteria were relatively rare within the clay samples. Sequencing of DNA extracted from the SRB culture revealed that the taxon present in the culture was affiliated with the genus Desulfosporosinus, which has been found in related bentonite clay analyses. Although the crystalline rock and Opalinus Clay samples were associated with inconsistent, likely spurious 16S rRNA gene profiles, we show evidence for viable and detectable microorganisms within several Tsukinuno natural analogue bentonite samples.

Investigation of mixed species biofilm on corrosion of X65 steel in seawater environment

Microbiologically influenced corrosion (MIC) is a complex process involving the cooperative effect of different bacterial species that coexist in the biofilm. Early studies focused on the MIC of single bacterial communities. However, in natural and industrial fields, biofilms are mostly composed of a variety of species. In this work, the effect of interspecific interaction on corrosion of X65 steel was investigated through the mixed culture of sulfate reducing bacteria (SRB) and iron oxidizing bacteria (IOB). Results demonstrated that the mixed microbial consortia created a cooperative effect to aggravate the local corrosion of X65 steel. Compared with the single species, the presence of IOB increased the growth activity of SRB cells and promoted the role of SRB in steel corrosion. The corrosion form on the surface of X65 steel gradually changed to annular pits induced by anaerobic SRB. The succession of dominant bacteria and the development of mixed species biofilm led to an increase in corrosion rate and local corrosion. The corrosion mechanism of X65 steel by mixed species biofilm at different stages was carefully elucidated.

Optimisation of the operational parameters for a comprehensive bioelectrochemical treatment of acid mine drainage

Bioelectrochemical systems provide a promising tool for the treatment of acid mine drainage (AMD). Biological sulphate reduction powered with electrical energy consumes acidity and produces sulphide, which can precipitate metals. However, the produced sulphide and the changes in pH resulting from the biological processes affect the efficiency and the environmental impacts of this treatment significantly. In this work, the effects of pH and sulphur speciation on the sulphate reduction rate (SRR) and comprehensive AMD treatment were evaluated in two-chamber microbial electrolysis cells at a cathode potential of -0.8 V vs. NHE. The increase of initial sulphate concentration from below 1000 mg to above 1500 mg S-SO₄^2-/L increased SRR from 121 ± 25 to 177 ± 19 mg S-SO₄^2-/L/d. SRR further increased to 347 mg S-SO₄^2-/L/d when the operation mode was changed from batch to periodical addition of sulphate and acidity (363 mg S-SO₄^2-/L/d and 22.6 mmol H⁺/L/d, respectively). The average SRR remained above 150 mg S-SO₄^2-/L/d even at pH above 8.5 and with the total dissolved sulphide concentration increasing above 1300 mg S-TDSu/L. Operation at pH above 8 enabled the recovery of over 90% of the sulphur as dissolved sulphide and thus assisted in minimising the formation and release of toxic H₂S.

Oxygen consumption of individual cable bacteria

The electric wires of cable bacteria possibly support a unique respiration mode with a few oxygen-reducing cells flaring off electrons, while oxidation of the electron donor and the associated energy conservation and growth is allocated to other cells not exposed to oxygen. Cable bacteria are centimeter-long, multicellular, filamentous Desulfobulbaceae that transport electrons across oxic-anoxic interfaces in aquatic sediments. From observed distortions of the oxic-anoxic interface, we derived oxygen consumption rates of individual cable bacteria and found biomass-specific rates of unheard magnitude in biology. Tightly controlled behavior, possibly involving intercellular electrical signaling, was found to generally keep <10% of individual filaments exposed to oxygen. The results strengthen the hypothesis that cable bacteria indeed have evolved an exceptional way to take the full energetic advantages of aerobic respiration and let >90% of the cells metabolize in the convenient absence of oxidative stress.

