Nitrate reduction and the nitrogen cycle in archaea

Nitrogen fixation by methanogenic Archaea, literature review and DNA database-based analysis; significance in face of climate change

Archaea represents a significant population of up to 10% in soil microbial communities. The role of Archaea in soil is often overlooked mainly due to its unculturability. Among the three domains of life biological nitrogen fixation (BNF) is mainly a trait of Eubacteria and some Archaea. Archaea mediated processes like BNF may become even more important in the face of global Climate change. Although there are reports on nitrogen fixation by Archaea, to best of our knowledge there is no comprehensive report on BNF by Archaea under environmental stresses typical to climate change. Here we report a survey of literature and DNA database to study N2-fixation among Archaea. A total of 37 Archaea belonging to Methanogens of the phylum Euryarchaeota within the class Methanococcus, Methanomicrobia Methanobacteria, and Methanotrophic ANME2 lineages either contain genes for BNF or are known to fix atmospheric N2. Archaea were found to have their nif genes arranged as clusters of 6-8 genes in a single operon. The genes code for commonly found Mo-nitrogenase while in some archaea the genes for alternative metal nitrogenases like vnf were also found. The nifHDK gene similarity matrices show that Archaea shared the highest similarity with the nifHDK gene of anaerobic Clostridium beijerinckii. Although there are various theories about the origin of N2-fixation in Archaea, the most acceptable is the origin of N2-fixation first in bacteria and its subsequent transfer to Archaea. Since Archaea can survive under extreme environmental conditions their role in BNF should be studied especially in soil under environmental stress.

The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis

Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories.

IMPORTANCE

Recent studies have revealed that halophilic microorganism is a promising microbial factory for the next-generation industrialization. Among them, halophilic archaea are advantageous as microbial factories due to their low contamination risk and low freshwater consumption. The halophilic archaea usually accumulate long chain C50 carotenoids, which are barely found in other organisms. Bacterioruberin (BR), the major C50 carotenoid, has multi-bioactivities, allowing potential application in food, cosmetic, and biomedical industries. However, the low yield impedes its large-scale application. This work figured out the BR synthesis characteristics and mechanism, and proposed several strategies for BR yield improvement, encouraging halophilic archaea to function as microbial factories for BR production. Meanwhile, the archaea have special evolutionary status and unique characteristics in taxonomy, the revelation of BR biosynthesis mechanism is beneficial for a better understanding of archaea.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations

Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.

Ammonia leakage can underpin nitrogen-sharing among soil microorganisms

Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.

Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert

The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.

Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River

Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.

Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland

Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.

Effects of nitrogen input on soil bacterial community structure and soil nitrogen cycling in the rhizosphere soil of Lycium barbarum L

Lycium barbarum L., goji berry, is a precious traditional Chinese medicine and it is homology of medicine and food. Its growth is heavily dependent on nitrogen. The use of chemical fertilizers has significantly promoted the yield of goji berry and the development of the L. barbarum L. industry. However, crop plants are inefficient in the acquisition and utilization of applied nitrogen, it often leads to excessive application of nitrogen fertilizers by producers, which cause negatively impact to the environment ultimately. The exploration of an interaction model which deals with crops, chemical fertilizers, and rhizosphere microbes to improve nitrogen use efficiency, is, therefore, an important research objective to achieve sustainable development of agriculture greatly. In our study, we explored the effects of nitrogen input on soil microbial community structure, soil nitrogen cycling, and the contents of nutrients in L. barbarum fruits. The structure and composition of the bacterial community in the rhizosphere soil of L. barbarum were significantly different under different nitrogen supply conditions, and high nitrogen addition inhibited the diversity and stability of bacterial communities. Low nitrogen input stimulated the relative abundance of ammonia-oxidizing bacteria (AOB), such as Nitrosospira, catalyzing the first step of the ammonia oxidation process. The results of the GLMM model showed that the level of nitrogen fertilizer (urea) input, the relative abundance of AOB, the relative abundance of Bradyrhizobium, and their combinations had significant effects on the soil nitrogen cycling and contents of nutrients in L. barbarum fruits. Therefore, we believe that moderately reducing the use of urea and other nitrogen fertilizers is more conducive to improving soil nitrogen use efficiency and Goji berry fruit quality by increasing the nitrogen cycling potential of soil microorganisms.

Insight into the shaping of microbial communities in element sulfur-based denitrification at different temperatures

