Use of “Specific” Inhibitors in Biogeochemistry and Microbial Ecology

Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge

In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.

Targeting the human gut microbiome with small-molecule inhibitors

The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.

Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis

Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the 'methane paradox'), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.

Suppressing Methane Production to Boost High-Purity Hydrogen Production in Microbial Electrolysis Cells

Hydrogen gas (H₂) is an attractive fuel carrier due to its high specific enthalpy; moreover, it is a clean source of energy because in the combustion reaction with oxygen (O₂) it produces water as the only byproduct. The microbial electrolysis cell (MEC) is a promising technology for producing H₂ from simple or complex organics present in wastewater and solid wastes. Methanogens and non-archaeal methane (CH₄)-producing microorganisms (NAMPMs) often grow in the MECs and lead to rapid conversion of produced H₂ to CH₄. Moreover, non-archaeal methane production (NAMP) catalyzed by nitrogenase of photosynthetic bacteria was always overlooked. Thus, suppression of CH₄ production is required to enhance H₂ yield and production rate. This review comprehensively addresses the principles and current state-of-the-art technologies for suppressing methanogenesis and NAMP in MECs. Noteworthy, specific strategies aimed at the inhibition of methanogenic enzymes and nitrogenase could be a more direct approach than physical and chemical strategies for repressing the growth of methanogenic archaea. In-depth studies on the multiomics of CH₄ metabolism can possibly provide insights into sustainable and efficient approaches for suppressing metabolic pathways of methanogenesis and NAMP. The main objective of this review is to highlight key concepts, directions, and challenges related to boosting H₂ generation by suppressing CH₄ production in MECs. Finally, perspectives are briefly outlined to guide and advance the future direction of MECs for production of high-purity H₂ based on genetic and metabolic engineering and on the interspecific interactions.

Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields

Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.

Effects and mechanisms of organic matter regulating the methylmercury dynamics in mangrove sediments

Mangrove ecosystems serve as an important carbon sink but also could be a hotspot that produces neurotoxic methylmercury (MeHg). Although many studies have focused on mercury (Hg) contamination in this carbon-rich ecosystem, our understanding of the effects and mechanisms of the organic matter (OM) regulation of MeHg production in mangrove sediments is still limited. Here, we examined the effects of Hg contamination and OM enrichment on MeHg production in anoxic mangrove sediments and identified the major microbial guilds attending this process. The mangrove sediments possessed a high potential for producing MeHg, but this was counterbalanced by its rapid degradation. Sulfate-reducing bacteria (SRB) such as Desulfobacterales, Desulfovibrionales, and Syntrophobacterales were the major methylators. OM diagenesis significantly changed the biogeochemical conditions, accelerating MeHg degradation in the sediments. The enhanced MeHg degradation could be attributed to the abundant sulfide produced during OM decomposition, which could potentially inhibit the Hg methylation by immobilization of inorganic Hg, abiotically degrade MeHg, and favor the non-mer-mediated degradation of MeHg by SRB. Our study provides both geochemical and microbial clues that can partly explain the low MeHg levels widely observed in mangrove sediments.

Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.

Microbial mercury transformations: Molecules, functions and organisms

Mercury (Hg) methylation, methylmercury (MeHg) demethylation, and inorganic redox transformations of Hg are microbe-mediating processes that determine the fate and cycling of Hg and MeHg in many environments, and by doing so influence the health of humans and wild life. The discovery of the Hg methylation genes, hgcAB, in the last decade together with advances in high throughput and genome sequencing methods, have resulted in an expanded appreciation of the diversity of Hg methylating microbes. This review aims to describe experimentally confirmed and recently discovered hgcAB gene-carrying Hg methylating microbes; phylogenetic and taxonomic analyses are presented. In addition, the current knowledge on transformation mechanisms, the organisms that carry them out, and the impact of environmental parameters on Hg methylation, MeHg demethylation, and inorganic Hg reduction and oxidation is summarized. This knowledge provides a foundation for future action toward mitigating the impact of environmental Hg pollution.

Methanogenesis pathways of methanogens and their responses to substrates and temperature in sediments from the South Yellow Sea

Although coastal sediments are major contributors to the production of atmospheric methane, the effects of environmental conditions on methanogenesis and the community of methanogenic archaea are not well understood. Here, we investigated the methanogenesis pathways in nearshore and offshore sediments from the South Yellow Sea (SYS). Moreover, the effects of the supply of methanogenic substrates (H₂/CO₂, acetate, trimethylamine (TMA), and methanol) and temperature on methanogenesis and the community of methanogenic archaea were further determined. Methylotrophic, hydrogenotrophic and acetotrophic methanogenesis were found to be responsible for biogenic methane production in nearshore sediments. In the offshore sediments, methylotrophic methanogenesis was the predominant methanogenic pathway. The changes in methanogenic community structure under different substrate amendments were characterized. Lower diversities were detected in substrate-amended samples with methanogenic activity. Hydrogenotrophic Methanogenium, multitrophic Methanosarcina, methylotrophic Methanococcoide, Methanococcoide or methylotrophic Methanolobus were dominant in H₂/CO₂-, acetate-, TMA- and methanol-amended sediment slurries, respectively. PCoA showed that the methanogen community in H₂/CO₂ and acetate amendments exhibited greater differences than those in other treatments. Lower temperature (10 °C) limits hydrogenotrophic and acetoclastic methanogenesis, but methylotrophic methanogenesis is much less affected. The response of methanogen diversity to the incubation temperature varied among the different substrate-amended slurries. The multitrophic methanogen Methanosarcina became increasingly abundant in H₂/CO_2- and acetate-amended sediment slurries when the temperature increased from 10 to 30 °C.

