Nitrogen, carbon, and sulfur metabolism in natural thioploca samples

Phylogeny and Metabolic Potential of New Giant Sulfur Bacteria of the Family Beggiatoaceae from Coastal-Marine Sulfur Mats of the White Sea

The family Beggiatoaceae is currently represented by 25 genera in the Genome Taxonomy Database, of which only 6 have a definite taxonomic status. Two metagenome-assembled genomes (MAGs), WS_Bin1 and WS_Bin3, were assembled from metagenomes of the sulfur mats coating laminaria remnants in the White Sea. Using the obtained MAGs, we first applied phylogenetic analysis based on whole-genome sequences to address the systematics of Beggiatoaceae, which clarify the taxonomy of this family. According to the average nucleotide identity (ANI) and average amino acid identity (AAI) values, MAG WS_Bin3 was assigned to a new genus and a new species in the family Beggiatoaceae, namely, 'Candidatus Albibeggiatoa psychrophila' gen. nov., sp. nov., thus providing the revised taxonomic status of the candidate genus 'BB20'. Analysis of 16S rRNA gene homology allowed us to identify MAG WS_Bin1 as the only currently described species of the genus 'Candidatus Parabeggiatoa', namely, 'Candidatus Parabeggiatoa communis', and consequently assign the candidate genus 'UBA10656', including four new species, to the genus 'Ca. Parabeggiatoa'. Using comparative whole-genome analysis of the members of the genera 'Candidatus Albibeggiatoa' and 'Ca. Parabeggiatoa', we expanded information on the central pathways of carbon, sulfur and nitrogen metabolism in the family Beggiatoaceae.

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China

Multicellularity is key to the functional and ecological success of the Eukarya, underpinning much of their modern diversity in both terrestrial and marine ecosystems. Despite the widespread occurrence of simple multicellular organisms among eukaryotes, when this innovation arose remains an open question. Here, we report cellularly preserved multicellular microfossils (Qingshania magnifica) from the ~1635-million-year-old Chuanlinggou Formation, North China. The fossils consist of large uniseriate, unbranched filaments with cell diameters up to 190 micrometers; spheroidal structures, possibly spores, occur within some cells. In combination with spectroscopic characteristics, the large size and morphological complexity of these fossils support their interpretation as eukaryotes, likely photosynthetic, based on comparisons with extant organisms. The occurrence of multicellular eukaryotes in Paleoproterozoic rocks not much younger than those containing the oldest unambiguous evidence of eukaryotes as a whole supports the hypothesis that simple multicellularity arose early in eukaryotic history, as much as a billion years before complex multicellular organisms diversified in the oceans.

Quantifying potential N turnover rates in hypersaline microbial mats by 15N tracer techniques

Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using ¹⁵N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.

Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps

Carbonate rocks at marine methane seeps are commonly colonized by sulfur-oxidizing bacteria that co-occur with etch pits that suggest active dissolution. We show that sulfur-oxidizing bacteria are abundant on the surface of an exemplar seep carbonate collected from Del Mar East Methane Seep Field, USA. We then used bioreactors containing aragonite mineral coupons that simulate certain seep conditions to investigate plausible in situ rates of carbonate dissolution associated with sulfur-oxidizing bacteria. Bioreactors inoculated with a sulfur-oxidizing bacterial strain, Celeribacter baekdonensis LH4, growing on aragonite coupons induced dissolution rates in sulfidic, heterotrophic, and abiotic conditions of 1773.97 (±324.35), 152.81 (±123.27), and 272.99 (±249.96) μmol CaCO₃ • cm⁻² • yr⁻¹, respectively. Steep gradients in pH were also measured within carbonate-attached biofilms using pH-sensitive fluorophores. Together, these results show that the production of acidic microenvironments in biofilms of sulfur-oxidizing bacteria are capable of dissolving carbonate rocks, even under well-buffered marine conditions. Our results support the hypothesis that authigenic carbonate rock dissolution driven by lithotrophic sulfur-oxidation constitutes a previously unknown carbon flux from the rock reservoir to the ocean and atmosphere.

Research on enhancement of zero-valent iron on dissimilatory nitrate/nitrite reduction to ammonium of Desulfovibrio sp. CMX

The process of nitrate dissimilation to ammonium (DNRA) is an important way for storing nitrogen in nature and DNRA is a key step in efficient recovery of nitrogen in wastewater. However, in view of the low conversion efficiency of DNRA, zero-valent iron (ZVI) was used to enhance the DNRA process of Desulfovibrio sp. CMX. ZVI can obviously promote the nitrate/nitrite reduction. The experiment indicated that 5 g/L 300 mesh ZVI could convert 5 mmol/L nitrate or nitrite to ammonium in 48 h or 36 h respectively, and the conversion ratio of NO₂^- to NH₄⁺ could reach more than 90%. The ZVI provided a suitable growth environment for the Desulfovibrio sp. CMX through chemical reduction of nitrite, production of divalent iron (Fe²⁺), reduction of oxidation-reduction potential (ORP) and adjustment of pH, which strengthened the DNRA performance. This experiment is advantageous for increasing efficiency of DNRA and provides a new idea for efficient recovery of nitrogen resources.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

Controls of H2S, Fe2 +, and Mn2 + on Microbial NO3 --Reducing Processes in Sediments of an Eutrophic Lake

