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Abstract Inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. Previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. To compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea (Nitrosopumilus maritimus and Nitrosotalea devanaterra) and bacteria (Nitrosomonas europaea and Nitrosospira multiformis) were determined at different light intensities under continuous illumination and light/dark cycles. All strains were inhibited by continuous illumination at the highest intensity (500 μE m−2 s−1). At lower light intensities, archaeal growth was much more photosensitive than bacterial growth, with greater inhibition at 60 μE m−2 s−1 than at 15 μE m−2 s−1, where bacteria were unaffected. Archaeal ammonia oxidizers were also more sensitive to cycles of 8-h light/16-h darkness at two light intensities (60 and 15 μE m−2 s−1) and, unlike bacterial strains, showed no evidence of recovery during dark phases. The findings provide evidence for niche differentiation in aquatic environments and reduce support for photoinhibition as an explanation of nitrite maxima in the ocean.

Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.

Chemolithotrophic ammonia-oxidising bacteria (AOB) present in oil-contaminated landfarming soil were studied over two growing seasons in 1999 and 2000. The number of AOB (4–9 × 10 5 cells g −1 of dry soil) determined with the quantitative polymerase chain reaction (real-time PCR) and the rate of potential ammonium oxidation ( 0 . 05 – 0 . 28 μ g NO 2 - – N g - 1 of dry soil h - 1 ) indicated the presence of stable AOB populations. Denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified AOB 16S rRNA genes showed dominance of Nitrosospira-like sequences in clusters 2 and 3. The present results from the chronically oil-contaminated landfarming soil support the suggested importance of Nitrosospira-like AOB in terrestrial environments.

This research was conducted to compare chemical and microbiological properties during aerobic composting (AC) and vermicomposting (VC) of green waste. Relative to AC, VC significantly decreased the pH and lignin and cellulose contents, and significantly increased the electrical conductivity and total N and available P contents. For AC, BIrii41_norank (order Myxococcales) was the major bacterial genus at 30 d and again became dominant genus from 90-150 d, with relative abundances of 2.88% and 4.77-5.19%, respectively; at 45 d and 60 d, the dominant bacterial genus was Nitrosomonadaceae_uncultured (order Nitrosomonadales) with relative abundances of 2.83-7.17%. For VC, the dominant bacterial genus was BIrii41_norank (except at 45 d), which accounted for 2.11-7.96% of the total reads. The dominant fungal class was Sordariomycetes in AC (relative abundances 39.2-80.6%) and VC (relative abundances 42.1-69.5%). The abundances of microbial taxa and therefore the bacterial and fungal community structures differed between VC and AC. The quality of the green waste compost product was higher with VC than with AC. These results will also help to achieve further composting technology breakthroughs in reducing the composting time and improving compost quality.

To predict the effects of nitrogen deposition on nitrogen-mineralizing enzyme activity and soil microbial community structure in artificial temperate forests in northern China, we studied the soil properties, nitrogen-mineralizing enzyme activity, and microbial community structure in the soil of a Korean pine plantation in which different concentrations (0, 20, 40, 80 kg N ha−1 year−1) of ammonium nitrate were applied for 5 consecutive years. The results showed that nitrogen addition at different concentrations did not significantly affect the soil pH. High nitrogen addition (80 kg N ha−1 year−1) significantly increased the soil organic matter, ammonium nitrogen, and nitrate nitrogen content in the Korean pine plantation, and ammonium nitrogen was the key factor that influenced the soil fungal community structure. The urease activity under the moderate nitrogen addition treatment (40 kg N ha−1 year−1) was significantly lower than that under the control (0 kg N ha−1 year−1), and the protease activity in the three treatments was also significantly lower than that in the control. There was no significant correlation between microbial community structure and the four mineralizing enzymes. After nitrogen addition at different concentrations, the Simpson and Shannon indexes of soil bacteria decreased significantly under low nitrogen addition (20 kg N ha−1 year−1), but the α-diversity index of soil fungi did not show significant differences under nitrogen addition. The microbial community composition was significantly changed by the different treatments. PLS-DA analysis showed that Tardiphaga was an important genus that made the greatest contribution to the differences in bacterial community composition among treatments, as was Taeniolella for fungal community composition. The low level of nitrogen addition inhibited nitrogen mineralization in the Korean pine plantation by reducing the relative abundances of Nitrosomonadaceae and Betaproteobacteriales and by reducing the abundances of symbiotrophic fungi. Berkelbacteria and Polyporales were bacteria and fungi, respectively, that changed significantly under the high nitrogen addition treatment (80 kg N ha−1 year−1). This study provides more data to support predictions of the changes in nitrogen-mineralizing enzyme activity and microbial community structure in artificial temperate forest soils in response to increased nitrogen deposition.