Putative Nickel-Dependent Anaerobic Carbon Monoxide Uptake Occurs Commonly in Soils and Sediments at Ambient Temperature and Might Contribute to Atmospheric and Sub-Atmospheric Carbon Monoxide Uptake During Anoxic Conditions

Carbon monoxide (CO) occurs naturally in the atmosphere where it plays a critical role in tropospheric chemistry. Atmospheric CO uptake by soils has been well documented as an important CO sink and has been attributed to a group of aerobic bacteria that possess a molybdenum-dependent CO dehydrogenase (Mo-CODH). CO can also be oxidized by obligate Ni-dependent anaerobes (Ni-COX) that possess nickel-dependent CODHs (Ni-CODH) but relatively little is known about their ecology or their potential to contribute to CO dynamics within soils and sediments or to soil-atmosphere CO exchanges. Results from a series of assays undertaken with diverse soils and sediments and CO concentrations of 10 ppm and 25% with incubation temperatures of 10, 25, and 60°C revealed anaerobic uptake rates with 10 ppm CO that were comparable to those measured under oxic conditions; further, anaerobic CO uptake occurred without a lag and at atmospheric and sub-atmospheric CO concentrations. Assays with 25% CO revealed previously undocumented activity at 10°C and showed extensive activity at 25°C. Results from prior studies with isolates and soils suggest that anaerobic uptake at both 10 ppm and 25% CO concentrations might be attributed to Ni-COX. Collectively the results considerably expand the ecological range for Ni-COX and indicate that they could play previously unsuspected roles in soil CO dynamics.

An outlook on suicide enzyme inhibition and drug design

There have been recent renewed interests in the importance of suicide enzyme inhibition. The principal objective of this review is to investigate all types of suicide inhibitions for natural enzymes, artificial biocatalysts as well as therapeutic potential of enzyme suicide inhibition. It is discussed the suicide inhibition beneficial in drug design and treatments and non-beneficial achievements for some industrial enzymes such as HRP peroxidase enzyme. The design of biomimetic artificial enzymes explained to prevent inhibition by protecting the active site via environmental conditions. Suicide enzyme inhibition development can be the key mechanism against sever diseases such as SARS. In this report, suicide enzyme inactivation classes are classified based on target enzyme groups via their substrates.

The role of seaweed as a potential dietary supplementation for enteric methane mitigation in ruminants: Challenges and opportunities

Seaweeds are macroalgae, which can be of many different morphologies, sizes, colors, and chemical profiles. They include brown, red, and green seaweeds. Brown seaweeds have been more investigated and exploited in comparison to other seaweed types for their use in animal feeding studies due to their large sizes and ease of harvesting. Recent in vitro and in vivo studies suggest that plant secondary compound-containing seaweeds (e.g., halogenated compounds, phlorotannins, etc.) have the potential to mitigate enteric methane (CH4) emissions from ruminants when added to the diets of beef and dairy cattle. Red seaweeds including Asparagopsis spp. are rich in crude protein and halogenated compounds compared to brown and green seaweeds. When halogenated-containing red seaweeds are used as the active ingredient in ruminant diets, bromoform concentration can be used as an indicator of anti-methanogenic properties. Phlorotannin-containing brown seaweed has also the potential to decrease CH4 production. However, numerous studies examined the possible anti-methanogenic effects of marine seaweeds with inconsistent results. This work reviews existing data associated with seaweeds and in vitro and in vivo rumen fermentation, animal performance, and enteric CH4 emissions in ruminants. Increased understanding of the seaweed supplementation related to rumen fermentation and its effect on animal performance and CH4 emissions in ruminants may lead to novel strategies aimed at reducing greenhouse gas emissions while improving animal productivity.

Nutrient Inputs Stimulate Mercury Methylation by Syntrophs in a Subarctic Peatland

Climate change dramatically impacts Arctic and subarctic regions, inducing shifts in wetland nutrient regimes as a consequence of thawing permafrost. Altered hydrological regimes may drive changes in the dynamics of microbial mercury (Hg) methylation and bioavailability. Important knowledge gaps remain on the contribution of specific microbial groups to methylmercury (MeHg) production in wetlands of various trophic status. Here, we measured aqueous chemistry, potential methylation rates (k_meth), volatile fatty acid (VFA) dynamics in peat-soil incubations, and genetic potential for Hg methylation across a groundwater-driven nutrient gradient in an interior Alaskan fen. We tested the hypotheses that (1) nutrient inputs will result in increased methylation potentials, and (2) syntrophic interactions contribute to methylation in subarctic wetlands. We observed that concentrations of nutrients, total Hg, and MeHg, abundance of hgcA genes, and rates of methylation in peat incubations (k_meth) were highest near the groundwater input and declined downgradient. hgcA sequences near the input were closely related to those from sulfate-reducing bacteria (SRB), methanogens, and syntrophs. Hg methylation in peat incubations collected near the input source (FPF2) were impacted by the addition of sulfate and some metabolic inhibitors while those down-gradient (FPF5) were not. Sulfate amendment to FPF2 incubations had higher k_meth relative to unamended controls despite no effect on k_meth from addition of the sulfate reduction inhibitor molybdate. The addition of the methanogenic inhibitor BES (25 mM) led to the accumulation of VFAs, but unlike molybdate, it did not affect Hg methylation rates. Rather, the concurrent additions of BES and molybdate significantly decreased k_meth, suggesting a role for interactions between SRB and methanogens in Hg methylation. The reduction in k_meth with combined addition of BES and molybdate, and accumulation of VFA in peat incubations containing BES, and a high abundance of syntroph-related hgcA sequences in peat metagenomes provide evidence for MeHg production by microorganisms growing in syntrophy. Collectively the results suggest that wetland nutrient regimes influence the activity of Hg methylating microorganisms and, consequently, Hg methylation rates. Our results provide key information about microbial Hg methylation and methylating communities under nutrient conditions that are expected to become more common as permafrost soils thaw.