Nitrate pollution is an important cause of eutrophication and ecological disruption. Recently, element sulfur-based denitrification (ESDeN) has attracted increasing attention because of its non-carbon source dependence, low sludge yield, and cost-effectiveness. Although the denitrification performance of sulfur autotrophic denitrifying bacteria at different temperatures has been widely studied, there are still many unknown factors about the adaptability and the shaping of microbial community. In this study, we comprehensively understood the shaping of ESDeN microbial communities under different temperature conditions. Results revealed that microbial communities cultivated at temperatures ranging from 10 °C to 35 °C could be classified as high-temperature (35 °C), middle-temperature (30, 25 and 20 °C), and low-temperature (15 and 10 °C) communities. Dissolved oxygen in water was an important factor that, in combination with temperature, shaped microbial community structure. According to network analysis, the composition of keystone taxa was different for the three groups of communities. Some bacteria that did not have sulfur compound oxidation function were identified as the "keystone species". The abundances of carbon, nitrogen, and sulfur metabolism of the three microbial communities were significantly changed, which was reflected in that the high-temperature and middle-temperature communities were dominated by dark oxidation of sulfur compounds and dark sulfide oxidation, while the low-temperature community was dominated by chemoheterotrophy and aerobic chemoheterotrophy. The fact that the number of microorganisms with dark oxidation of sulfur compounds capacity was quite higher than that of microorganisms with dark sulfur oxidation capacity suggested that the sulfur bioavailability at different temperatures, especially low temperature, was the main challenge for the development of efficient ESDeN process. This study provided a biological basis for developing a high-efficiency ESDeN process to cope with temperature changes in different seasons or regions.

Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment

Research focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. While several studies have focused on understanding the fundamental ecology of these springs, the small molecule profiles of thermoalkaline springs have largely been overlooked. To better understand how geochemistry, small molecule composition, and microbial communities are connected, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry-based metabolite and extracellular small molecule characterization. Integration of the four datasets facilitated a comprehensive analysis of the interwoven thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen- and sulfur-containing extracellular small molecules and fluctuations in metabolic pathways associated with nitrogen cycling. This multi-factorial analysis demonstrates that the microbial community composition is more closely correlated with pools of extracellular small molecules than with the geochemistry of the thermal springs. This is a novel finding and suggests that a previously overlooked component of thermal springs may have a significant impact on microbial community composition.

Archaea from the gut microbiota of humans: Could be linked to chronic diseases?

Archaea comprise a unique domain of organisms with distinct biochemical and genetic differences from bacteria. Methane-forming archaea, methanogens, constitute the predominant group of archaea in the human gut microbiota, with Methanobrevibacter smithii being the most prevalent. However, the effect of methanogenic archaea and their methane production on chronic disease remains controversial. As perturbation of the microbiota is a feature of chronic conditions, such as cardiovascular disease, neurodegenerative diseases and chronic kidney disease, assessing the influence of archaea could provide a new clue to mitigating adverse effects associated with dysbiosis. In this review, we will discuss the putative role of archaea in the gut microbiota in humans and the possible link to chronic diseases.

Effects of microplastics on greenhouse gas emissions and microbial communities in sediment of freshwater systems

Microplastics can regulate greenhouse gas emissions from environmental systems and affect microbes in the environment. However, the effect of microplastics in freshwater sediment system is still not well studied. In this paper, polyethylene terephthalate (PET) particles with six different diameters of 5-2000 µm were added to freshwater sediment, PET exposing for 90 days was carried out and its effect on greenhouse gas emissions, nutrients cycle and microbial communities were studied. In the 5 µm experimental group, carbon dioxide (CO₂) emissions were significantly promoted in the 7-30 days and nitrogen monoxide (N₂O) emissions were significantly promoted in the 7 days after cultivation. Microplastics in the range of 300-800 µm significantly promoted CO₂ emissions after three days of culture. In addition, microplastics increased the total organic carbon (TOC) content in freshwater sediment and changed microbial diversity, especially increased the microorganisms capable of degrading complex organics such as Saprospiraceae. There was a positive correlation between N₂O emission and nitrate (NO₃^-) content in sediment after 3 days of culture, while greenhouse gas emission was mainly related to TOC content after 90 days of culture. These results showed that microplastics could affect the carbon and nitrogen cycling process of shallow lake ecosystem.

Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China

A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2-) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.

Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments

This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs.

IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.

Anaerobic degradation of benzene and other aromatic hydrocarbons in a tar-derived plume: Nitrate versus iron reducing conditions

The anaerobic degradation of aromatic hydrocarbons in a plume originating from a Pintsch gas tar-DNAPL zone was investigated using molecular, isotopic- and microbial analyses. Benzene concentrations diminished at the relatively small meter scale dimensions of the nitrate reducing plume fringe. The ratio of benzene to toluene, ethylbenzene, xylenes and naphthalene (BTEXN) in the fringe zone compared to the plume zone, indicated relatively more loss of benzene in the fringe zone than TEXN. This was substantiated by changes in relative concentrations of BTEXN, and multi-element compound specific isotope analysis for δ²H and δ¹³C. This was supported by the presence of (abcA) genes, indicating the presumed benzene carboxylase enzyme in the nitrate-reducing plume fringe. Biodegradation of most hydrocarbon contaminants at iron reducing conditions in the plume core, appears to be quantitatively of greater significance due to the large volume of the plume core, rather than relatively faster biodegradation under nitrate reducing conditions at the smaller volume of the plume fringe. Contaminant concentration reductions by biodegradation processes were shown to vary distinctively between the source, plume (both iron-reducing) and fringe (nitrate-reducing) zones of the plume. High anaerobic microbial activity was detected in the plume zone as well as in the dense non aqueous phase liquid (DNAPL) containing source zone. Biodegradation of most, if not all, other water-soluble Pintsch gas tar aromatic hydrocarbon contaminants occur at the relatively large dimensions of the anoxic plume core. The highest diversity and concentrations of metabolites were detected in the iron-reducing plume core, where the sum of parent compounds of aromatic hydrocarbons was greater than 10 mg/L. The relatively high concentrations of metabolites suggest a hot spot for anaerobic degradation in the core of the plume downgradient but relatively close to the DNAPL containing source zone.