Ammonia-oxidizing bacteria are believed to be an important source of the climatically important trace gas nitrous oxide (N₂O). The genes for nitrite reductase (nirK) and nitric oxide reductase (norB), putatively responsible for nitrous oxide production, have been identified in several ammonia-oxidizing bacteria, but not in Nitrosospira strains that may dominate ammonia-oxidizing communities in soil. In this study, sequences from nirK and norB genes were detected in several cultured Nitrosospira species and the diversity and phylogeny of these genes were compared with those in other ammoniaoxidizing bacteria and in classical denitrifiers. The nirK and norB gene sequences obtained from Nitrosospira spp. were diverse and appeared to be less conserved than 16S rRNA genes and functional ammonia monooxygenase (amoA) genes. The nirK and norB genes from some Nitrosospira spp. were not phylogenetically distinct from those of denitrifiers, and phylogenetic analysis suggests that the nirK and norB genes in ammonia-oxidizing bacteria have been subject to lateral transfer.

Aims Seeds are involved in the transmission of microorganisms from one plant generation to the next, acting as initial inoculum for the plant microbiome, therefore provide a key source of variability in plants. This study aimed to characterize the seed bacteria and fungi communities in Elymus nutans , a dominant perennial grass growing in the Qinghai Tibet Plateau (QTP) and explore the effects of plant growth location on the seed microbiome. Methods Seeds were collected from plants growing in four locations in the QTP. The seed microbial community was examined by Illumina MiSeq sequencing of DNA extracted from the surface sterilized seeds. Results The seed bacterial community was dominated by the bacteria phylum Proteobacteria (98%) and fungal phyla Ascomycota (83%) and Basidiomycota (15%). At the lower taxonomic level, the bacterial genus Pseudomonas dominated in all four locations with an average relative abundance of 83% whereas the fungal genera that dominated the seed microbiome was diverse, the most prominent being Epichloë , Pyrenophora , Mycosphaerella and Bullera . Ecologically important bacterial family Nitrosomonadaceae (nitrifiers) and fungal phylum Glomeromycota (arbuscular mycorrhizal fungi) were detected in this study for the first time as seed endophytes. The Elymus nutans seed bacterial community was not impacted by the plant growth location, in contrast, the seed fungal community varied significantly in four locations. Conclusions The seeds of Elymus nutans host diverse endophytic bacteria and fungi. Unlike the bacteria, the host plant selection of seed fungal endophytes was observed to have been affected by plant growth location. Positive and negative associations in the Elymus nutans seed microbiome were observed.

Low-energy nitrogen removal from ammonium-rich wastewater is crucial in preserving the water environment. A one-stage nitritation/anammox process with two inflows treating ammonium-containing wastewater, supplied from inside and outside the wound filter, is expected to stably remove nitrogen. Laboratory-scale reactors were operated using different start-up strategies; the first involved adding nitritation inoculum after anammox biomass formation in the filter, which presented a relatively low nitrogen removal rate (0.171 kg N/m3 · d), at a nitrogen loading rate of 1.0 kg N/m3 · d. Conversely, the second involved the gradual cultivation of anammox and nitritation microorganisms, which increased the nitrogen removal rate (0.276 kg N/m3 · d). Furthermore, anammox (Candidatus Brocadia) and nitritation bacteria (Nitrosomonadaceae) coexisted in the biofilm formed on the filter surface. The abundance of nitritation bacteria (10.5%) in the reactor biofilm using the second start-up strategy was higher than that using the first (3.7%). Thus, the two-inflow nitritation/anammox process effectively induced habitat segregation using a suitable start-up strategy.

For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.

How the root metabolic profiles and rhizosphere bacterial communities of dioecious plants respond to soil properties and sex identity is largely unknown. In this study, we analyzed root phenolic metabolomes and rhizosphere bacterial microbiomes of Populus euphratica females and males in two P. euphratica plantations with different soil properties to reveal the relative importance of soil and sex effects, and to decipher associations of certain phenolic compounds with specific bacterial taxa. We found that the relative abundances of bacterial OTUs and phenolic metabolites were closely linked to soil properties and sex identity. Soil is the main filter influencing the root phenolic metabolic profiles and rhizosphere bacterial communities of P. euphratica, while sexes and their interactions with soil properties are secondary factors. Differences in the diversity and evenness of phenolic metabolites were affected by plant sex, but not by soil properties. Conversely, the diversity and evenness of bacterial communities were affected by soil properties independent of plant sex. A multiple regression model indicated the presence of associations between root phenolic metabolites and specific soil bacteria taxa. Furthermore, all bacterial phyla and families correlated with at least one phenolic metabolite. Especially, both Nitrosomonadaceae and Cytophagaceae positively correlated with salicylic acid. Thus, our study provides new insights into the ecological mechanism that maintains rhizosphere bacterial communities in P. euphratica plantations in the desert area.