Understanding the biogeochemical controls on the partitioning between nitrogen (N) removal through denitrification and anaerobic ammonium oxidation (anammox), and N recycling via dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) is crucial for constraining lacustrine N budgets. Besides organic carbon, inorganic compounds may serve as electron donors for NO3 - reduction, yet the significance of lithotrophic NO3 - reduction in the environment is still poorly understood. Conducting incubation experiments with additions of 15N-labeled compounds and reduced inorganic substrates (H2S, Fe2+, Mn2+), we assessed the role of alternative electron donors in regulating the partitioning between the different NO3 --reducing processes in ferruginous surface sediments of Lake Lugano, Switzerland. In sediment slurry incubations without added inorganic substrates, denitrification and DNRA were the dominant NO3 --reducing pathways, with DNRA contributing between 31 and 46% to the total NO3 - reduction. The contribution of anammox was less than 1%. Denitrification rates were stimulated by low to moderate additions of ferrous iron (Fe2+ ≤ 258 μM) but almost completely suppressed at higher levels (≥1300 μM). Conversely, DNRA was stimulated only at higher Fe2+ concentrations. Dissolved sulfide (H2S, i.e., sum of H2S, HS- and S2-) concentrations up to ∼80 μM, strongly stimulated denitrification, but did not affect DNRA significantly. At higher H2S levels (≥125 μM), both processes were inhibited. We were unable to find clear evidence for Mn2+-supported lithotrophic NO3 - reduction. However, at high concentrations (∼500 μM), Mn2+ additions inhibited NO3 - reduction, while it did not affect the balance between the two NO3 - reduction pathways. Our results provide experimental evidence for chemolithotrophic denitrification or DNRA with Fe2+ and H2S in the Lake Lugano sediments, and demonstrate that all tested potential electron donors, despite the beneficial effect at low concentrations of some of them, can inhibit NO3 - reduction at high concentration levels. Our findings thus imply that the concentration of inorganic electron donors in lake sediments can act as an important regulator of both benthic denitrification and DNRA rates, and suggest that they can exert an important control on the relative partitioning between microbial N removal and N retention in lakes.

Denitrification and dissimilatory nitrate reduction to ammonium in freshwater lakes of the Eastern Plain, China: Influences of organic carbon and algal bloom

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are critical dissimilatory nitrate reduction pathways that determine nitrogen (N) removal and internal recycling in aquatic environments. However, the relative important of DNRA, and the influences of environmental factors on DNF and DNRA, have not been widely studied in freshwater lakes. In our study, we used N isotope-tracing to investigate the potential rates of DNF and DNRA in 27 lakes from the Eastern Plain Lake Zone (EPL), China. In the EPL lakes, DNF was the dominant nitrate reduction process, however DNRA was still important, accounting for around 4.3%-21.9% of total nitrate reduction. The sediment organic carbon was the primary factor controlling the rates of dissimilatory nitrate reduction, accounting for 28.3% and 37.9% of the variance in DNF and DNRA rates, respectively. High algal biomass accelerated DNF rates, while indirectly affected DNRA via changing the quality of organic carbon. The greater contributions of DNRA to dissimilatory nitrate reduction were found in lakes with higher sulfate concentrations. DNRA coupled to sulfur cycling may play an important role in lakes with high sulfate concentrations and high sediment organic carbon. This study highlights the important role played by DNRA in total nitrate reduction pathways of freshwater lakes. Mitigation strategies for N pollution and algal blooms should not only target decrease of nutrient input, strategies should also create a suitable environment for improving N removal and inhibit N recycling.

The nitrogen reduction in eutrophic water column driven by Microcystis blooms

During the bloom seasons, the dissolved inorganic nitrogen declines, which results in the occurrence of nitrogen limitation. It is unclear where the nitrogen goes. Our enclosure experiments and batch tests suggested that Microcystis blooms could significantly reduce the nitrogen in water bodies and the key mechanisms for the nitrogen reduction in different layers were different. The assimilation was the main pathway for nitrogen reduction in the surface layer, while denitrification played an important role both at the sediment-water interface and in the overlying water. Stable nitrogen isotope experiments showed that the nitrate reduction efficiency at sediment-water interface was enhanced by Microcystis, reaching to 76.5∼84.7 %. Dissimilation accounted for 63.8∼67.3 % of the nitrate reduction, and the denitrification rate was 7.4∼8.5 times of DNRA rate. In the water column, the Microcystis bloom facilitated the formation of dark/anoxic condition, which favored the denitrification. The Microcystis aggregates collected from the field showed a great potential in removing nitrogen, and the TN in the overly water was reduced by 3.76∼6.03 mg L^-1 within two days. This study provided field evidences and deeper insights into the relationship between Microcystis blooms and nitrogen reduction in the whole water column and gave more details about the enhancing effects of Microcystis on nitrogen reduction.

Division of labor and growth during electrical cooperation in multicellular cable bacteria

Cable bacteria form centimeter-long, multicellular filaments whose energy metabolism involves cooperation among cells that separately perform oxidation of the electron donor and reduction of the electron acceptor. This cooperative division of labor is facilitated via long-range electrical currents that run from cell to cell along a network of conductive fibers. Here we show that biomass synthesis shows a surprising asymmetry along the filament: only the cells oxidizing the electron donor conserve energy for growth, while the other cells reduce electron acceptors without biosynthesis. Our study hence provides insights into the physiology of an unconventional chemolithotroph, which forms a multicellular electrically connected system with unique functional differentiation, integration, and coordination.