Pathways of soil N2O uptake, consumption, and its driving factors: a review

Nitrous oxide (N₂O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N₂O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N₂O uptake and consumption. N₂O emissions at the soil surface are the result of gross N₂O production, uptake, and consumption, which are co-occurring processes. Soil N₂O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N₂O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N₂O uptake and consumption and their driving factors and measurement techniques. This systematic review of N₂O uptake and consumption will help to further understand N transformations and soil N₂O emissions.

Spotlight on FtsZ-based cell division in Archaea

Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.

Effects of 3,6-dichlorocarbazole on microbial ecology and its degradation in soil

The emerging contaminants polyhalogenated carbazoles (PHCZs) have been verified to be present in soils and sediments globally, and they show dioxin-like toxicity. However, there is a lack of soil ecological risk assessments on PHCZs despite their high detection rate and concentration in soils. The present study investigated the degradation and soil microbial influence of 3,6-dichlorocarbazole (3,6-DCCZ, a frequently detected PHCZ) in soil. The results showed that the half-lives of 3,6-DCCZ at concentrations of 0.100 mg/kg and 1.00 mg/kg were 7.75 d and 16.73 d, respectively. We found that 3,6-DCCZ was transformed into 3-chlorocarbazole (3-CCZ) by dehalogenation in soil. Additionally, intermediate products with higher molecular weights were detected, presumably because the -H on the carbazole ring was replaced by -CH₃, -CH₂-O-CH₃, or -CH₂-O-CH₂CH₃. 3,6-DCCZ exposure slightly increased the soil bacterial abundance and diversity and clearly changed the soil bacterial community structure. Through a comprehensive analysis of FAPROTAX, functional gene qPCR and soil enzyme tests, we concluded that 3,6-DCCZ exposure inhibited nitrification and nitrogen fixation but promoted denitrification, carbon dioxide fixation and hydrocarbon degradation processes in soil. This study provides valuable data for clarifying the PHCZ ecological risk in soil.

Genomic features underlying the evolutionary transitions of Apibacter to honey bee gut symbionts

The gut bacteria of honey bee recognized as a mutualistic partner with the insect host might have originated from a free-living or parasitic lifestyle. However, little is known about the genomic features underlying this lifestyle transition. Here we compared the genomes of bee gut bacteria Apibacter with their close relatives living in different lifestyles. We found that despite general reduction in the Apibacter genome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which is putatively beneficial to the host. Interestingly, the microaerobic Apibacter species specifically acquired genes encoding for the nitrate respiration (NAR). These together with nitrate transporter and enzymatic cofactor synthesis genes were found clustered in the genomes. The NAR system is also conserved in the cohabitating bee gut microbe Snodgrassella, although with a different structure. This convergence suggests a key role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation were found partially or completely lost in Apibacter. Particularly, genes encoding for the conversion to the toxic intermediates in phenylacetate degradation, as well as other potential virulence factors, are specifically lost in Apibacter group. Antibiotic resistance genes are only sporadically distributed among Apibacter species, but are prevalent in their relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advanced our knowledge of genomic features specialized to bee gut symbionts.

Nitric oxide-secreting probiotics as sustainable bio-cleaners for reverse osmosis membrane systems

Membrane biofouling in water purification plants is a serious issue of worldwide concern. Various chemical, physical, and biochemical processes are practised for membrane clean-up. A high-dosage treatment adversely affects the life expectancy of the membrane, and minimum dosage seems unable to deteriorate the biofilms on the membrane. It is reported that quorum quenchers like nitric oxide (NO) disrupt biofilm signals through metabolic rewiring, and also NO is known to be secreted by probiotics (good bacteria). In the present review, it is hypothesized that if probiotic biofilms secreting NO are used, other microbes that aggregate on the filtration membrane could be mitigated. The concept of probiotic administration on filtration membrane seeks to be encouraged because probiotic bacteria will not be hazardous, even if released during filtration. The fundamental motive to present probiotics as a resource for sequestering NO may serve as multifunctional bioweapons for membrane remediation, which will virtually guarantee their long-term sustainability and green approach.

Evolution of Thermophilic Microbial Communities from a Deep-Sea Hydrothermal Chimney under Electrolithoautotrophic Conditions with Nitrate

Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on electrotrophic enrichment with nitrate as electron acceptor. The biofilm density, community composition, production of organic compounds, and electrical consumption were monitored by FISH confocal microscopy, qPCR, metabarcoding, NMR, and potentiostat measurements. A statistical analysis by PCA showed the correlation between the different parameters (qPCR, organic compounds, and electron acceptors) in three distinct temporal phases. In our conditions, the Archaeoglobales have been shown to play a key role in the development of the community as the first colonizers on the cathode and the first producers of organic compounds, which are then used as an organic source by heterotrophs. Finally, through subcultures of the community, we showed the development of a greater biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal contexts, where energy sources are transient and unstable.