Deltaproteobacterium Strain KaireiS1, a Mesophilic, Hydrogen-Oxidizing and Sulfate-Reducing Bacterium From an Inactive Deep-Sea Hydrothermal Chimney

A novel deltaproteobacterial, mesophilic, hydrogen-oxidizing, and sulfate-reducing bacterium (strain KaireiS1) was highly enriched from an inactive chimney located in the active zone of the Kairei hydrothermal vent field (Central Indian Ridge) in the Indian Ocean. Based on 16S rRNA gene analyses, strain KaireiS1 is the currently only cultured representative of a cluster of uncultured Deltaproteobacteria, positioned within the Desulfobulbaceae family, between the Desulfobulbus genus and the “Cable Bacteria.” A facultative autotrophic lifestyle of KaireiS1 is indicated by its growth in the absence of organic compounds, measurements of CO₂-fixation rates, and activity measurements of carbon monoxide dehydrogenase, the key enzyme of the reductive Acetyl-CoA pathway. Apart from hydrogen, strain KaireiS1 can also use propionate, lactate, and pentadecane as electron donors. However, the highest cell numbers were reached when grown autotrophically with molecular hydrogen. Hydrogen uptake activity was found in membrane and soluble fractions of cell-free extracts and reached up to 2,981±129 nmol H₂*min⁻¹*mg⁻¹ of partially purified protein. Commonly, autotrophic sulfate-reducing bacteria from the Deltaproteobacteria class, thriving in hydrothermal vent habitats are described as thermophiles. Given its physiological characteristics and specific isolation source, strain KaireiS1 demonstrates a previously unnoticed potential for microbial sulfate reduction by autotrophs taking place at moderate temperatures in hydrothermal vent fields.

"Biomethanation of syngas by enriched mixed anaerobic consortium in pressurized agitated column"

In a circular economy approach, heterogeneous wastes can be upgraded to energy in the form of syngas via pyrogasification, and then to methane via biomethanation. Working at high pressure is a promising approach to intensify the process and to reduce gas-liquid transfer limitations. However, raising the pressure could lead to reaching the CO inhibition threshold of the microorganisms involved in syngas-biomethanation. To investigate the impact on pressure on the process, a 10L continuous stirred tank reactor working at 4 bars and 55 °C was implemented. Syngas (40% CO, 40% H₂, 20% CO₂) biomethanation was performed successfully and methane productivity as high as 6.8 mmol_CH4/L_reactor/h with almost full conversion of CO (97%) and H₂ (98%) was achieved. CO inhibition was investigated and carboxydotrophs appeared less resistant to high CO exposition than methanogens.

Effects of antimony on anaerobic methane oxidization and microbial community in an antimony-contaminated paddy soil: A microcosm study

Anaerobic methane oxidation (AOM) plays an important role in sinking global methane and thereby in constraining climate change. Anthropogenic activities in antimony (Sb) mines have resulted in Sb contamination in rice fields, which are among the dominant methane sources. However, the knowledge of effects of Sb on AOM in paddy soils and the microbiota involved in this process remains limited. Herein, Sb was amended into the paddy soil to investigate the effects of Sb contamination on AOM and the microbial communities such as methanotrophs. Significant inhibition of AOM was observed in the treatment with Sb addition in comparison with the treatment without Sb addition. The significant increases in the abundance of the mcrA genes, responsible for methane production and oxidation, were observed in the treatment with/without Sb addition. In contrast, no significant increases in the copy number of the mcrA gene were detected in the treatment with the addition of the methanogenic and methanotrophic inhibitor 2-bromoethanesulfonate (BES). These results suggested that Sb contamination might inhibit only AOM but not methane production. In addition, amplicon high-throughput sequencing showed that the Sb addition impaired the diversity of microbial communities and impacted the biotic interactions in the soil. However, the abundance of bacterial methane-oxidizing phylum NC10 and its biotic connections with other microbes were enhanced by the addition of Sb. Pseudogulbenkiania and Methanosarcina dominated the bacterial and archaeal communities in the treatment without Sb addition, while the bacteria Ramlibacter and Geothrix and the archaea Methanomethylovorans were the most abundant genera in the treatment with Sb addition. These analyses of microbial communities indicated that Sb addition had significant effects on both the compositions of bacterial and archaeal communities. This study expands our knowledge of the effects of Sb contamination on AOM and the microbial (especially methanotrophs) diversity and composition in paddy soils.

Got acetylene: a personal research retrospective

In research, sometimes sheer happenstance and serendipity make for an unexpected discovery. Once revealed and if interesting enough, such a finding and its follow-up investigations can lead to advances by others that leave its originators 'scooped' and mulling about what next to do with their unpublished data, specifically what journals could it still be published in and be perceived as original. This is what occurred with us nearly 40 years ago with regard to our follow-up observations of acetylene fermentation and led us to concoct a 'cock-and-bull' story. We hypothesized about a plausible role for acetylene metabolism in the primordial biogeochemistry of Earth and the possibility of acetylene serving as a key life-sustaining substrate for alien microbes dwelling in the orbs of the outer solar system. With the passage of time, advances were made in whole-genome sequencing coupled with major in silico progress in bioinformatics. In parallel came the results of explorations of the outer solar system (i.e. the Cassini mission to Saturn and its moons). It now appears that these somewhat harebrained ideas of ours, arisen at first out of a sense of desperation, actually ring true in fact, and particularly well in song: 'Tell a tale of cock and bull, Of convincing detail full Tale tremendous, Heav'n defend us! What a tale of cock and bull!' From 'The Yeoman of the Guard' by Gilbert & Sullivan.

Composition and Activity of N2-Fixing Microorganisms in Mangrove Forest Soils

Mangrove forests are considered to be a highly productive ecosystem, but they are also generally nitrogen (N)-limited. Thus, soil N2 fixation can be important for the stability of both mangrove ecosystem functions and upland N supply. This study evaluates the N2 fixation activity and composition of relevant microorganisms in two coastal mangrove forests—the Guandu mangrove in an upstream estuary and the Bali mangrove in a downstream estuary—using the acetylene reduction method, real-time polymerase chain reaction, and next-generation sequencing. The results demonstrated that ambient nitrogenase activity was higher in downstream mangrove forests (13.2–15.6 nmol h−1 g−1 soil) than in upstream mangrove forests (0.2–1.4 nmol h−1 g−1 soil). However, both the maximum potential nitrogenase activity and nitrogenase gene (nifH gene) copy number were found to be higher in the upstream than in the downstream mangrove forests, implying that the nitrogenase activity and diazotrophic abundance may not necessarily be positively correlated. In addition, amended MoO4 (which inhibits the activity of sulfate-reducing bacteria in N2-fixation) yielded low nitrogenase activity, and sulfate-reducing bacteria made up 20–50% of the relative diazotrophic abundance in the mangrove forests, indicating that these bacteria might be the major active diazotrophs in this environment.