Multicellularity is a key evolutionary innovation, leading to coordinated activity and resource sharing among cells, which generally occurs via the physical exchange of chemical compounds. However, filamentous cable bacteria display a unique metabolism in which redox transformations in distant cells are coupled via long-distance electron transport rather than an exchange of chemicals. This challenges our understanding of organismal functioning, as the link among electron transfer, metabolism, energy conservation, and filament growth in cable bacteria remains enigmatic. Here, we show that cells within individual filaments of cable bacteria display a remarkable dichotomy in biosynthesis that coincides with redox zonation. Nanoscale secondary ion mass spectrometry combined with ¹³C (bicarbonate and propionate) and ¹⁵N-ammonia isotope labeling reveals that cells performing sulfide oxidation in deeper anoxic horizons have a high assimilation rate, whereas cells performing oxygen reduction in the oxic zone show very little or no label uptake. Accordingly, oxygen reduction appears to merely function as a mechanism to quickly dispense of electrons with little to no energy conservation, while biosynthesis and growth are restricted to sulfide-respiring cells. Still, cells can immediately switch roles when redox conditions change, and show no differentiation, which suggests that the “community service” performed by the cells in the oxic zone is only temporary. Overall, our data reveal a division of labor and electrical cooperation among cells that has not been seen previously in multicellular organisms.

Comparison of Community and Function of Dissimilatory Nitrate Reduction to Ammonium (DNRA) Bacteria in Chinese Shallow Lakes with Different Eutrophication Degrees

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in controlling nitrogen (N) loading in lake ecosystems. However, studies on the linkage between DNRA bacterial community structure and lake eutrophication remain unclear. We examined the community and abundance of DNRA bacteria at six basins of four shallow lakes with different degrees of eutrophication in China. Measurements of the different forms of N and phosphorus (P) in the water column and interstitial water as well as total organic carbon (TOC) and sulfide in the sediments in summer (July 2016) were performed. The nutritional status of Lake Chaohu was more serious than that of the lakes in Wuhan, including Lake Qingling, Lake Houguan, and Lake Zhiyin by comparing geochemical and physical parameters. We found a higher abundance of the nrfA gene, which is a function gene of DNRA bacteria in sediments with higher contents of TOC and sulfide. Moreover, nitrate was a significant factor influencing the DNRA bacterial community structure. A significant difference of the DNRA bacterial community structure between Lake Chaohu and the lakes in Wuhan was discovered. Furthermore, DNRA bacterial abundance and community positively correlated with NH4+ and Chl a concentrations in Lake Chaohu, in which a percent abundance of dominant populations varied along eutrophication gradients. Overall, the abundance and community structure of the DNRA bacteria might be important regulators of eutrophication and cyanobacteria bloom in Lake Chaohu.

Identification, Expression and Activity of Candidate Nitrite Reductases From Orange Beggiatoaceae, Guaymas Basin

Orange filamentous Beggiatoaceae form massive microbial mats on hydrothermal sediments in Guaymas Basin; these bacteria are considered to oxidize sulfide with nitrate and nitrite as electron acceptors. From a previously analyzed genome of an orange Beggiatoaceae filament, three candidate genes for enzymes with nitrite-reducing function - an orange octaheme cytochrome, a nirS nitrite reductase, and a nitrite/tetrathionate-reducing octaheme cytochrome - were cloned and expressed in Escherichia coli. The expressed and purified orange cytochrome showed reduced nitrite-reducing activity compared to the multifunctional native protein obtained from microbial mats. The nirS gene product showed in vitro but no in-gel nitrite-reducing activity; and the nitrite/tetrathionate-reducing octaheme cytochrome was capable of reducing both nitrite and tetrathionate in vitro. Phylogenetic analysis shows that the orange Beggiatoaceae nirS, in contrast to the other candidate nitrite reductases, does not form monophyletic lineages with its counterparts in other large sulfur-oxidizing bacteria, and most likely represents a recent acquisition by lateral gene transfer. The nitrite/tetrathionate-reducing enzyme of the orange Beggiatoaceae is related to nitrite- and tetrathionate reductases harbored predominantly by Gammaproteobacteria, including obligate endosymbionts of hydrothermal vent tubeworms. Thus, the orange Guaymas Basin Beggiatoaceae have a repertoire of at least three different functional enzymes for nitrite reduction. By demonstrating the unusual diversity of enzymes with a potential role in nitrite reduction, we show that bacteria in highly dynamic, sulfide-rich hydrothermal vent habitats adapt to these conditions that usually prohibit nitrate and nitrite reduction. In the case of the orange Guaymas Beggiatoaceae, classical denitrification appears to be replaced by different multifunctional enzymes for nitrite and tetrathionate reduction; the resulting ecophysiological flexibility provides a new key to the dominance of these Beggiatoaceae in hydrothermal hot spots.

Mechanisms of nitrogen attenuation from seawater by two microbial mats

Microbial mats, due to their high microbial diversity, have the potential to express most biogeochemical cycling processes, highlighting their prospective use in bioremediation of various environmental contaminants. In this study the mechanisms of nitrogen attenuation were investigated in naturally occurring microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico. Key processes responsible for this removal were evaluated using quantification of functional genes related to nitrification, denitrification, and nitrogen fixation. Both microbial mats were capable of removing high (up to 2 mM) concentrations of ammonium and nitrate. Ammonium assimilation rates measured for Elkhorn Slough mats showed that this process was responsible for most of the ammonium uptake in these mats. While Elkhorn Slough mats did not show any evidence of nitrogen removal pathways other than microbial assimilation, Baja mats exhibited the potential for nitrification, denitrification, and DNRA as well as assimilation. The results of this study demonstrate the potential of microbial mats for bioremediation of nitrogenous pollutants independent of the mechanisms responsible for their removal.

Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: possible implications for their ecology

The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO₂ fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency. One possible answer is that GD17 cells store high-energy-containing polyphosphate during favorable nutrient conditions to survive periods of nutrient starvation. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy to investigate potential substrate enrichments in single GD17 cells collected from Baltic Sea redox zones. More specific substrate enrichment features were identified in experiments using Sulfurimonas gotlandica GD1^T, a GD17 representative. Sulfurimonas cells accumulated polyphosphate both in situ and in vitro. Combined genome and culture-dependent analyses suggest that polyphosphate serves as an energy reservoir to maintain cellular integrity at unfavorable substrate conditions. This redox-independent energy supply would be a precondition for sustaining the r-strategy lifestyle of GD17 and may represent a newly identified survival strategy for chemolithoautotrophic prokaryotes occupying eutrophic redox zones.

Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms

Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1.6 cm into the sediment. Intracellular nitrate contents were particularly high at stations where chlorophyll contents suggested high settling rates of pelagic primary production. The depth distribution of intracellular nitrate matched that of the diatom-specific photopigment fucoxanthin in the upper 1.6 cm and calculations support that diatoms are the major nitrate-storing microbes in these sediments. In contrast, other known nitrate-storing microbes, such as sulfide-oxidizing bacteria and foraminifers, played only a minor role, if any. Strikingly, 18S rRNA gene sequencing revealed that the majority of the diatoms in the sediment were pelagic species. We conclude that intracellular nitrate stored by pelagic diatoms is transported to the seafloor by settling phytoplankton blooms, implying a so far overlooked 'biological nitrate pump'.

Filamentous Giant Beggiatoaceae from the Guaymas Basin Are Capable of both Denitrification and Dissimilatory Nitrate Reduction to Ammonium

Whether large sulfur bacteria of the family Beggiatoaceae reduce NO₃⁻ to N₂ via denitrification or to NH₄⁺ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N₂ production removes bioavailable nitrogen from the ecosystem, whereas NH₄⁺ production retains it. For this reason, the topic of environmental controls on the competition for NO₃⁻ between N₂-producing and NH₄⁺-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO₃⁻ reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

Filamentous large sulfur-oxidizing bacteria (FLSB) of the family Beggiatoaceae are globally distributed aquatic bacteria that can control geochemical fluxes from the sediment to the water column through their metabolic activity. FLSB mats from hydrothermal sediments of Guaymas Basin, Mexico, typically have a “fried-egg” appearance, with orange filaments dominating near the center and wider white filaments at the periphery, likely reflecting areas of higher and lower sulfide fluxes, respectively. These FLSB store large quantities of intracellular nitrate that they use to oxidize sulfide. By applying a combination of ¹⁵N-labeling techniques and genome sequence analysis, we demonstrate that the white FLSB filaments were capable of reducing their intracellular nitrate stores to both nitrogen gas and ammonium by denitrification and dissimilatory nitrate reduction to ammonium (DNRA), respectively. On the other hand, our combined results show that the orange filaments were primarily capable of DNRA. Microsensor profiles through a laboratory-incubated white FLSB mat revealed a 2- to 3-mm vertical separation between the oxic and sulfidic zones. Denitrification was most intense just below the oxic zone, as shown by the production of nitrous oxide following exposure to acetylene, which blocks nitrous oxide reduction to nitrogen gas. Below this zone, a local pH maximum coincided with sulfide oxidation, consistent with nitrate reduction by DNRA. The balance between internally and externally available electron acceptors (nitrate) and electron donors (reduced sulfur) likely controlled the end product of nitrate reduction both between orange and white FLSB mats and between different spatial and geochemical niches within the white FLSB mat.

IMPORTANCE Whether large sulfur bacteria of the family Beggiatoaceae reduce NO₃⁻ to N₂ via denitrification or to NH₄⁺ via DNRA has been debated in the literature for more than 25 years. We resolve this debate by showing that certain members of the Beggiatoaceae use both metabolic pathways. This is important for the ecological role of these bacteria, as N₂ production removes bioavailable nitrogen from the ecosystem, whereas NH₄⁺ production retains it. For this reason, the topic of environmental controls on the competition for NO₃⁻ between N₂-producing and NH₄⁺-producing bacteria is of great scientific interest. Recent experiments on the competition between these two types of microorganisms have demonstrated that the balance between electron donor and electron acceptor availability strongly influences the end product of NO₃⁻ reduction. Our results suggest that this is also the case at the even more fundamental level of enzyme system regulation within a single organism.

Enhanced nitrogen removal using solid carbon source in constructed wetland with limited aeration

In this study, the performances of nitrogen removal in constructed wetlands using solid carbon source with limited aeration were investigated. The blends of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) and polyacetic acid (PLA) were used as the carbon source and biofilm support. The performances of nitrogen removal, microbial abundance and microbial community structure in the biofilm attached on PHBV/PLA were investigated. Higher ammonia removal efficiency (91.00%) and total nitrogen removal efficiency (97.03%) than non-aerated constructed wetland (System NA) were achieved in constructed wetland with limited aeration (System A). The limited aeration decreased the average concentrations of COD in effluent. And, System A had higher microbial abundance than System NA. Pyrosequencing analysis showed that denitrifying bacteria Brevinema (41.85%) and Thiothrix (12.33%) were the predominant genus in the biofilm attached on the carbon source in System NA and System A, respectively.

Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 36°S). Studies show that primeval sulfuretums held diverse prokaryotic life, and, while rare today, still sustain species-rich giant sulfur-oxidizing bacterial communities. We here present the genomic features of a new bacteria of the HS, "Candidatus Venteria ishoeyi" ("Ca. V. ishoeyi") in the family Thiotrichaceae.Three identical filaments were micro-manipulated from reduced sediments collected off central Chile; their DNA was extracted, amplified, and sequenced by a Roche 454 GS FLX platform. Using three sequenced libraries and through de novo genome assembly, a draft genome of 5.7 Mbp, 495 scaffolds, and a N50 of 70 kbp, was obtained. The 16S rRNA gene phylogenetic analysis showed that "Ca. V. ishoeyi" is related to non-vacuolate forms presently known as Beggiatoa or Beggiatoa-like forms. The complete set of genes involved in respiratory nitrate-reduction to dinitrogen was identified in "Ca. V. ishoeyi"; including genes likely leading to ammonification. As expected, the sulfur-oxidation pathway reported for other sulfur-oxidizing bacteria were deduced and also, key inorganic and organic carbon acquisition related genes were identified. Unexpectedly, the genome of "Ca. V. ishoeyi" contained numerous CRISPR repeats and an I-F CRISPR-Cas type system gene coding array. Findings further show that, as a member of an eons-old marine ecosystem, "Ca. V. ishoeyi" contains the needed metabolic plasticity for life in an increasingly oxygenated and variable ocean.

Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp

The largest known bacteria, Thiomargarita spp., have yet to be isolated in pure culture, but their large size allows for individual cells to be monitored in time course experiments or to be individually sorted for omics-based investigations. Here we investigated the metabolism of individual cells of Thiomargarita spp. by using a novel application of a tetrazolium-based dye that measures oxidoreductase activity. When coupled with microscopy, staining of the cells with a tetrazolium-formazan dye allows metabolic responses in Thiomargarita spp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity of Thiomargarita sp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox dye-based assay suggest that Thiomargarita is the most metabolically versatile under anoxic conditions, where it appears to express cellular oxidoreductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H₂, and H₂S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate and likely acetate, citrate, and H₂S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H₂S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies of Candidatus Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular oxidoreductase response of bacteria attached to the exterior of Thiomargarita also supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts.

The metabolic potential of many microorganisms that cannot be grown in the laboratory is known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolism with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation-independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

Denitrification and dissimilatory reduction to ammonium (DNRA) are competing nitrate-reduction processes that entail important biogeochemical consequences for nitrogen retention/removal in natural and man-made ecosystems. The nature of the available carbon source and electron donor have been suggested to play an important role on the outcome of this microbial competition. In this study, the influence of lactate as fermentable carbon source on the competition for nitrate was investigated for varying ratios of lactate and nitrate in the influent (Lac/N ratio). The study was conducted in an open chemostat culture, enriched from activated sludge, under strict anoxia. The mechanistic explanation of the conversions observed was based on integration of results from specific batch tests with biomass from the chemostat, molecular analysis of the biomass enriched, and a computational model. At high Lac/N ratio (2.97 mol/mol) both fermentative and respiratory nitrate reduction to ammonium occurred, coupled to partial oxidation of lactate to acetate, and to acetate oxidation respectively. Remaining lactate was fermented to propionate and acetate. At a decreased Lac/N ratio (1.15 mol/mol), the molar percentage of nitrate reduced to ammonium decreased to 58%, even though lactate was supplied in adequate amounts for full ammonification and nitrate remained the growth limiting compound. Data evaluation at this Lac/N ratio suggested conversions were comparable to the higher Lac/N ratio, except for lactate oxidation to acetate that was coupled to denitrification instead of ammonification. Respiratory DNRA on acetate was likely catalyzed by two Geobacter species related to G. luticola and G. lovleyi. Two Clostridiales members were likely responsible for lactate fermentation and partial lactate fermentation to acetate coupled to fermentative DNRA. An organism related to Propionivibrio militaris was identified as the organism likely responsible for denitrification. The results of this study clearly show that not only the ratio of available substrates, but also the nature of the electron donor influences the outcome of competition between DNRA and denitrification. Apparently, fermentative bacteria are competitive for the electron donor and thereby alter the ratio of available substrates for nitrate reduction.

Sinks and Sources of Intracellular Nitrate in Gromiids

A substantial nitrate pool is stored within living cells in various benthic marine environments. The fate of this bioavailable nitrogen differs according to the organisms managing the intracellular nitrate (ICN). While some light has been shed on the nitrate carried by diatoms and foraminiferans, no study has so far followed the nitrate kept by gromiids. Gromiids are large protists and their ICN concentration can exceed 1000x the ambient nitrate concentration. In the present study we investigated gromiids from diverse habitats and showed that they contained nitrate at concentrations ranging from 1 to 370 mM. We used ¹⁵N tracer techniques to investigate the source of this ICN, and found that it originated both from active nitrate uptake from the environment and from intracellular production, most likely through bacterial nitrification. Microsensor measurements showed that part of the ICN was denitrified to N₂ when gromiids were exposed to anoxia. Denitrification seemed to be mediated by endobiotic bacteria because antibiotics inhibited denitrification activity. The active uptake of nitrate suggests that ICN plays a role in gromiid physiology and is not merely a consequence of the gromiid hosting a diverse bacterial community. Measurements of aerobic respiration rates and modeling of oxygen consumption by individual gromiid cells suggested that gromiids may occasionally turn anoxic by their own respiration activity and thus need strategies for coping with this self-inflicted anoxia.

Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria

Respiratory ammonification of nitrate is the microbial process that determines the retention of nitrogen in an ecosystem. To date, sulfur-dependent dissimilatory nitrate reduction to ammonium has been demonstrated only with sulfide as an electron donor. We detected a novel pathway that couples the sulfur and nitrogen cycles. Thermophilic anaerobic bacteria Thermosulfurimonas dismutans and Dissulfuribacter thermophilus, isolated from deep-sea hydrothermal vents, grew autotrophically with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. The genomes of both bacteria contain a gene cluster that encodes a putative nitrate ammonification enzyme system. Nitrate reduction occurs via a Nap-type complex. The reduction of produced nitrite to ammonium does not proceed via the canonical Nrf system because nitrite reductase NrfA is absent in the genomes of both microorganisms. The genome of D. thermophilus encodes a complete sulfate reduction pathway, while the Sox sulfur oxidation system is missing, as shown previously for T. dismutans. Thus, in high-temperature environments, nitrate ammonification with elemental sulfur may represent an unrecognized route of primary biomass production. Moreover, the anaerobic oxidation of sulfur compounds coupled to growth has not previously been demonstrated for the members of Thermodesulfobacteria or Deltaproteobacteria, which were considered exclusively as participants of the reductive branch of the sulfur cycle.

Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO₂ fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na⁺-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome.

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism

Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.

Two new Beggiatoa species inhabiting marine mangrove sediments in the Caribbean

Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperate waters, as well as hydrothermal vents, where they form dense mats on the floor. However, they have never been described in tropical marine mangroves. Here, we describe two new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangrove roots. We combined phylogenetic and lipid analysis with electron microscopy in order to describe these organisms. Furthermore, oxygen and sulphide measurements in and ex situ were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as Candidatus Maribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves.

Strong influence of the littoral zone on sedimentary lipid biomarkers in a meromictic lake

Planktonic sulfur bacteria growing in zones of photic zone euxinia (PZE) are important primary producers in stratified, sulfur-rich environments. The potential for export and burial of microbial biomass from anoxic photic zones remains relatively understudied, despite being of fundamental importance to interpreting the geologic record of bulk total organic carbon (TOC) and individual lipid biomarkers. Here we report the relative concentrations and carbon isotope ratios of lipid biomarkers from the water column and sediments of meromictic Mahoney Lake. The data show that organic matter in the central basin sediments is indistinguishable from material at the lake shoreline in both its lipid and carbon isotopic compositions. However, this material is not consistent with either the lipid profile or carbon isotope composition of biomass obtained directly from the region of PZE. Due to the strong density stratification and the intensive carbon and sulfur recycling pathways in the water column, there appears to be minimal direct export of the sulfur-oxidizing planktonic community to depth. The results instead suggest that basinal sediments are sourced via the littoral environment, a system that integrates an indigenous shoreline microbial community, the degraded remains of laterally rafted biomass from the PZE community, and detrital remains of terrigenous higher plants. Material from the lake margins appears to travel downslope, traverse the strong density gradient, and become deposited in the deep basin; its final composition may be largely heterotrophic in origin. This suggests an important role for clastic and/or authigenic minerals in aiding the burial of terrigenous and mat-derived organic matter in euxinic systems. Downslope or mineral-aided transport of anoxygenic, photoautotrophic microbial mats may have been a significant sedimentation process in early Earth history.

Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments

Salt marshes are highly productive ecosystems hosting an intense sulfur (S) cycle, yet little is known about S-oxidizing microorganisms in these ecosystems. Here, we studied the diversity and transcriptional activity of S-oxidizers in salt marsh sediments colonized by the plant Spartina alterniflora, and assessed variations with sediment depth and small-scale compartments within the rhizosphere. We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays. We identified a diverse assemblage of S-oxidizers, with Chromatiales and Thiotrichales being dominant. The detection of transcripts from S-oxidizers was mostly confined to the upper 5 cm sediments, following the expected distribution of root biomass. A common pool of species dominated by Gammaproteobacteria transcribed S-oxidation genes across roots, rhizosphere, and surrounding sediment compartments, with rdsrAB transcripts prevailing over soxB. However, the root environment fine-tuned the abundance and transcriptional activity of the S-oxidizing community. In particular, the global transcription of soxB was higher on the roots compared to mix and rhizosphere samples. Furthermore, the contribution of Epsilonproteobacteria-related S-oxidizers tended to increase on Spartina roots compared to surrounding sediments. These data shed light on the under-studied oxidative part of the sulfur cycle in salt marsh sediments and indicate small-scale heterogeneities are important factors shaping abundance and potential activity of S-oxidizers in the rhizosphere.

Development of HuMiChip for functional profiling of human microbiomes

Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.

Response of the ubiquitous pelagic diatom Thalassiosira weissflogii to darkness and anoxia

Thalassiosira weissflogii, an abundant, nitrate-storing, bloom-forming diatom in the world's oceans, can use its intracellular nitrate pool for dissimilatory nitrate reduction to ammonium (DNRA) after sudden shifts to darkness and anoxia, most likely as a survival mechanism. T. weissflogii cells that stored 4 mM (15)N-nitrate consumed 1.15 (±0.25) fmol NO3 (-) cell(-1) h(-1) and simultaneously produced 1.57 (±0.21) fmol (15)NH4 (+) cell(-1) h(-1) during the first 2 hours of dark/anoxic conditions. Ammonium produced from intracellular nitrate was excreted by the cells, indicating a dissimilatory rather than assimilatory pathway. Nitrite and the greenhouse gas nitrous oxide were produced at rates 2-3 orders of magnitude lower than the ammonium production rate. While DNRA activity was restricted to the first few hours of darkness and anoxia, the subsequent degradation of photopigments took weeks to months, supporting the earlier finding that diatoms resume photosynthesis even after extended exposure to darkness and anoxia. Considering the high global abundance of T. weissflogii, its production of ammonium and nitrous oxide might be of ecological importance for oceanic oxygen minimum zones and the atmosphere, respectively.

