Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Proteomic response of the marine ammonia-oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity

Dissolved iron (Fe) is vanishingly low in the oceans, with ecological success conferred to microorganisms that can restructure their biochemistry to maintain high growth rates during Fe scarcity. Chemolithoautotrophic ammonia-oxidising archaea (AOA) are highly abundant in the oceans, constituting ~30% of cells below the photic zone. Here we examine the proteomic response of the AOA isolate Nitrosopumilus maritimus to growth-limiting Fe concentrations. Under Fe limitation, we observed a significant reduction in the intensity of Fe-dense ferredoxins associated with respiratory complex I whilst complex III and IV proteins with more central roles in the electron transport chain remain unchanged. We concomitantly observed an increase in the intensity of Fe-free functional alternatives such as flavodoxin and plastocyanin, thioredoxin and alkyl hydroperoxide which are known to mediate electron transport and reactive oxygen species detoxification, respectively. Under Fe limitation, we found a marked increase in the intensity of the ABC phosphonate transport system (Phn), highlighting an intriguing link between Fe and P cycling in N. maritimus. We hypothesise that an elevated uptake of exogenous phosphonates under Fe limitation may either supplement N. maritimus' endogenous methylphosphonate biosynthesis pathway - which requires Fe - or enhance the production of phosphonate-containing exopolysaccharides known to efficiently bind environmental Fe.

Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches

Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.

Induced fusion and aggregation of bacterial outer membrane vesicles: Experimental and theoretical analysis

Recombinantly engineered bacterial outer membrane vesicles (OMVs) are promising vaccine delivery vehicles. The diversity of exogenous antigens delivered by OMVs can be enhanced by induced fusion of OMV populations. To date there are no reports of induced fusion of bacterial OMVs. Here we measure the pH and salt-induced aggregation and fusion of OMVs and analyze the processes against the Derjaguin-Landau-Verwey-Overbeek (DLVO) colloidal stability model. Vesicle aggregation and fusion kinetics were investigated for OMVs isolated from native E. coli (Nissle 1917) and lipopolysaccharide (LPS) modified E. coli (ClearColi) strains to evaluate the effect of lipid type on vesicle aggregation and fusion. Electrolytes and low pHs induced OMV aggregation for both native and modified LPS constructs, approaching a calculated fusion efficiency of ~25% (i.e. ~1/4 of collision events lead to fusion). However, high fusion efficiency was achieved for Nissle OMVs solely with decreased pH as opposed to a combination of low pH and increased divalent counterion concentration for ClearColi OMVs. The lipid composition of the OMVs from Nissle negatively impacted fusion in the presence of electrolytes, causing higher deviations from DLVO-predicted critical coagulation concentrations with monovalent counterions. The outcome of the work is a defined set of conditions under which investigators can induce OMVs to fuse and make various combinations of vesicle compositions.

Improved Gastric Acid Resistance and Adhesive Colonization of Probiotics by Mucoadhesive and Intestinal Targeted Konjac Glucomannan Microspheres

The low survival rate in harsh stomach conditions and short retention in intestine of probiotics greatly limit their health benefits. To solve this problem, thiolated oxidized konjac glucomannan (sOKGM) microspheres is designed with pH responsive and mucoadhesive properties. First, an increased survival rate of probiotics by sOKGM microspheres encapsulation in simulated gastric fluid (SGF) is discovered in contrast to the zero‐survival rate of naked probiotics. sOKGM/probiotics even show a higher survival rate in SGF compared with commercial Bb12 formulation. Further, an enhanced mucoadhesion of probiotics to intestinal mucus by mediated interactions with sOKGM is confirmed by isotherm titration calorimetry, rheology, and tensile measurements. The in vivo intestinal transition experiment indicates a prolonged retention of probiotics at intestine by sOKGM encapsulation. Moreover, in vivo evaluation of enhanced colonization and proliferation by sOKGM/probiotics is demonstrated by the fecal and intestinal bacteria copy number via quantitative polymerase chain reaction (qPCR) detection. Further investigation of the alleviation of constipation by sOKGM containing Bifidobacterium animalis subsp. lactis A6 suggests that sOKGM increases the abundance of Bifidobacterium, balanced intestinal flora, and alleviated constipation in mice compared with other formulations. sOKGM with both enhanced gastric acid resistance and adhesion colonization at intestine can effectively improve the function of probiotics.