Macroalgal detrital systems: an overlooked ecological niche for heterotrophic nitrogen fixation

Diazotrophic macroalgal associations (DMAs) can contribute fixed nitrogen (N) to the host macroalgae. Biological nitrogen fixation (BNF) rates investigated using acetylene reduction assays with living macroalgae surrounding Santa Catalina Island were low (maximum: 36 nmol N × g^-1 (dw) × h^-1 ) and probably insufficient towards helping meet macroalgal N demand. However, DMAs were observed during periods of low nitrate availability in Southern California coastal waters, highlighting the potential importance of diazotrophs during N depleted conditions. Eleven long-term (16-32 days) litter bag decomposition experiments with various macroalgae, especially those with high (> 10) C:N ratios, resulted in much higher BNF rates (maximum: 693 nmol N × g^-1 (dw) × h^-1 ) than observed with living macroalgae. BNF rates were lower at the beginning of macroalgal decomposition but rapidly increased during the second phase before declining towards the end of decomposition. Labile carbon availability is likely influencing BNF rates throughout macroalgal degradation and limits BNF in the final decomposition stage. Comparable dark and light BNF rates with most macroalgae surveyed suggest macroalgal detrital systems are an overlooked, potentially global, niche for heterotrophic N₂ fixation. Lastly, suppressed BNF rates with sodium molybdate additions highlight the prevalence of sulfate reducing diazotrophs.

Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs

Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for > 98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for > 90% of overall N2 fixation, whereas corals contributed to more than half of reef denitrification. Total N2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.

Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum

High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity.

Widespread Use of the Nitrification Inhibitor Nitrapyrin: Assessing Benefits and Costs to Agriculture, Ecosystems, and Environmental Health

Agricultural production and associated applications of nitrogen (N) fertilizers have increased dramatically in the last century, and current projections to 2050 show that demands will continue to increase as the human population grows. Applied in both organic and inorganic fertilizer forms, N is an essential nutrient in crop productivity. Increased fertilizer applications, however, create the potential for more N loss before plant uptake. One strategy for minimizing N loss is the use of enhanced efficiency fertilizers, fortified with a nitrification inhibitor, such as nitrapyrin. In soils and water, nitrapyrin inhibits the activity of ammonia monooxygenase, a microbial enzyme that catalyzes the first step of nitrification from ammonium to nitrite. Potential benefits of using nitrification inhibitors range from reduced nitrate leaching and nitrous oxide emissions to increased crop yield. The extent of these benefits, however, depends on environmental conditions and management practices. Thus, such benefits are not always realized. Additionally, nitrapyrin has been shown to transport off-field, and it is unknown what effects environmental nitrapyrin could have on nontarget organisms and the ecological nitrogen cycle. Here, we review the agronomic and environmental benefits and costs of nitrapyrin use and present a series of research questions and considerations to be addressed with future nitrification inhibitor research.

Novel Mode of Molybdate Inhibition of Desulfovibrio vulgaris Hildenborough

Sulfate-reducing microorganisms (SRM) are found in multiple environments and play a major role in global carbon and sulfur cycling. Because of their growth capabilities and association with metal corrosion, controlling the growth of SRM has become of increased interest. One such mechanism of control has been the use of molybdate (MoO4 2-), which is thought to be a specific inhibitor of SRM. The way in which molybdate inhibits the growth of SRM has been enigmatic. It has been reported that molybdate is involved in a futile energy cycle with the sulfate-activating enzyme, sulfate adenylyl transferase (Sat), which results in loss of cellular ATP. However, we show here that a deletion of this enzyme in the model SRM, Desulfovibrio vulgaris Hildenborough, remained sensitive to molybdate. We performed several subcultures of the ∆sat strain in the presence of increasing concentrations of molybdate and obtained a culture with increased resistance to the inhibitor (up to 3 mM). The culture was re-sequenced and three single nucleotide polymorphisms (SNPs) were identified that were not present in the parental strain. Two of the SNPs seemed unlikely candidates for molybdate resistance due to a lack of conservation of the mutated residues in homologous genes of closely related strains. The remaining SNP was located in DVU2210, a protein containing two domains: a YcaO-like domain and a tetratricopeptide-repeat domain. The SNP resulted in a change of a serine residue to arginine in the ATP-hydrolyzing motif of the YcaO-like domain. Deletion mutants of each of the three genes apparently enriched with SNPs in the presence of inhibitory molybdate and combinations of these genes were generated in the Δsat and wild-type strains. Strains lacking both sat and DVU2210 became more resistant to molybdate. Deletions of the other two genes in which SNPs were observed did not result in increased resistance to molybdate. YcaO-like proteins are distributed across the bacterial and archaeal domains, though the function of these proteins is largely unknown. The role of this protein in D. vulgaris is unknown. Due to the distribution of YcaO-like proteins in prokaryotes, the veracity of molybdate as a specific SRM inhibitor should be reconsidered.

Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China

Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture-dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confirmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more flexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.

A mixed consortium of methanotrophic archaea and bacteria boosts methane-dependent selenate reduction

Though methane-based selenate reduction has been reported, neither the selenate load nor the removal rate could satisfy practical applications, thus limiting this technique to bio-remediate selenate pollution. In the present study, using a membrane biofilm batch reactor (MBBR), we successfully enriched a consortium performing methane-dependent selenate reduction, with enhanced reduction rates from 16.1 to 28.9 μM-day^-1 under a comparable Se concentration to industrial wastewaters (i.e., ~500 μM). During active reduction, 16S rRNA gene copies of Archaea and Bacteria were both increased more than one order of magnitude. Clone library construction and high-throughput sequencing indicated that Methanosarcina and Methylocystis were the only methane-oxidizing microorganisms. The presence of 20 mM bromoethanesulphonate or 0.15 mM acetylene both significantly, but not completely, inhibited methane-dependent selenate reduction, indicating the concurrent contributions of methanotrophic archaea and bacteria. Fluorescence in situ hybridization (FISH) revealed that archaea directly adhered to the surface of the membrane while bacteria were in the outer layer, together forming the mature biofilm. This study highlights the crucial role of both methanotrophic archaea and bacteria in methane-dependent selenate reduction, and lays foundations in applying methane to bio-remediate practical selenate pollution.

Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps

Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.

Biogeochemical Processes of C and N in the Soil of Mangrove Forest Ecosystems

The mangrove forest provides various ecosystem services in tropical and subtropical regions. Many of these services are driven by the biogeochemical cycles of C and N, and soil is the major reservoir for these chemical elements. These cycles may be influenced by the changing climate. The high plant biomass in mangrove forests makes these forests an important sink for blue C storage. However, anaerobic soil conditions may also turn mangrove forests into an environmentally detrimental producer of greenhouse gases (such as CH4 and N2O), especially as air temperatures increase. In addition, the changing environmental factors associated with climate change may also influence the N cycles and change the patterns of N2 fixation, dissimilatory nitrate reduction to ammonium, and denitrification processes. This review summarizes the biogeochemical processes of C and N cycles in mangrove forest soils based on recently published studies, and how these processes may respond to climate change, with the aim of predicting the impacts of climate change on the mangrove forest ecosystem.

Rates and Microbial Players of Iron-Driven Anaerobic Oxidation of Methane in Methanic Marine Sediments

The flux of methane, a potent greenhouse gas, from the seabed is largely controlled by anaerobic oxidation of methane (AOM) coupled to sulfate reduction (S-AOM) in the sulfate methane transition (SMT). S-AOM is estimated to oxidize 90% of the methane produced in marine sediments and is mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria. An additional methane sink, i.e., iron oxide coupled AOM (Fe-AOM), has been suggested to be active in the methanic zone of marine sediments. Geochemical signatures below the SMT such as high dissolved iron, low to undetectable sulfate and high methane concentrations, together with the presence of iron oxides are taken as prerequisites for this process. So far, Fe-AOM has neither been proven in marine sediments nor have the governing key microorganisms been identified. Here, using a multidisciplinary approach, we show that Fe-AOM occurs in iron oxide-rich methanic sediments of the Helgoland Mud Area (North Sea). When sulfate reduction was inhibited, different iron oxides facilitated AOM in long-term sediment slurry incubations but manganese oxide did not. Especially magnetite triggered substantial Fe-AOM activity and caused an enrichment of ANME-2a archaea. Methane oxidation rates of 0.095 ± 0.03 nmol cm-3 d-1 attributable to Fe-AOM were obtained in short-term radiotracer experiments. The decoupling of AOM from sulfate reduction in the methanic zone further corroborated that AOM was iron oxide-driven below the SMT. Thus, our findings prove that Fe-AOM occurs in methanic marine sediments containing mineral-bound ferric iron and is a previously overlooked but likely important component in the global methane budget. This process has the potential to sustain microbial life in the deep biosphere.

Denitrification Aligns with N2 Fixation in Red Sea Corals

Denitrification may potentially alleviate excess nitrogen (N) availability in coral holobionts to maintain a favourable N to phosphorous ratio in the coral tissue. However, little is known about the abundance and activity of denitrifiers in the coral holobiont. The present study used the nirS marker gene as a proxy for denitrification potential along with measurements of denitrification rates in a comparative coral taxonomic framework from the Red Sea: Acropora hemprichii, Millepora dichotoma, and Pleuractis granulosa. Relative nirS gene copy numbers associated with the tissues of these common corals were assessed and compared with denitrification rates on the holobiont level. In addition, dinitrogen (N2) fixation rates, Symbiodiniaceae cell density, and oxygen evolution were assessed to provide an environmental context for denitrification. We found that relative abundances of the nirS gene were 16- and 17-fold higher in A. hemprichii compared to M. dichotoma and P. granulosa, respectively. In concordance, highest denitrification rates were measured in A. hemprichii, followed by M. dichotoma and P. granulosa. Denitrification rates were positively correlated with N2 fixation rates and Symbiodiniaceae cell densities. Our results suggest that denitrification may counterbalance the N input from N2 fixation in the coral holobiont, and we hypothesize that these processes may be limited by photosynthates released by the Symbiodiniaceae.

Anion transport as a target of adaption to perchlorate in sulfate-reducing communities

Inhibitors can be used to control the functionality of microbial communities by targeting specific metabolisms. The targeted inhibition of dissimilatory sulfate reduction limits the generation of toxic and corrosive hydrogen sulfide across several industrial systems. Sulfate-reducing microorganisms (SRM) are specifically inhibited by sulfate analogs, such as perchlorate. Previously, we showed pure culture SRM adaptation to perchlorate stress through mutation of the sulfate adenylyltransferase, a central enzyme in the sulfate reduction pathway. Here, we explored adaptation to perchlorate across unconstrained SRM on a community scale. We followed natural and bio-augmented sulfidogenic communities through serial transfers in increasing concentrations of perchlorate. Our results demonstrated that perchlorate stress altered community structure by initially selecting for innately more resistant strains. Isolation, whole-genome sequencing, and molecular biology techniques allowed us to define subsequent genetic mechanisms of adaptation that arose across the dominant adapting SRM. Changes in the regulation of divalent anion:sodium symporter family transporters led to increased intracellular sulfate to perchlorate ratios, allowing SRM to escape the effects of competitive inhibition. Thus, in contrast to pure-culture results, SRM in communities cope with perchlorate stress via changes in anion transport and its regulation. This highlights the value of probing evolutionary questions in an ecological framework, bridging the gap between ecology, evolution, genomics, and physiology.