Role of diatoms in the spatial-temporal distribution of intracellular nitrate in intertidal sediment

Intracellular nitrate storage allows microorganisms to survive fluctuating nutrient availability and anoxic conditions in aquatic ecosystems. Here we show that diatoms, ubiquitous and highly abundant microalgae, represent major cellular reservoirs of nitrate in an intertidal flat of the German Wadden Sea and are potentially involved in anaerobic nitrate respiration. Intracellular nitrate (ICNO₃) was present year-round in the sediment and was spatially and temporally correlated with fucoxanthin, the marker photopigment of diatoms. Pyrosequencing of SSU rRNA genes of all domains of life confirmed that ICNO₃ storage was most likely due to diatoms rather than other known nitrate-storing microorganisms (i.e., large sulfur bacteria and the eukaryotic foraminifers and gromiids). Sedimentary ICNO₃ concentrations reached up to 22.3 µmol dm^-3 at the sediment surface and decreased with sediment depth to negligible concentrations below 5 cm. Similarly, the ICNO₃/fucoxanthin ratio and porewater nitrate (PWNO₃) concentrations decreased with sediment depth, suggesting that ICNO₃ of diatoms is in equilibrium with PWNO₃, but is enriched relative to PWNO₃ by 2-3 orders of magnitude. Cell-volume-specific ICNO₃ concentrations in a diatom mat covering the sediment surface during spring were estimated at 9.3-46.7 mmol L^-1. Retrieval of 18S rRNA gene sequences related to known nitrate-storing and nitrate-ammonifying diatom species suggested that diatoms in dark and anoxic sediment layers might be involved in anaerobic nitrate respiration. Due to the widespread dominance of diatoms in microphytobenthos, the total nitrate pool in coastal marine sediments may generally be at least two times larger than derived from porewater measurements and partially be recycled to ammonium.

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament

A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria--anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species--in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca-anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Phylogenetic and morphologic complexity of giant sulphur bacteria

The large sulphur bacteria, first discovered in the early nineteenth century, include some of the largest bacteria identified to date. Individual cells are often visible to the unaided eye and can reach 750 μm in diameter. The cells usually feature light-refracting inclusions of elemental sulphur and a large internal aqueous vacuole, which restricts the cytoplasm to the outermost periphery. In some taxa, it has been demonstrated that the vacuole can also serve for the storage of high millimolar concentrations of nitrate. Over the course of the past two centuries, a wide range of morphological variation within the family Beggiatoaceae has been found. However, representatives of this clade are frequently recalcitrant to current standard microbiological techniques, including 16S rRNA gene sequencing and culturing, and a reliable classification of these bacteria is often complicated. Here we present a summary of the efforts made and achievements accomplished in the past years, and give perspectives for investigating the heterogeneity and possible evolutionary developments in this extraordinary group of bacteria.

Macplocimine A, a new 18-membered macrolide isolated from the filamentous sulfur bacteria Thioploca sp

Macplocimine A (1), a rare naturally occurring 18-membered macrolide, was isolated from the marine-derived filamentous sulfur bacteria Thioploca sp. The structure was determined by a combination of spectroscopic techniques, including HRESIMS, 1D and 2D NMR analyses. 1 features a thymine group, which is attached to an aromatic fused 18-membered macrolide ring structure derived from a polyketide synthase biosynthetic pathway.

Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008

Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus sp. strain MCC0008, isolated from a consortium enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of the genome is 5,609,456 bp, with a G+C content of 35.1%.

Why orange Guaymas Basin Beggiatoa spp. are orange: single-filament-genome-enabled identification of an abundant octaheme cytochrome with hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities

Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange Beggiatoa ("Candidatus Maribeggiatoa") filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC-MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.

Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydrothermally altered sediments

We measured potential nitrate removal and denitrification rates in hydrothermally altered sediments inhabited by Beggiatoa mats and adjacent brown oil stained sediments from the Guaymas Basin, Gulf of California. Sediments with Beggiatoa maintained slightly higher rates of potential denitrification than did brown sediments at 31.2 ± 12.1 versus 21.9 ± 1.4 µM N day⁻¹, respectively. In contrast, the nitrate removal rates in brown sediments were higher than those observed in mat-hosting sediments at 418 ± 145 versus 174 ± 74 µM N day⁻¹, respectively. Additional experiments were conducted to assess the responses of denitrifying communities to environmental factors [i.e., nitrate, sulfide, and dissolved organic carbon (DOC) concentration)]. The denitrifying community had a high affinity for nitrate (K_m = 137 ± 91 µM NO3−), in comparison to other environmental communities of denitrifiers, and was capable of high maximum rates of denitrification (V_max = 1164 ± 153 µM N day⁻¹). The presence of sulfide resulted in significantly lower denitrification rates. Microorganisms with the potential to perform denitrification were assessed in these sediments using the bacterial 16S rRNA gene and nitrous oxide reductase (nosZ) functional gene libraries. The bacterial 16S rRNA gene clone library was dominated by Epsilonproteobacteria (38%), some of which (e.g., Sulfurimonas sp.) have a potential for sulfide-dependent denitrification. The nosZ clone library did not contain clones similar to pure culture denitrifiers; these clones were most closely associated with environmental clones.