Electrochemical Characterization of a Complex FeFe Hydrogenase, the Electron-Bifurcating Hnd From Desulfovibrio fructosovorans

Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H₂ to both the exergonic reduction of NAD⁺ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O₂-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H₂, diffusion and reaction at the active site of CO and O₂) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.

Hydrogen sulfide toxicity in the gut environment: Meta-analysis of sulfate-reducing and lactic acid bacteria in inflammatory processes

BACKGROUND

Hydrogen sulfide is the final product of sulfate-reducing bacteria metabolism. Its high concentration in the gut can affect adversely bowel environment and intestinal microbiota by toxicity and pH lowering.

AIM OF REVIEW

The aim of the review was to give observations related to the properties of bacterial communities inhabiting the gut, with the emphasis on sulfate-reducing bacteria and lactic acid bacteria.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The conduction of meta-analysis was another goal, since it gave statistical observation of the relevant studies. The review literature consisted of more than 160 studies, published from 1945 to 2019. Meta-analysis included 16 studies and they were chosen from the Web of Science database. The systematic review gave important information about the development of gut inflammation, with emphasis on sulfate-reducing and lactic acid bacteria. Oppositely from sulfate-reducing bacteria, probiotic properties of lactic acid bacteria are effective inhibitors against inflammatory bowel disease development, including ulcerative colitis. These facts were confirmed by the conducted meta-analysis. The results and observations gained from the systematic review represent the emphasized importance of gut microbiota for bowel inflammation. On the other side, it should be stated that more studies in the future will provide even better confirmations.

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments

Microbial sulfate reduction and sulfur oxidation are vital processes to enhance organic matter degradation in sediments. However, the diversity and composition of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their environmental driving factors are still poorly understood in aquaculture ponds, which received mounting of organic matter. In this study, bacterial communities, SRB and SOB from sediments of aquaculture ponds with different sizes of grass carp (Ctenopharyngodon idellus) were analysed using high-throughput sequencing and quantitative real-time PCR (qPCR). The results indicated that microbial communities in aquaculture pond sediments of large juvenile fish showed the highest richness and abundance of SRB and SOB, potentially further enhancing microbial sulfur cycling. Specifically, SRB were dominated by Desulfobulbus and Desulfovibrio, whereas SOB were dominated by Dechloromonas and Leptothrix. Although large juvenile fish ponds had relatively lower concentrations of sulfur compounds (i.e. total sulfur, acid-volatile sulfide and elemental sulfur) than those of larval fish ponds, more abundant SRB and SOB were found in the large juvenile fish ponds. Further redundancy analysis (RDA) and linear regression indicated that sulfur compounds and sediment suspension are the major environmental factors shaping the abundance and community structure of SRB and SOB in aquaculture pond sediments. Findings of this study expand our current understanding of microbial driving sulfur cycling in aquaculture ecosystems and also provide novel insights for ecological and green aquaculture managements.

Organohalide-respiring Desulfoluna species isolated from marine environments

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1^T and D. butyratoxydans MSL71^T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.

Distribution of reactive oxygen species defense mechanisms across domain bacteria

Bacteria are the most diverse and numerous organisms on the planet, inhabiting environments from the deep subsurface to particles in clouds. Across this range of conditions, bacteria have evolved a diverse suite of enzymes to mitigate cellular damage from reactive oxygen species (ROS). Here, we review the diversity and distribution of ROS enzymatic defense mechanisms across the domain Bacteria, using both peer-reviewed literature and publicly available genome databases. We describe the specific strategies used by well-characterized organisms in order to highlight differences in oxidative stress responses between aerobic, facultatively anaerobic, and anaerobic lifestyles. We present evidence from genome minimization experiments to suggest that ROS defenses are obligately required for life. This review clarifies the variability in ROS defenses across Bacteria, including the novel diversity found in currently uncharacterized Candidate Phyla.

How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth

One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O₂), 2) O₂-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O₂ in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O₂ in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O₂ tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O₂-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O₂/ROS tolerant anaerobes, where the role of the O₂/ROS detoxification system is separated from O₂-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O₂/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O₂/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O₂/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.