Sulfate-reducing bacteria and methanogens are involved in arsenic methylation and demethylation in paddy soils

Microbial arsenic (As) methylation and demethylation are important components of the As biogeochemical cycle. Arsenic methylation is enhanced under flooded conditions in paddy soils, producing mainly phytotoxic dimethylarsenate (DMAs) that can cause rice straighthead disease, a physiological disorder occurring widely in some rice growing regions. The key microbial groups responsible for As methylation and demethylation in paddy soils are unknown. Three paddy soils were incubated under flooded conditions. DMAs initially accumulated in the soil porewater, followed by a rapid disappearance coinciding with the production of methane. The soil from a rice straighthead disease paddy field produced a much larger amount of DMAs than the other two soils. Using metabolic inhibition, quantification of functional gene transcripts, microbial enrichment cultures and 13C-labeled DMAs, we show that sulfate-reducing bacteria (SRB) and methanogenic archaea are involved in As methylation and demethylation, respectively, controlling the dynamics of DMAs in paddy soils. We present a model of As biogeochemical cycle in paddy soils, linking the dynamics of changing soil redox potential with arsenite mobilization, arsenite methylation and subsequent demethylation driven by different microbial groups. The model provides a basis for controlling DMAs accumulation and incidence of straighthead disease in rice.

Methane and nitrous oxide temporal and spatial variability in two midwestern USA streams containing high nitrate concentrations

Concentrations and emissions of greenhouse gases CO₂, CH₄, and N₂O commonly are examined individually in aquatic environments in which each is expected to be relatively important; however, their co-occurrence and dynamic interactions in fluvial settings could provide important information about their controlling biogeochemical processes and potential contributions to global climate change. Spatial and temporal variability of CH₄, N₂O, and CO₂ concentrations were measured from June 1999 to September 2003 in two nitrate-rich (40-1200 μM) streams draining agricultural land in the midwestern USA that differed ~13-fold in flow. Seasonal (biweekly), diel (hourly), and transport-oriented (reach-scale) sampling approaches were compared. Dissolved gas concentrations exceeded atmospheric equilibrium values up to 700- and 16-fold, for CH₄ and N₂O, respectively. Mean concentrations were higher in the larger stream than in the smaller stream. In both streams, CH₄ emissions were generally higher in summer-fall and negatively correlated with flow and NO₃^- concentration while N₂O emissions were generally higher in winter/spring and positively correlated with flow and NO₃^-. In the small stream, diel variations in the concentrations, emissions, and isotopic compositions of CH₄, N₂O, and NO₂^- resulted from diel variations in sources, sinks, and air-water gas exchange velocities. Seasonal mean total (CH₄ + N₂O) area-normalized emission rates, expressed as CO₂ warming potential equivalents, were similar for the two streams, but the total reach-scale emission rate for the larger stream, including CO₂, was about 2.9 times that of the smaller stream (131.6 vs 46.0 kg CO₂ equivalents km^-1 day^-1, respectively). The CH₄ contribution to this flux was 9-28%, despite the relatively high NO₃^- and O₂ concentrations in the streams, indicating contributions from upwelling groundwater or reactions in streambed sediment.

Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments

Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm⁻³ d⁻¹) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm⁻³ d⁻¹ and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm⁻³ d⁻¹. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.

Microbial sulfate reduction decreases arsenic mobilization in flooded paddy soils with high potential for microbial Fe reduction

Arsenic (As) tends to mobilize in flooded paddy soil due to the reductive dissolution of the iron (oxyhydr)oxides to which As sorbs, resulting in elevated As accumulation in rice that poses a potential risk to the food safety and human health. Microbial sulfate reduction is an important biogeochemical process in paddy soils, but its impact on As mobilization remains poorly understood. In this study, we incubated eight As-contaminated paddy soils under flooded conditions to investigate the effect of sulfate addition on As mobility. Porewater Fe and As concentrations and As species were determined. Among the eight soils, an addition of 50 mg S kg^-1 as sodium sulfate decreased porewater arsenite only in two soils, which also showed a high mobilization of Fe²⁺. Further experiments showed that the addition of sulfate to these two soils stimulated microbial sulfate reduction but decreased porewater concentrations of both arsenite and Fe²⁺. Additionally, the supply of sulfate increased the fractions of As associated with acid volatile sulfides in the solid phase and decreased As uptake by rice in pot experiments under similar conditions. The effect of sulfate addition on porewater As was diminished by the addition of molybdate, an inhibitor of sulfate reducing bacteria. These results suggest the formation of secondary FeS minerals which co-precipitate or sorb arsenite as a likely mechanism of As immobilization, which was also supported by thermodynamic modeling of the pore water. Thus, sulfate additions can immobilize As and reduce its availability to rice plants in paddy soils containing a high potential for microbial Fe reduction, providing an efficient way to mitigate the As transfer to the food chain.

Resistance and Resilience of Sulfidogenic Communities in the Face of the Specific Inhibitor Perchlorate

Hydrogen sulfide is a toxic and corrosive gas, produced by the activity of sulfate-reducing microorganisms (SRM). Owing to the environmental, economic and human-health consequences of sulfide, there is interest in developing specific inhibitors of SRM. Recent studies have identified perchlorate as a promising emerging inhibitor. The aim of this work is to quantitatively dissect the inhibitory dynamics of perchlorate. Sulfidogenic mixed continuous-flow systems were treated with perchlorate. SRM number, sulfide production and community structure were monitored pre-, during and post-treatment. The data generated was compared to a simple mathematical model, where SRM growth slows as a result of inhibition. The experimental data supports the interpretation that perchlorate largely acts to suppress SRM growth rates, rendering planktonic SRM increasingly susceptible to wash-out. Surface-attachment was identified as an important parameter preventing SRM wash-out and thus governing inhibitory dynamics. Our study confirmed the lesser depletion of surface-attached SRM as compared to planktonic SRM during perchlorate treatment. Indirect effects of perchlorate (bio-competitive exclusion of SRM by dissimilatory perchlorate-reducing bacteria, DPRB) were also assayed by amending reactors with DPRB. Indeed, low concentrations of perchlorate coupled with DRPB amendment can drive sulfide concentrations to zero. Further, inhibition in a complex community was compared to that in a pure culture, highlighting similarities and differences between the two scenarios. Finally, we quantified susceptibility to perchlorate across SRM in various culture conditions, showing that prediction of complex behavior in continuous systems from batch results is possible. This study thus provides an overview of the sensitivity of sulfidogenic communities to perchlorate, as well as mechanisms underlying these patterns.