Transport Properties of Nanoporous, Chemically Forced Biological Lattices

Permselective nanochannels are ubiquitous in biological systems, controlling ion transport and maintaining a potential difference across a cell surface. Surface layers (S-layers) are proteinaceous, generally charged lattices punctuated with nanoscale pores that form the outermost cell envelope component of virtually all archaea and many bacteria. Ammonia oxidizing archaea (AOA) obtain their energy exclusively from oxidizing ammonia directly below the S-layer lattice, but how the charged surfaces and nanochannels affect availability of NH₄⁺ at the reaction site is unknown. Here, we examine the electrochemical properties of negatively charged S-layers for asymmetrically forced ion transport governed by Michaelis-Menten kinetics at ultralow concentrations. Our 3-dimensional electrodiffusion reaction simulations revealed that a negatively charged S-layer can invert the potential across the nanochannel to favor chemically forced NH₄⁺ transport, analogous to polarity switching in nanofluidic field-effect transistors. Polarity switching was not observed when only the interior of the nanochannels was charged. We found that S-layer charge, nanochannel geometry, and enzymatic turnover rate are finely tuned to elevate NH₄⁺ concentration at the active site, potentially enabling AOA to occupy nutrient-poor ecological niches. Strikingly, and in contrast to voltage-biased systems, magnitudes of the co- and counterion currents in the charged nanochannels were nearly equal and amplified disproportionally to the NH₄⁺ current. Our simulations suggest that engineered arrays of crystalline proteinaceous membranes could find unique applications in industrial energy conversion or separation processes.

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins

Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH₄⁺), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH₄⁺ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH₄⁺ availability, with broad implications for comparisons of ecologically distinct populations.

Archaeal S-Layers: Overview and Current State of the Art

In contrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S-layers, few reports have employed archaea as a study model. As such, archaeal S-layers represent an area for exploration in both basic and applied research.

Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria

Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05).

Variability of the transporter gene complement in ammonia-oxidizing archaea

Ammonia-oxidizing archaea (AOA) are a widespread and abundant component of microbial communities in many different ecosystems. The extent of physiological differences between individual AOA is, however, unknown. Here, we compare the transporter gene complements of six AOA, from four different environments and two major clades, to assess their potential for substrate uptake and efflux. Each of the corresponding AOA genomes encode a unique set of transporters and although the composition of AOA transporter complements follows a phylogenetic pattern, few transporter families are conserved in all investigated genomes. A comparison of ammonia transporters encoded by archaeal and bacterial ammonia oxidizers highlights the variance among AOA lineages as well as their distinction from the ammonia-oxidizing bacteria, and suggests differential ecological adaptations.

Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil

Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interactions between nitrifying communities dominated by ammonia-oxidizing archaea (AOA) and Nitrospira-like nitrite-oxidizing bacteria (NOB), and communities of MOB in controlled microcosm experiments with two levels of ammonium and methane availability. We observed strong stimulatory effects of elevated ammonium concentration on the processes of nitrification and methane oxidation as well as on the abundances of autotrophically growing nitrifiers. However, the key players in nitrification and methane oxidation, identified by stable-isotope labeling using (13)CO2 and (13)CH4, were the same under both ammonium levels, namely type 1.1a AOA, sublineage I and II Nitrospira-like NOB and Methylomicrobium-/Methylosarcina-like MOB, respectively. Ammonia-oxidizing bacteria were nearly absent, and ammonia oxidation could almost exclusively be attributed to AOA. Interestingly, although AOA functional gene abundance increased 10-fold during incubation, there was very limited evidence of autotrophic growth, suggesting a partly mixotrophic lifestyle. Furthermore, autotrophic growth of AOA and NOB was inhibited by active MOB at both ammonium levels. Our results suggest the existence of a previously overlooked competition for nitrogen between nitrifiers and methane oxidizers in soil, thus linking two of the most important biogeochemical cycles in nature.

Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments

Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. “Nitrosopumilus koreensis” AR1 and “Nitrosopumilus sediminis” AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.