Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (“comammox”), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia-and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies Pjevac et al.Comammox amoA-Targeted PCR Primers of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.

Recently, it has been shown that boar acrosin exhibits a carbohydrate-binding activity with a specificity to fucose, by which it can bind to the oocyte zona pellucida. By limited autoproteolysis of a high-molecular mass acrosin (55/53 kDa), designated as alpha-acrosin, a 15 kDa fragment was generated which interacts strongly with the porcine zona pellucida. Zona-binding was demonstrated on protein blots and by the solid-phase zona-binding assay utilizing biotinylated zona proteins. The zona-binding peptide was isolated by reversed-phase HPLC and analyzed for amino acid sequence. Its single N-terminal sequence corresponded to that of the acrosin B-chain (heavy chain). These data indicate that the zona-binding properties of acrosin are associated with the N-terminal peptide of the acrosin heavy chain.

Acrosin is a multifunctional enzyme combining several functional properties within a single molecule: the catalytic triad of the proteinase, hydrophobic domains responsible for the special membrane-associating character of the enzyme and the carbohydrate binding sites by which the molecule can bind to the zona pellucida. Acrosin occurs in the sperm acrosome as an inactive precursor, proacrosin, with a molecular mass of 53-55 kDa. Proacrosin is activated by a single proteolytic clip between Arg23 and Val24 generating the high molecular mass acrosin. The activation of proacrosin to the biologically active enzyme which occurs concomitantly with the acrosome reaction appears to be regulated on and by the zona pellucida. It is hypothesized that alternating cycles of binding to the zona, digestion of the zona and release from the zona together with the forward motility of the spermatozoon would be required to achieve penetration. Zusammenfassung. Acrosin ist ein multifunktionelles Enzym, das in sich verschiedeneEigenschaften kombiniert: die katalytische Triade einer Proteinase, hydrophobe Domanen, die fur die spezielle Membran-Affinitat wesentlich sind und Kohlenhydrat-Bindungsstellen, uber die das Enzym an der Zona pellucida binden kann. Acrosin kommt im Spermien-Akrosom als inaktive Vorstufe, Proacrosin, mit einer molekularen Masse von 53-55 kDa vor. Proacrosin wird durch einen proteolytischen Schnitt zwischen Arg23 und Val24 aktiviert und bildet das hohermolekulare Akrosin. Die Aktivierung von Proacrosin zum biologisch aktiven Enzym verlauft parallel zur akrosomalen Reaktion und scheint durch und an der Zona pellucida reguliert zu werden. Es wird hypothetisch angenommen, daB alternierende Zyklen von Bindung an der Zona, Verdauung des Zonamaterials und Freisetzung von der Zona gemeinsam mit der Vorwartsmotilitat der Spermien fur die Penetration erforderlich sind. Acrosomal proteins 111