Pyrite formation from FeS and H2S is mediated through microbial redox activity

Pyrite is the most abundant iron−sulfur mineral in sediments. Over geological times, its burial controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. However, the mechanism of pyrite formation in sediments is still being debated. We show that lithotrophic microorganisms can mediate the transformation of FeS and H₂S to FeS₂ at ambient temperature if metabolically coupled to methane-producing archaea. Our results provide insights into a metabolic relationship that could sustain part of the deep biosphere and lend support to the iron−sulfur-world theory that postulated FeS transformation to FeS₂ as a key energy-delivering reaction for life to emerge.

The exergonic reaction of FeS with H₂S to form FeS₂ (pyrite) and H₂ was postulated to have operated as an early form of energy metabolism on primordial Earth. Since the Archean, sedimentary pyrite formation has played a major role in the global iron and sulfur cycles, with direct impact on the redox chemistry of the atmosphere. However, the mechanism of sedimentary pyrite formation is still being debated. We present microbial enrichment cultures which grew with FeS, H₂S, and CO₂ as their sole substrates to produce FeS₂ and CH₄. Cultures grew over periods of 3 to 8 mo to cell densities of up to 2 to 9 × 10⁶ cells per mL⁻¹. Transformation of FeS with H₂S to FeS₂ was followed by ⁵⁷Fe Mössbauer spectroscopy and showed a clear biological temperature profile with maximum activity at 28 °C and decreasing activities toward 4 °C and 60 °C. CH₄ was formed concomitantly with FeS₂ and exhibited the same temperature dependence. Addition of either penicillin or 2-bromoethanesulfonate inhibited both FeS₂ and CH₄ production, indicating a coupling of overall pyrite formation to methanogenesis. This hypothesis was supported by a 16S rRNA gene-based phylogenetic analysis, which identified at least one archaeal and five bacterial species. The archaeon was closely related to the hydrogenotrophic methanogen Methanospirillum stamsii, while the bacteria were most closely related to sulfate-reducing Deltaproteobacteria, as well as uncultured Firmicutes and Actinobacteria. Our results show that pyrite formation can be mediated at ambient temperature through a microbially catalyzed redox process, which may serve as a model for a postulated primordial iron−sulfur world.

A theoretical framework for controlling complex microbial communities

Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states.

Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding

Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis - and potentially assimilatory sulfate pathways - relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.

Acetylenotrophy: a hidden but ubiquitous microbial metabolism?

Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C2H2). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.

Widespread nitrogen fixation in sediments from diverse deep-sea sites of elevated carbon loading

Nitrogen fixation, the biological conversion of N₂ to NH₃ , is critical to alleviating nitrogen limitation in many marine ecosystems. To date, few measurements exist of N₂ fixation in deep-sea sediments. Here, we conducted > 400 bottle incubations with sediments from methane seeps, whale falls and background sites off the western coast of the United States from 600 to 2893 m water depth to investigate the potential rates, spatial distribution and biological mediators of benthic N₂ fixation. We found that N₂ fixation was widespread, yet heterogeneously distributed with sediment depth at all sites. In some locations, rates exceeded previous measurements by > 10×, and provided up to 30% of the community anabolic growth requirement for nitrogen. Diazotrophic activity appeared to be inhibited by pore water ammonium: N₂ fixation was only observed if incubation ammonium concentrations were ≤ 25 μM, and experimental additions of ammonium reduced diazotrophy. In seep sediments, N₂ fixation was dependent on CH₄ and coincident with sulphate reduction, consistent with previous work showing diazotrophy by microorganisms mediating sulphate-coupled methane oxidation. However, the pattern of diazotrophy was different in whale-fall and associated reference sediments, where it was largely unaffected by CH₄ , suggesting catabolically different diazotrophs at these sites.

Seasonal changes in peryphytic microbial metabolism determining mercury methylation in a tropical wetland

Mercury (Hg) methylation, a key process in the biogeochemical cycle of Hg, is mainly attributed to sulfate-reducing bacteria and methanogenic Archaea. However, environmental regulation by these groups has not yet been ascertained in tropical environments, especially in respect to the seasonal flood flooding. This work evaluated the variation of net methylmercury production potential in relation to biological characteristics of the periphyton, environmental factors, and flood pulse seasons. Our results indicate that there is a seasonal change between metabolic groups as main Hg methylators, sulfate-reducing bacteria in the dry season and methanogenic Archaea in the flood season. In addition, there was a positive relationship between dissolved organic carbon (DOC), phosphorus, cyanobacteria biovolume, and periphytic Hg methylation potential. These results shed a new light on MeHg production plasticity, mediated by landscape and flood pulses in tropical wetlands, as well as on ecological relationships within the periphyton.

Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park

Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter However, the abundances and activities of such organisms in the native microbial community are unknown. Here, we used stable isotope probing experiments combined with 16S rRNA gene amplicon and shotgun metagenomic sequencing to gain an understanding of the in situ Fe(III)-reducing microbial community at CP. Fe-Si oxide precipitates collected near the hot spring vent were incubated with unlabeled and ¹³C-labeled acetate to target active FeRB. We searched reconstructed genomes for homologs of genes involved in known extracellular electron transfer (EET) systems to identify the taxa involved in Fe redox transformations. Known FeRB taxa containing putative EET systems (Geobacter, Ignavibacteria) increased in abundance under acetate-amended conditions, whereas genomes related to Ignavibacterium and Thermodesulfovibrio that contained putative EET systems were recovered from incubations without electron donor. Our results suggest that FeRB play an active role in Fe redox cycling within Fe-Si oxide-rich deposits located at the hot spring vent.IMPORTANCE The identification of past near-surface hydrothermal environments on Mars emphasizes the importance of using modern Earth environments, such as CP, to gain insight into potential Fe-based microbial life on other rocky worlds, as well as ancient Fe-rich Earth ecosystems. By combining stable carbon isotope probing techniques and DNA sequencing technology, we gained insight into the pathways of microbial Fe redox cycling at CP. The results suggest that microbial Fe(III) oxide reduction is prominent in situ, with important implications for the generation of geochemical and stable Fe isotopic signatures of microbial Fe redox metabolism within Fe-rich circumneutral-pH thermal spring environments on Earth and Mars.