Identification of Natural and Anthropogenic Geochemical Processes Determining the Groundwater Quality in Port del Comte High Mountain Karst Aquifer (SE, Pyrenees)

The Port del Comte Massif (SE, Pyrenees) contains one of the most important vulnerable and strategic karst aquifers for supplying freshwater to the city of Barcelona (Spain). It is a fragile system, whose possible environmental impact is highly conditioned by land use. To improve the hydrogeological knowledge of the system, between September 2013 and October 2015, a detailed fieldwork was carried out for the revision of the geological model, the inventory of water points, and the in situ physico-chemical characterization on major elements and isotopes of up to a total of 43 springs, as well as precipitation water. This paper focuses on the characterization of the geochemical processes that allow explanation of the observed chemical variability of groundwater drained by the pristine aquifer system to determine the origin of salinity. The results show that the main process is the dissolution of calcite and dolomite, followed by gypsum and halite, and a minor cation exchange-like process. Sulfur and oxygen isotopes from dissolved sulfate in the studied springs point out a geogenic origin related to the dissolution of gypsum from Triassic and Tertiary materials, and that the contribution from anthropogenic sources, like fertilizers, is lower. Nitrate in groundwater is not an important issue, with a few localized cases related with agricultural activities. The multidisciplinary approach has allowed the development of a consistent hydrogeological conceptual model of the functioning of the aquifer system, which can be replicated in other places to understand the geogenic character of the hydrogeochemistry.

Complete genome sequence of a nitrate reducing bacteria, Algoriphagus sp. Y33 isolated from the water of the Indian Ocean

Algoriphagus sp. Y33, is a nitrate-reducing bacterium isolated from the water of Indian Ocean. Here, we present the complete genome sequence of strain Y33. The genome has one circular chromosome of 6,378,979 bp, with an average GC content of 41.86%, and 5757 coding sequences. According to the annotation analysis, strain Y33 encodes 32 proteins related to nitrogen metabolism. To our knowledge, this is the first report of Algoriphagus sp. isolated from the Indian Ocean with the capacity of nitrate reduction, which will provide insights into regulatory mechanisms of nitrate uptake by heterotrophic bacteria and the global nitrogen cycling.

Metagenomic analysis revealed the sulfur- and iron- oxidation capabilities of heterotrophic denitrifying sludge

Heterotrophic denitrification is widely applied in wastewater treatment processes to remove nitrate. However, the ability of the heterotrophic denitrifying sludge to use inorganic matter as electron donors to perform autotrophic denitrification has rarely been investigated. In this study, we enriched heterotrophic denitrifying sludge and demonstrated its sulfur- and iron- oxidizing abilities and denitrification performance with batch experiments. Based on high-throughput sequencing of 16S rRNA genes, high diversity and abundance of sulfur-oxidizing bacteria (SOB) (e.g., Sulfuritalea, Thiobacillus, and Thiothrix) and iron (II)-oxidizing bacteria (FeOB) (e.g., Azospira and Thiobacillus) were observed. Metagenomic sequencing and genome binning results further suggested that the SOB in the heterotrophic denitrifying sludge were mainly Alphaproteobacteria and Betaproteobacteria instead of Gammaproteobacteria and Epsilonproteobacteria. The similarities of potential iron-oxidizing genes with known sequences were very low (32-51%), indicating potentially novel FeOB species in this system. The findings of this study suggested that the heterotrophic denitrifying sludge harbors diverse mixotrophic denitrifying bacterial species, and based on this finding, we proposed that organic carbon and inorganic electron donors (e.g., sulfur, thiosulfate, and iron) could be jointly used in engineering practices according to the quality and quantity of wastewater to balance the cost and efficiency of the denitrification process.

Inhibited Methanogenesis in the Rumen of Cattle: Microbial Metabolism in Response to Supplemental 3-Nitrooxypropanol and Nitrate

3-Nitrooxypropanol (3-NOP) supplementation to cattle diets mitigates enteric CH₄ emissions and may also be economically beneficial at farm level. However, the wider rumen metabolic response to methanogenic inhibition by 3-NOP and the NO2- intermediary metabolite requires further exploration. Furthermore, NO3- supplementation potently decreases CH₄ emissions from cattle. The reduction of NO3- utilizes H₂ and yields NO2-, the latter of which may also inhibit rumen methanogens, although a different mode of action than for 3-NOP and its NO2- derivative was hypothesized. Our objective was to explore potential responses of the fermentative and methanogenic metabolism in the rumen to 3-NOP, NO3- and their metabolic derivatives using a dynamic mechanistic modeling approach. An extant mechanistic rumen fermentation model with state variables for carbohydrate substrates, bacteria and protozoa, gaseous and dissolved fermentation end products and methanogens was extended with a state variable of either 3-NOP or NO3-. Both new models were further extended with a NO2- state variable, with NO2- exerting methanogenic inhibition, although the modes of action of 3-NOP-derived and NO3--derived NO2- are different. Feed composition and intake rate (twice daily feeding regime), and supplement inclusion were used as model inputs. Model parameters were estimated to experimental data collected from the literature. The extended 3-NOP and NO3- models both predicted a marked peak in H₂ emission shortly after feeding, the magnitude of which increased with higher doses of supplement inclusion. The H₂ emission rate appeared positively related to decreased acetate proportions and increased propionate and butyrate proportions. A decreased CH₄ emission rate was associated with 3-NOP and NO3- supplementation. Omission of the NO2- state variable from the 3-NOP model did not change the overall dynamics of H₂ and CH₄ emission and other metabolites. However, omitting the NO2- state variable from the NO3- model did substantially change the dynamics of H₂ and CH₄ emissions indicated by a decrease in both H₂ and CH₄ emission after feeding. Simulations do not point to a strong relationship between methanogenic inhibition and the rate of NO3- and NO2- formation upon 3-NOP supplementation, whereas the metabolic response to NO3- supplementation may largely depend on methanogenic inhibition by NO2-.