Effects of backwashing strategy and dissolved oxygen on arsenic removal to meet drinking water standards in a sulfidogenic attached growth reactor

Efficiency and feasibility of two backwashing methods (water-nitrogen and water-air assisted) on arsenic and its co-pollutants removal were assessed through running a sulfidogenic attached growth reactor (AGR) treating arsenic spiked simulated groundwater for about 600 days. Replacing water with nitrogen assisted backwashing (WNAB) by water with air assisted backwashing (WAAB) introduced dissolved oxygen (DO) as an additional electron acceptor, which required an increased empty bed contact time (EBCT) to retain the entire terminal electron accepting zones (DO, nitrate, arsenate and sulfate) within the reactor. Removal of arsenic to below 10 μg/L required a longer EBCT at higher influent DO in backwash water. Notably, MiSeq sequencing analysis confirmed the presence of diverse bacterial community on biofilm which can utilize multiple terminal electron acceptors present in the bioreactor.

Hydrogenases and H2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus

Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H₂ metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H₂ metabolism.

Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection

Human immunodeficiency virus (HIV)-1 infection causes severe gut and systemic immune damage, but its effects on the gut microbiome remain unclear. Previous shotgun metagenomic studies in HIV-negative subjects linked low-microbial gene counts (LGC) to gut dysbiosis in diseases featuring intestinal inflammation. Using a similar approach in 156 subjects with different HIV-1 phenotypes, we found a strong, independent, dose-effect association between nadir CD4+ T-cell counts and LGC. As in other diseases involving intestinal inflammation, the gut microbiomes of subjects with LGC were enriched in gram-negative Bacteroides, acetogenic bacteria and Proteobacteria, which are able to metabolize reactive oxygen and nitrogen species; and were depleted in oxygen-sensitive methanogenic archaea and sulfate-reducing bacteria. Interestingly, subjects with LGC also showed increased butyrate levels in direct fecal measurements, consistent with enrichment in Roseburia intestinalis despite reductions in other butyrate producers. The microbiomes of subjects with LGC were also enriched in bacterial virulence factors, as well as in genes associated with beta-lactam, lincosamide, tetracycline, and macrolide resistance. Thus, low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation.

Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O2 -driven experimental evolution

Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O₂ -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD⁺ /NADH, leading to an optimized O₂ reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.

High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure

Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 °C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O₂ L^-1). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O₂ L^-1) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox.

A novel aerobic sulfate reduction process in landfill mineralized refuse

It is thought that mineralized refuse could be excavated from almost-full landfill sites to provide space for the increasing burden of municipal solid waste. When excavating, however, the H₂S emissions from the mineralized waste need to be considered carefully. In an attempt to understand how H₂S emissions might change during this excavation process, we carried out a series of tests, including exposing anaerobic mineralized refuse to oxygen, isolating and determining possible functional bacteria, and characterizing the electron donors and/or acceptors. The results showed that H₂S would be released when landfill mineralized refuse was exposed to oxygen (O₂), and could reach concentrations of 6 mg m^-3, which was 3 times the concentrations of H₂S released from anaerobic mineralized refuse. Sulfur-metabolized microorganisms accounted for only 0.5% of the microbial functional bacteria (MFB) derived from the mineralized refuse when exposed to O₂ for 60 days, and SRB were not present. The MFB maintained H₂S production by aerobic sulfate reduction using SO₄^2- and S₂O₃^2- as electron acceptors, and sulfate-reducing rates of 16% and 55%, respectively, were achieved. Lactate and S₂O₃^2- were the preferred electron donor and acceptor, respectively. By enhancing the carbon source and electron transfer, MFB may undergo strong aerobic sulfate reduction even at low abundances of sulfur-metabolized microorganisms.

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.