Method for High Frequency Underway N2 Fixation Measurements: Flow-Through Incubation Acetylene Reduction Assays by Cavity Ring Down Laser Absorption Spectroscopy (FARACAS)

Because of the difficulty in resolving the large variability of N₂ fixation with current methods which rely on discrete sampling, the development of new methods for high-resolution measurements is highly desirable. We present a new method for high-frequency measurements of aquatic N₂ fixation by continuous flow-through incubations and spectral monitoring of the acetylene (C₂H_2, a substrate analog for N₂) reduction to ethylene (C₂H₄). In this method, named Flow-through Incubation Acetylene Reduction Assays by Cavity Ring-Down Laser Absorption Spectroscopy (FARACAS), dissolved C₂H₂ is continuously admixed with seawater upstream of a continuous-flow stirred-tank reactor (CFSR) in which C₂H₂ reduction takes place. Downstream of the flow-through incubator, the C₂H₄ gas is stripped using a bubble column contactor and circulated with a diaphragm pump into a wavelength-scanned cavity ring down laser absorption spectrometer (CRDS). Our method provides high-resolution and precise mapping of aquatic N₂ fixation, its diel cycle, and its response to environmental gradients, and can be adapted to measure other biological processes. The short-duration of the flow-through incubations without preconcentration of cells minimizes potential artifacts such as bottle containment effects while providing near real-time estimates for adaptive sampling. We expect that our new method will improve the characterization of the biogeography and kinetics of aquatic N₂ fixation rates.

Enzyme- and gene-based approaches for developing methanogen-specific compounds to control ruminant methane emissions: a review

Methane emissions from ruminants are of worldwide concern due to their potential to adversely affect climate patterns. Methane emissions can be mitigated in several ways, including dietary manipulation, the use of alternative hydrogen sinks, and by the direct inhibition of methanogens. In the present review, we summarise and emphasise studies where defined chemically synthesised compounds have been used to mitigate ruminant methane emissions by direct targeting of methanogens and discuss the future potential of such inhibitors. We also discuss experiments, where methanogen-specific enzymes and pure cultures of methanobacterial species have been used to aid development of inhibitors. Application of certain compounds can result in dramatic reductions of methane emissions from ruminant livestock, demonstrating ‘proof of principle’ of chemical inhibitors of methanogenesis. More recently, genome sequencing of rumen methanogens has enabled an in-depth analysis of the enzymatic pathways required for methane formation. Chemogenomic methods, similar to those used in the fight against cancer and infectious diseases, can now be used to specifically target a pathway or enzyme in rumen methanogens. However, few rumen methanogen enzymes have been structurally or biochemically characterised. Any compound, whether natural or man-made, that is used as a mitigation strategy will need to be non-toxic to the host animal (and humans), cost-effective, environmentally friendly, and not accumulate in host tissues or milk products. Chemically synthesised inhibitors offer potentially significant advantages, including high levels of sustained inhibition, the ability to be easily and rapidly produced for global markets, and have the potential to be incorporated into slow-release vehicles for grazing animals.

Microbial Processes Mediating the Evolution of Methylarsine Gases from Dimethylarsenate in Paddy Soils

Arsenic (As) biovolatilization is an important component of the global As biogeochemical cycle. Soils can emit various methylarsine gases, but the underlying microbial processes remain unclear. Here, we show that the addition of molybdate (Mo), an inhibitor of sulfate-reducing bacteria, greatly enhanced dimethylarsine evolution from dimethylarsenate [DMAs(V)] added to two paddy soils. Molybdate addition significantly affected the microbial community structure. The aerobic enrichment cultures from both soils volatilized substantial amounts of dimethylarsine from DMAs(V) in the presence of Mo, whereas the anaerobic enrichment cultures did not. A Bacillus strain (CZ-2) capable of reducing DMAs(V) to dimethylarsine was isolated from the aerobic enrichment culture, and its volatilization ability was enhanced by Mo. RNA-seq analysis identified 10 reductase genes upregulated by Mo. Addition of the reducing agent NADH increased dimethylarsine volatilization by strain CZ-2, suggesting that DMAs(V) reductase is an NADH-dependent enzyme. The strain could not methylate arsenite or convert monomethylarsenate and DMAs(V) to trimethylarsine. Our results show that dimethylarsine evolution from DMAs(V) is independent of the As methylation pathway and that Mo enhances dimethylarsine evolution from paddy soils by shifting the microbial community structure and enhancing the reduction of DMAs(V) to dimethylarsine, possibly through upregulating the expression of DMAs(V) reductase gene(s).

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to identify potent and selective inhibitors of SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Zinc pyrithione is the most potent inhibitor of sulfidogenesis that we identified, and is several orders of magnitude more potent than commonly used industrial biocides. Both zinc and copper pyrithione are also moderately selective against SRM. The high-throughput (HT) approach we present can be readily adapted to target SRM in diverse environments and similar strategies could be used to quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant to efforts to engineer environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments

The competition between sulfate reducing bacteria and methanogens over common substrates has been proposed as a critical control for methane production. In this study, we examined the co-existence of methanogenesis and sulfate reduction with shared substrates over a large range of sulfate concentrations and rates of sulfate reduction in estuarine systems, where these processes are the key terminal sink for organic carbon. Incubation experiments were carried out with sediment samples from the sulfate-methane transition zone of the Yarqon (Israel) estuary with different substrates and inhibitors along a sulfate concentrations gradient from 1 to 10 mM. The results show that methanogenesis and sulfate reduction can co-exist while the microbes share substrates over the tested range of sulfate concentrations and at sulfate reduction rates up to 680 μmol L-1 day-1. Rates of methanogenesis were two orders of magnitude lower than rates of sulfate reduction in incubations with acetate and lactate, suggesting a higher affinity of sulfate reducing bacteria for the available substrates. The co-existence of both processes was also confirmed by the isotopic signatures of δ34S in the residual sulfate and that of δ13C of methane and dissolved inorganic carbon. Copy numbers of dsrA and mcrA genes supported the dominance of sulfate reduction over methanogenesis, while showing also the ability of methanogens to grow under high sulfate concentration and in the presence of active sulfate reduction.