Chemolithoautotrophic denitrification of epsilonproteobacteria in marine pelagic redox gradients

Pelagic marine oxygen-depleted zones often exhibit a redox gradient, caused by oxygen depletion due to biological demand exceeding ventilation, and the accumulation of reduced chemical species, such as hydrogen sulfide. These redox gradients harbour a distinct assemblage of epsilonproteobacteria capable of fixing carbon dioxide autotrophically in the dark and potentially of utilizing hydrogen sulfide chemolithotrophically by oxidation with nitrate. Together, these two processes are referred to as chemolithoautotrophic denitrification. The focus of this study was the recently isolated and cultivated representative strain of pelagic epsilonproteobacteria, 'Sulfurimonas gotlandica' strain GD1, specifically dark carbon dioxide fixation and its substrate turnovers during chemolithotrophic denitrification. By connecting these processes stoichiometrically and comparing the results with those obtained for dark carbon dioxide fixation and nutrient concentrations measured in pelagic redox gradients of the Baltic Sea, we were able to estimate the role of chemolithoautotrophic denitrification in the environment. Evidence is provided for a defined zone where chemolithoautotrophic denitrification of these epsilonproteobacteria allows the complete removal of nitrate and hydrogen sulfide from the water column. This water layer is roughly equivalent in thickness to the average overlapping region of the two substrates, but slightly larger. Such a difference may be explained by a variety of reasons, including, e.g. utilization of substrates present at concentrations below the detection limit, alternative usage of other substrates as thiosulfate or nitrous oxide, or comparable activities of other microbes. However, the combined results of in vitro and in situ studies strongly suggest that epsilonproteobacteria are primarily responsible for hydrogen sulfide and nitrate removal from pelagic Baltic Sea redox gradients.

Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments

Marine gas and hydrocarbon seeps are hot spots of sulfate reduction which is fuelled by methane, other short-chain alkanes or a complex mixture of hydrocarbons. In this study, we investigated the global distribution and abundance of sulfate-reducing bacteria (SRB) in eight gas and hydrocarbon seeps by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH). The majority of Deltaproteobacteria were assigned to specific SRB groups, i.e. 83 ± 14% at gas seeps and 61 ± 35% at hydrocarbon seeps, indicating that the probe set used was sufficient for classification of marine SRB. Statistical analysis showed that SRB abundance and distribution were significantly influenced by habitat type and sediment depth. Members of the Desulfosarcina/Desulfococcus (DSS) clade strongly dominated all sites. Our data indicated the presence of many diverse and highly specialized DSS species of low abundance rather than a single abundant subgroup. In addition, SEEP-SRB2, an uncultured deep-branching deltaproteobacterial group, was ubiquitously found in high abundances at all sites. SEEP-SRB2 members occurred either in a novel association with methanotrophic archaea in shell-type ANME-2/SEEP-SRB2 consortia, in association with ANME-1 archaea in Black Sea microbial mats or as single cells. Two other uncultured groups, SEEP-SRB3 and SEEP-SRB4, were preferentially detected in surface sediments from mud volcanoes.

Physiological implications of hydrogen sulfide: a whiff exploration that blossomed

The important life-supporting role of hydrogen sulfide (H(2)S) has evolved from bacteria to plants, invertebrates, vertebrates, and finally to mammals. Over the centuries, however, H(2)S had only been known for its toxicity and environmental hazard. Physiological importance of H(2)S has been appreciated for about a decade. It started by the discovery of endogenous H(2)S production in mammalian cells and gained momentum by typifying this gasotransmitter with a variety of physiological functions. The H(2)S-catalyzing enzymes are differentially expressed in cardiovascular, neuronal, immune, renal, respiratory, gastrointestinal, reproductive, liver, and endocrine systems and affect the functions of these systems through the production of H(2)S. The physiological functions of H(2)S are mediated by different molecular targets, such as different ion channels and signaling proteins. Alternations of H(2)S metabolism lead to an array of pathological disturbances in the form of hypertension, atherosclerosis, heart failure, diabetes, cirrhosis, inflammation, sepsis, neurodegenerative disease, erectile dysfunction, and asthma, to name a few. Many new technologies have been developed to detect endogenous H(2)S production, and novel H(2)S-delivery compounds have been invented to aid therapeutic intervention of diseases related to abnormal H(2)S metabolism. While acknowledging the challenges ahead, research on H(2)S physiology and medicine is entering an exponential exploration era.

Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation

Except for several conspicuous cases, very little is known about sulfur oxidizers living in natural freshwater environments. Sulfuricella denitrificans skB26 is a psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a representative of a new genus in the class Betaproteobacteria. In this study, an approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and 3,133 coding sequences were identified. The identified genes include those required for sulfur oxidation, denitrification, and carbon fixation. Comparative proteomic analysis was conducted to assess cold adaptation mechanisms of this organism. From cells grown at 22°C and 5°C, proteins were extracted for analysis by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry. In the cells cultured at 5°C, relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box RNA helicases were increased in comparison to those at 22°C. These results suggest that maintenance of proper translation is critical for growth under low-temperature conditions, similar to the case for other cold-adapted prokaryotes.