Anaerobic digestion of sulphate-rich post-tanning wastewater at different COD/sulphate and F/M ratios

Anaerobic digestion of post-tanning wastewater was performed in batch anaerobic digester to evaluate the effect of COD/sulphate ratio [0.62, 0.69, and 1.20 (w/w) %] and F/M ratio [0.2, 0.3, 0.5, 0.7, 0.9, 1.1, 1.3, and 1.5 (w/w) %)] on the removal efficiency of COD. The F/M ratio of 0.3 was found to be the optimum ratio for the removal of COD by 53, 57, and 65%, respectively at COD/sulphate ratio of 0.62, 0.69, and 1.20. The maximum sulphate removal was observed at F/M ratio of 0.2 and the removal efficiency was 48, 50, and 58% at COD/sulphate ratio of 0.62, 0.69, and 1.20, respectively. The removal efficiency of COD and sulphate was increased with increase in COD/sulphate ratio from 0.62 to 1.20 and decreased with increase in F/M ratio from 0.2 to 1.5 in anaerobic digestion of post-tanning wastewater. The maximum concentration of sulphide formation was 784 mg/L at COD/sulphate ratio of 0.62 in anaerobic digestion process and the process was inhibited at this sulphide concentration. The microbial activity in the sludge was evaluated through live and dead cell assay using fluorescent microscopy. The maximum amount of dead microbes was observed in the anaerobic digester, which was operated at COD/sulphate ratio of 0.62 than other studied ratio.

Simultaneous use of caustic and oxygen for efficient sulfide control in sewers

Periodic caustic shock-loading is a commonly used method for sulfide control in sewers. Caustic shock-loading relies on the elevation of the sewage pH to ≥10.5 for several hours, thereby removing sewer pipe biofilms as well as deactivating SRB activity in the remaining biofilm. Although a widely used method, SRB activity is often not completely inhibited, and as such sulfide is still being generated. Here, we propose and experimentally demonstrate an innovative approach which combines caustic with oxygen, another commonly used method, as a dosing strategy for overcoming the drawbacks of caustic shock-loading. Six laboratory-scale rising main reactors were subjected to three dosing schemes over a period of three months, namely (i) simultaneous caustic and oxygen addition, (ii) caustic addition and (iii) no chemical addition. Our results showed that the combination of caustic and oxygen achieved efficient sulfide control, leading to a prolonged biofilm recovery period in between caustic shocks. In addition, methane emissions were reduced to a negligible level compared to caustic treatment only. To translate the findings to real-life application, the key parameters obtained during the long-term lab-scale experiments were subjected to extensive simulation studies using the SeweX model under a wide range of conditions commonly found in sewers. Overall, this study highlights the potential of periodic shock-loading and intermittent oxygen injection as combined dosing strategy for efficient sulfide control in sewers.

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.

Hydrogen Dynamics in Cyanobacteria Dominated Microbial Mats Measured by Novel Combined H2/H2S and H2/O2 Microsensors

Hydrogen may accumulate to micromolar concentrations in cyanobacterial mat communities from various environments, but the governing factors for this accumulation are poorly described. We used newly developed sensors allowing for simultaneous measurement of H2S and H2 or O2 and H2 within the same point to elucidate the interactions between oxygen, sulfate reducing bacteria, and H2 producing microbes. After onset of darkness and subsequent change from oxic to anoxic conditions within the uppermost ∼1 mm of the mat, H2 accumulated to concentrations of up to 40 μmol L-1 in the formerly oxic layer, but with high variability among sites and sampling dates. The immediate onset of H2 production after darkening points to fermentation as the main H2 producing process in this mat. The measured profiles indicate that a gradual disappearance of the H2 peak was mainly due to the activity of sulfate reducing bacteria that invaded the formerly oxic surface layer from below, or persisted in an inactive state in the oxic mat during illumination. The absence of significant H2 consumption in the formerly oxic mat during the first ∼30 min after onset of anoxic conditions indicated absence of active sulfate reducers in this layer during the oxic period. Addition of the methanogenesis inhibitor BES led to increase in H2, indicating that methanogens contributed to the consumption of H2. Both H2 formation and consumption seemed unaffected by the presence/absence of H2S.

Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes

Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.

Oxygen Reduction Reaction Affected by Sulfate-Reducing Bacteria: Different Roles of Bacterial Cells and Metabolites

Sulfate-reducing bacteria (SRB) were found to be capable of tolerating a certain amount of oxygen (O₂), but how they affect oxygen reduction reaction (ORR) has not been clear. The present work investigated the impact of SRB on ORR in 3.5 wt% sodium chloride solution with the cyclic voltammetry method. The addition of SRB culture solution hampered both the reduction of O₂ to superoxide (O₂^·-) and hydrogen peroxide (H₂O₂) to water (H₂O), and the influence of SRB metabolites was much larger than that of bacterial cells. Sulfide and extracellular polymeric substances (EPS), typical inorganic and organic metabolic products, had great impact on ORR. Sulfide played an important role in the decrease of cathodic current for H₂O₂ reduction due to its hydrolysis and chemical reaction activity with H₂O₂. EPS were sticky, easy to adsorb on the electrode surface and abundant in functional groups, which hindered the transformation of O₂ into O₂^·- and favored the reduction of H₂O₂ to H₂O.

Effects of electron acceptors on sulphate reduction activity in activated sludge processes

The concentration of sulphate present in wastewater can vary from 10 to 500 mg SO₄²⁻/L. During anaerobic conditions, sulphate is reduced to sulphide by sulphate-reducing bacteria (SRB). Sulphide generation is undesired in wastewater treatment plants (WWTPs). Previous research indicated that SRB are inhibited by the presence of electron acceptors (such as O₂, NO₃ and NO₂). However, the contact times and concentrations used in those studies are by far higher than occur in WWTPs. Since sulphide can influence the biological nitrogen and phosphorus removal processes, this research aimed to understand how the different electron acceptors commonly present in biological nutrient removal (BNR) systems can affect the proliferation of SRB. For this purpose, a culture of SRB was enriched in a sequencing batch reactor (approx. 88% of the total bacteria population). Once enriched, the SRB were exposed for 2 h to typical concentrations of electron acceptors like those observed in BNR systems. Their activity was assessed using three different types of electron donors (acetate, propionate and lactate). Oxygen was the most inhibiting electron acceptor regardless the carbon source used. After exposure to oxygen and when feeding acetate, an inactivation time in the sulphate reduction activity was observed for 1.75 h. Once the sulphate reduction activity resumed, only 60% of the original activity was recovered. It is suggested that the proliferation of SRB is most likely to occur in BNR plants with an anaerobic fraction higher than 15% and operating at sludge retention times higher than 20 days (at a temperature of 20 °C). These results can be used to implement strategies to control the growth of sulphate reducers that might compete for organic carbon with phosphate-accumulating organisms.

Growth of magnetotactic sulfate-reducing bacteria in oxygen concentration gradient medium

Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O₂ . For example, SRB remain viable in many aerobic environments while some even reduce O₂ to H₂ O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals. The ability of D. magneticus to grow aerobically in several different media under air where an O₂ concentration gradient formed, or under O₂ -free N₂ gas was tested. Under air, cells grew as a microaerophilic band of cells at the oxic-anoxic interface in media lacking sulfate. These results show that D. magneticus is capable of aerobic growth with O₂ as a terminal electron acceptor. This is the first report of consistent, reproducible aerobic growth of SRB. This finding is critical in determining important ecological roles SRB play in the environment. Interestingly, the crystal structure of the magnetite crystals of D. magneticus grown under microaerobic conditions showed significant differences compared with those produced anaerobically providing more evidence that environmental parameters influence magnetosome formation.