Deep Soil Layers of Drought-Exposed Forests Harbor Poorly Known Bacterial and Fungal Communities

Soil microorganisms such as bacteria and fungi play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of the soil microbiome to a depth of 2 m in Swiss drought-exposed forests of European beech and oaks on calcareous bedrock. We aimed to disentangle the effects of soil depth, tree (beech, oak), and substrate (soil, roots) on microbial abundance, diversity, and community structure. With increasing soil depth, organic carbon, nitrogen, and clay content decreased significantly. Similarly, fine root biomass, microbial biomass (DNA content, fungal abundance), and microbial alpha-diversity decreased and were consequently significantly related to these physicochemical parameters. In contrast, bacterial abundance tended to increase with soil depth, and the bacteria to fungi ratio increased significantly with greater depth. Tree species was only significantly related to the fungal Shannon index but not to the bacterial Shannon index. Microbial community analyses revealed that bacterial and fungal communities varied significantly across the soil layers, more strongly for bacteria than for fungi. Both communities were also significantly affected by tree species and substrate. In deep soil layers, poorly known bacterial taxa from Nitrospirae, Chloroflexi, Rokubacteria, Gemmatimonadetes, Firmicutes and GAL 15 were overrepresented. Furthermore, archaeal phyla such as Thaumarchaeota and Euryarchaeota were more abundant in subsoils than topsoils. Fungal taxa that were predominantly found in deep soil layers belong to the ectomycorrhizal Boletus luridus and Hydnum vesterholtii. Both taxa are reported for the first time in such deep soil layers. Saprotrophic fungal taxa predominantly recorded in deep soil layers were unknown species of Xylaria. Finally, our results show that the microbial community structure found in fine roots was well represented in the bulk soil. Overall, we recorded poorly known bacterial and archaeal phyla, as well as ectomycorrhizal fungi that were not previously known to colonize deep soil layers. Our study contributes to an integrated perspective on the vertical distribution of the soil microbiome at a fine spatial scale in drought-exposed forests.

Towards the Elucidation of Assimilative nasABC Operon Transcriptional Regulation in Haloferax mediterranei

The assimilatory pathway of the nitrogen cycle in the haloarchaeon Haloferax mediterranei has been well described and characterized in previous studies. However, the regulatory mechanisms involved in the gene expression of this pathway remain unknown in haloarchaea. This work focuses on elucidating the regulation at the transcriptional level of the assimilative nasABC operon (HFX_2002 to HFX_2004) through different approaches. Characterization of its promoter region using β-galactosidase as a reporter gene and site-directed mutagenesis has allowed us to identify possible candidate binding regions for a transcriptional factor. The identification of a potential transcriptional regulator related to nitrogen metabolism has become a real challenge due to the lack of information on haloarchaea. The investigation of protein–DNA binding by streptavidin bead pull-down analysis combined with mass spectrometry resulted in the in vitro identification of a transcriptional regulator belonging to the Lrp/AsnC family, which binds to the nasABC operon promoter (p.nasABC). To our knowledge, this study is the first report to suggest the AsnC transcriptional regulator as a powerful candidate to play a regulatory role in nasABC gene expression in Hfx. mediterranei and, in general, in the assimilatory nitrogen pathway.

Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases

Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (¹⁴N, ¹⁵N) and oxygen (¹⁶O, ¹⁸O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (¹⁸ε/¹⁵ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the ¹⁸ε/¹⁵ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of ¹⁸ε/¹⁵ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an ¹⁸ε/¹⁵ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in ¹⁸ε/¹⁵ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar ¹⁸ε/¹⁵ε signatures.

