Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought

Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling

Metagenome of a nitrite-oxidizing enrichment from Austrian saline-alkaline lake containing Nitrospira alkalitolerans

Via the enrichment and genomic analyis of a new, haloalkalitolerant Lineage IV Nitrospira species, which we refer to as "Candidatus Nitrospira alkalitolerans”, we revealed several features that show the adaptation of this organism to its extreme environment and may help in overcoming low proton motive force, aid in pH and ion homeostasis and counter-regulate osmotic pressure

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox nitrospira in the environment

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

Amplicon sequencing of genus Nitrospira from nine Austrian saline-alkaline lakes

To portray Nitrospira distribution, diversity, functionality, and adaptation in an extreme natural system we studied hypo- and subsaline, highly alkaline (pH 8.5-9.8) lakes of the Austrian national park “Neusiedler See-Seewinkel” by amplicon sequencing. Our results show surprisingly diverse Nitrospira populations from lineages I, II and IV inhabiting lake sediments with high alkalinity and elevated salinity and indicate a strong competitive advantage of Nitrospira lineage IV members at high pH

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are theprimary producers, providing most of the organic carbon needed for the animal host’s nutrition. We sequenced genomesof the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus.The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosyntheticsymbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbiontsof lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis werewithin the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts.The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogenavailability often limits primary productivity