Nitrate-responsive suppression of DMSO respiration in a facultative anaerobic haloarchaeon Haloferax volcanii

Haloferax volcanii is a facultative anaerobic haloarchaeon that can grow using nitrate or dimethyl sulfoxide (DMSO) as respiratory substrates in an anaerobic condition. Comparative transcriptome analysis of denitrifying and aerobic cells of H. volcanii indicated extensive changes in the gene expression involving activation of denitrification, suppression of DMSO respiration, and conversion of the heme biosynthetic pathway under denitrifying condition. Anaerobic growth of H. volcanii by DMSO respiration was inhibited at nitrate concentrations lower than 1 mM, whereas the nitrate-responsive growth inhibition was not observed in the ΔnarO mutant. A reporter assay experiment demonstrated that transcription of the dms operon was suppressed by nitrate. In contrast, anaerobic growth of the ΔdmsR mutant by denitrification was little affected by addition of DMSO. NarO has been identified as an activator of the denitrification-related genes in response to anaerobic conditions, and here we found that NarO is also involved in nitrate-responsive suppression of the dms operon. Nitrate-responsive suppression of DMSO respiration is known in several bacteria, such as Escherichia coli and photosynthetic Rhodobacter sp. This is the first report to show that a regulatory mechanism that suppresses DMSO respiration in response to nitrate exists not only in bacteria but also in the haloarchaea.IMPORTANCE Haloferax volcanii can grow anaerobically by denitrification (nitrate respiration) or DMSO respiration. In the facultative anaerobic bacteria that can grow by both nitrate respiration and DMSO respiration, nitrate respiration is preferentially induced when both nitrate and DMSO are available as respiratory substrates. The results of transcriptome analysis, growth phenotyping, and reporter assay indicated that DMSO respiration is suppressed in response to nitrate in H. volcanii The haloarchaea-specific regulator NarO, which activates denitrification under anaerobic conditions, is suggested to be involved in the nitrate-responsive suppression of DMSO respiration.

Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea

The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.

Nitrate Is Crucial for the Proliferation of Gut Escherichia coli Caused by H9N2 AIV Infection and Effective Regulation by Chinese Herbal Medicine Ageratum-Liquid

H9N2 avian influenza virus (AIV) infection in chickens is often accompanied by secondary bacterial infection, but the mechanism is unclear. The aim of the present study was to reveal that mechanism and explore non-antibiotic treatment. 16s rRNA sequencing and metabonomics were performed in the intestinal contents of chickens infected with H9N2 AIV or H9N2 AIV and fed with ageratum-liquid (AL) to reveal the metabolite that promote intestinal Escherichia coli (E. coli) proliferation caused by H9N2 AIV, as well as to determine the regulatory effect of AL. It was found that H9N2 AIV infection led E. coli to become the dominant gut microbe and promoted E. coli translocation from the intestinal tract to the visceral tissue through the damaged intestinal barrier. H9N2 AIV infection induces inflammation in the intestinal mucosa and promotes the secretion and release of nitrate from the host intestinal epithelium. In addition, nitrate promoted E. coli proliferation in the inflamed intestinal tract following H9N2 AIV infection. Furthermore, Chinese herbal medicine AL can restore intestinal homeostasis, inhibit the production of nitrate in the intestinal epithelium and effectively prevent the proliferation and translocation of E. coli in the intestines. This is the first report on the mechanism of E. coli secondary infection induced by H9N2 AIV, where herbal medicine AL was shown to have a good preventive effect on the secondary infection.

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (K_D) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [K_D (Mo) 27.0 nM, K_D (W) 26.7 nM] and E. coli K12[(K_D (Mo) 25.0 nM, K_D (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.

Archaea, tiny helpers of land plants

Archaea are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome. Only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. This review discusses recent progress in identifying how archaea contribute to plant traits such as growth, adaptation to abiotic stresses, and immune activation. We synthesized the most recent functional and molecular data on archaea, including root colonization and the volatile emission to activate plant systemic immunity. These data represent a paradigm shift in our understanding of plant-microbiota interactions.

Transcriptomic Analysis of Staphylococcus aureus Under the Stress Condition Caused by Litsea cubeba L. Essential Oil via RNA Sequencing

Litsea cubeba L. essential oil (LCEO) is a natural essential oil with considerable antimicrobial activity, and it can gradually replace some chemical additives in the food industry. However, the genetic evidences of stress response of bacteria under sub-lethal treatment with LCEO is limited. To this end, transcriptomic analysis of Staphylococcus aureus 29213 under a low concentration of LCEO was performed. Bacterial RNA samples were extracted from 1/4 MIC (0.07 μL/mL) of LCEO-treated and non-treated S. aureus 29213. The transcriptional results were obtained by RNA sequencing (RNA-Seq). After treated with LCEO of S. aureus 29213, 300, and 242 genes were significantly up and down-regulated. Up-regulated genes were mainly related to cell membrane (wall) stress stimulon including genes related to two-component regulatory system (VraS), histidine metabolism (hisABCD etc.) and L-lysine biosynthesis (thrA, lysC, asd etc.). Significant differences were also founded between LCEO-treated and non-treated groups in peptidoglycan biosynthesis related pathways. Down-regulated genes were related to nitrogen metabolism (NarGHIJ etc.), carotenoid biosynthesis (all) and pyruvate metabolism (phdA, pflB, pdhC etc.) of S. aureus 29213 in an LCEO-existing environment compared to the control. At the same time, we confirmed that LCEO can significantly affect the staphyloxanthin level of S. aureus 29213 for the first time, which is closely related to the redox state of S. aureus 29213. These evidences expanded the knowledge of stress response of S. aureus 29213 strain under sub-lethal concentration of LCEO.

The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks

The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.

Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant

The Seine-Morée wastewater treatment plant (SM_WWTP), with a capacity of 100,000 population-equivalents, was fed with raw domestic wastewater during all of its start-up phase. Its microbiome resulted from the spontaneous evolution of wastewater-borne microorganisms. This rare opportunity allowed us to analyze the sequential microbiota colonization and implantation follow up during the start-up phase of this WWTP by means of regular sampling carried out over 8 months until the establishment of a stable and functional ecosystem. During the study, biological nitrification–denitrification and dephosphatation occurred 68 days after the start-up of the WWTP, followed by flocs decantation 91 days later. High throughput sequencing of 18S and 16S rRNA genes was performed using Illumina's MiSeq and PGM Ion Torrent platforms respectively, generating 584,647 16S and 521,031 18S high-quality sequence rDNA reads. Analyses of 16S and 18S rDNA datasets show three colonization phases occurring concomitantly with nitrification, dephosphatation and floc development processes. Thus, we could define three microbiota profiles that sequentially colonized the SM_WWTP: the early colonizers, the late colonizers and the continuous spectrum population. Shannon and inverse Simpson diversity indices indicate that the highest microbiota diversity was reached at days 133 and 82 for prokaryotes and eukaryotes respectively; after that, the structure and complexity of the wastewater microbiome reached its functional stability. This study demonstrates that physicochemical parameters and microbial metabolic interactions are the main forces shaping microbial community structure, gradually building up and maintaining a functionally stable microbial ecosystem.

Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO₂ fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H⁺/Na⁺ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'

Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum

The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001-0.005 fmol%) proteins for polypeptides' hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures.

Responses of Methanosarcina barkeri to acetate stress

BACKGROUND

Anaerobic digestion of easily degradable biowaste can lead to the accumulation of volatile fatty acids, which will cause environmental stress to the sensitive methanogens consequently. The metabolic characteristics of methanogens under acetate stress can affect the overall performance of mixed consortia. Nevertheless, there exist huge gaps in understanding the responses of the dominant methanogens to the stress, e.g., Methanosarcinaceae. Such methanogens are resistant to environmental deterioration and able to utilize multiple carbon sources. In this study, transcriptomic and proteomic analyses were conducted to explore the responses of Methanosarcina barkeri strain MS at different acetate concentrations of 10, 25, and 50 mM.

RESULTS

The trend of OD600 and the regulation of the specific genes in 50 mM acetate, indicated that high concentration of acetate promoted the acclimation of M. barkeri to acetate stress. Acetate stress hindered the regulation of quorum sensing and thereby eliminated the advantages of cell aggregation, which was beneficial to resist stress. Under acetate stress, M. barkeri allocated more resources to enhance the uptake of iron to maintain the integrities of electron-transport chains and other essential biological processes. Comparing with the initial stages of different acetate concentrations, most of the genes participating in acetoclastic methanogenesis did not show significantly different expressions except hdrB1C1, an electron-bifurcating heterodisulfide reductase participating in energy conversion and improving thermodynamic efficiency. Meanwhile, vnfDGHK and nifDHK participating in nitrogen fixation pathway were upregulated.

CONCLUSION

In this work, transcriptomic and proteomic analyses are combined to reveal the responses of M. barkeri to acetate stress in terms of central metabolic pathways, which provides basic clues for exploring the responses of other specific methanogens under high organics load. Moreover, the results can also be used to gain insights into the complex interactions and geochemical cycles among natural or engineered populations. Furthermore, these findings also provide the potential for designing effective and robust anaerobic digesters with high organic loads.

Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes

Nitrogen (N) fertilization in agricultural soils has been receiving worldwide attention due to its detrimental effects on ecosystem services, particularly on microbial N transformation. However, few studies provide a complete picture of N-fertilization effects on the N transformation cycle within a single agricultural ecosystem. Here, we explored the main steps of the microbial N cycle, using targeted gene abundances as proxies, in relation to soil properties, following 35 years of N-fertilization at increasing rates (0, 202 and 269 kg N/ha) in continuous corn (Zea mays L.) and corn-soybean [Glycine max (L.) Merr.] rotations. We used real-time quantitative polymerase chain reaction (qPCR) for the quantification of phylogenetic groups and functional gene screening of the soil microbial communities, including genes encoding critical enzymes of the microbial N cycle: nifH (N₂ fixation), amoA (first step of nitrification), nirK and nirS (first step of denitrification), and nosZ (last step of denitrification). Our results showed that long term N-fertilization increased the abundance of fungal communities likely related to decreases in pH, and an enrichment of Al³⁺ and Fe³⁺ in exchange sites at the expense of critical macro and micronutrients. At the same time, long term N-fertilization damaged potential biological N₂ fixation by significantly reducing the abundance of nifH genes in both continuous and rotated corn systems, while accelerating potential nitrification activities under continuous corn by increasing the abundance of bacterial amoA. Fertilization did not affect the abundance of denitrifying groups. Altogether, these results suggest that N fertilization in corn crops potentially decreases N₂ acquisition by free-living soil microbes and stimulates nitrification activities, thus creating a vicious loop that makes the overall agricultural system even more dependent on external N inputs.

Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses

Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.

Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater

With the increase in industrial and agricultural activities, a large amount of nitrogenous compounds are released into the environment, leading to nitrate pollution. The perilous effects of nitrate present in the environment pose a major threat to human and animal health. Bioremediation provides a cost-effective and environmental friendly method to deal with this problem. The process of aerobic denitrification can reduce nitrate compounds to harmless dinitrogen gas. This review provides a brief view of the exhaustive role played by aerobic denitrifiers for tackling nitrate pollution under different ecological niches and their dependency on various environmental parameters. It also provides an understanding of the enzymes involved in aerobic denitrification. The role of aerobic denitrification to solve the issues faced by the conventional method (aerobic nitrification-anaerobic denitrification) in treating nitrogen-polluted wastewaters is elaborated.

Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity

The persistent and undiscriminating application of chemicals as means to improve crop growth, development and yields for several years has become problematic to agricultural sustainability because of the adverse effects these chemicals have on the produce, consumers and beneficial microbes in the ecosystem. Therefore, for agricultural productivity to be sustained there are needs for better and suitable preferences which would be friendly to the ecosystem. The use of microbial metabolites has become an attractive and more feasible preference because they are versatile, degradable and ecofriendly, unlike chemicals. In order to achieve this aim, it is then imperative to explore microbes that are very close to the root of a plant, especially where they are more concentrated and have efficient activities called the rhizosphere. Extensive varieties of bacteria, archaea, fungi and other microbes are found inhabiting the rhizosphere with various interactions with the plant host. Therefore, this review explores various beneficial microbes such as bacteria, fungi and archaea and their roles in the environment in terms of acquisition of nutrients for plants for the purposes of plant growth and health. It also discusses the effect of root exudate on the rhizosphere microbiome and compares the three domains at molecular levels.

The Structure and Species Co-Occurrence Networks of Soil Denitrifying Bacterial Communities Differ Between A Coniferous and A Broadleaved Forests

Acacia mangium (AM) and Pinus massoniana (PM) are widely planted in tropical regions, whereas their effects on soil microbial communities remain unclear. We did a comprehensive investigation of soil denitrifying bacterial communities in AM and PM monoculture plantations in Southern China based on the high throughput sequencing data of their functional genes: nirK, nirS, and nosZ. The average abundance of nosZ (1.3 × 10⁷) was significantly higher than nirS (5.6 × 10⁶) and nirK (4.9 × 10⁵). Shannon estimator revealed a markedly higher α-diversity of nirS and nosZ communities in PM than in AM plantations. The AM and PM plantations were dominated by different nirS and nosZ taxa belonging to proteobacteria, actinobacteria, thermoleophilia, chloroflexia, and acidobacteria, while the dominant nirK taxa were mainly categorized into proteobacteria in both types of plantations. The structure of nirS and nosZ communities shifted substantially from AM to PM plantations with changes in soil moisture, NH₄⁺, and microbial biomass nitrogen content. The species co-occurrence network of nirK community was better organized in a more modular manner compared to nirS and nosZ communities, and the network keystone species mostly occurred in PM plantations. These results indicated a highly species corporation of nirK community in response to environmental changes, especially in PM plantations. AM and PM plantations can form different soil denitrifying microbial communities via altering soil physicochemical properties, which may further affect soil N transformations.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.

Microbial Community Structures and Important Associations Between Soil Nutrients and the Responses of Specific Taxa to Rice-Frog Cultivation

Rice-frog cultivation is a traditional farming system in China and has been reintroduced as an agricultural practice in China in recent years. The microbial community in paddy rhizospheric soils has attracted much attention because many microorganisms participate in functional processes in soils. In this study, Illumina MiSeq sequencing-based techniques were used to investigate soil microbial communities and functional gene patterns across samples obtained by conventional rice cultivation (CR) and rice-frog cultivation (RF). The results showed that RF significantly affected the microbial community composition and richness, which indicated that the rhizospheric microorganisms responded to the introduction of tiger frogs into the paddy fields. Operational taxonomic units (OTUs) from Sandaracinaceae, Anaerolineaceae, Candidatus Nitrososphaera, Candidatus Nitrosotalea, Candidatus Nitrosoarchaeum and some unclassified OTUs from Euryarchaeota and Agaricomycetes were significantly enriched by RF. The abiotic parameters soil organic carbon (SOC), nitrate nitrogen (NO3 --N), and available phosphorus (AP) changed under RF treatment and played essential roles in establishing the soil bacterial, archaeal, and fungal compositions. Correlations between environmental factors and microbial communities were described using network analysis. SOC was strongly correlated with Anaerolineaceae, Methanosaeta, and Scutellinia. NO3 --N showed strong positive correlations with Opitutus, Geobacter, and Methanosaeta. NH4 ++-N was strongly positively associated with Sideroxydans, and TN was strongly positively correlated with Candidatus Nitrotoga. Compared to conventional CR, RF greatly enriched specific microbial taxa. These taxa may be involved in the decomposition of complex organic matter and the transformation of soil nutrients, thus promoting plant growth by improving nutrient cycling. The unique patterns of microbial taxonomic and functional composition in soil profiles suggested functional redundancy in these paddy soils. RF could significantly affect the bacterial, archaeal, and fungal communities though changing SOC and AP levels.

DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.