Recent studies point to the importance of oxygen (O ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O tension in oceanic oxygen minimum zones (OMZs), and O availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O concentrations, characteristic of suboxic regions of OMZs (<10 µM O ), and that atmospheric concentrations of O may inhibit the growth of some environmental populations. We quantify the increasing N O production by marine AOA with decreasing O tensions, consistent with the plausibility of an AOA contribution to the accumulation of N O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.

The disruption of mutualisms between plants and mycorrhizal fungi is a potentially powerful mechanism by which invasives can negatively impact native species, yet our understanding of this mechanism's role in exotic species invasion is still in its infancy. Here, we provide several lines of evidence indicating that invasive tamarisk (Tamarix sp.) negatively affects native cottonwoods (Populus fremontii) by disrupting their associations with arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. At a field site in the early stages of tamarisk invasion, cottonwoods with tamarisk neighbors had reduced EM colonization and altered EM fungal community composition relative to cottonwoods with native neighbors, leading to reductions in EM propagule abundance in the soil beneath tamarisk. Similarly, AM colonization of cottonwoods was reduced with a tamarisk neighbor, but there were no significant changes in AM fungal spore communities or propagule abundance. Root colonization by nonmycorrhizal fungi, including potential pathogens, was higher in cottonwoods with tamarisk neighbors. A greenhouse experiment in which AM and EM inoculation and plant neighbor were manipulated in a fully factorial design showed that cottonwoods benefited from mycorrhizas, especially EM, in terms of shoot biomass when grown with a conspecific, but shoot biomass was similar to that of nonmycorrhizal controls when cottonwoods were grown with a tamarisk neighbor. These results are partially explained by a reduction in EM but not AM colonization of cottonwoods by a tamarisk neighbor. Tamarisk neighbors negatively affected cottonwood specific leaf area, but not chlorophyll content, in the field. To pinpoint a mechanism for these changes, we measured soil chemistry in the field and the growth response of an EM fungus (Hebeloma crustuliniforme) to salt-amended media in the laboratory. Tamarisk increased both NO3- concentrations and electrical conductivity 2.5-fold beneath neighboring cottonwoods in the field. Salt-amended media did not affect the growth of H. crustuliniforme. Our findings demonstrate that a nonnative species, even in the early stages of invasion, can negatively affect a native species by disrupting its mycorrhizal symbioses. Some of these changes in mycorrhizal fungal communities may remain as legacy effects of invasives, even after their removal, and should be considered in management and restoration efforts.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase (amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB.

Anaerobic ammonia-oxidizing (Anammox) bacteria (AnAOB) rely on nitrite supplied by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Affinities for ammonia and oxygen play a crucial role in AOA/AOB competition and their association with AnAOB. In this work we measured the affinity constants for ammonia and oxygen (half-saturation; k m) of two freshwater AOA enrichments, an AOA soil isolate (N. viennensis), and a freshwater AnAOB enrichment. The AOA enrichments had similar kinetics (μ max ≈ 0.36 d −1 , k m,NH4 ≈ 0.78 µM, and k m,O2 ≈ 2.9 µM), whereas N. viennensis had similar k m values but lower μ max (0.23 d −1). In agreement with the current paradigm, these AOA strains showed a higher affinity for ammonia (lower k m,NH4 ; 0.34-1.27 µM) than published AOB measurements (>20 µM). The slower growing AnAOB (μ max ≈ 0.16 d −1) had much higher k m values (k m,NH4 ≈ 132 µM, k m,NO2 ≈ 48 µM) and were inhibited by oxygen at low levels (halfoxygen inhibition; k i,O2 ≈ 0.092 µM). The higher affinity of AOA for ammonia relative to AnAOB, suggests AOA/AnAOB cooperation is only possible where AOA do not outcompete AnAOB for ammonia. Using a biofilm model, we show that environments of ammonia/oxygen counter diffusion, such as stratified lakes, favors this cooperation.

Climate change-induced droughts have contributed to large-scale die-offs of dominant tree species throughout much of the southwestern United States. These mortality events provide ecologists with the opportunity to determine whether afterlife effects associated with the die-off occur and the potential implications for future ecosystem changes. We studied both the afterlife and interaction effects of condition (dead trees, living trees, and open areas) on understory vegetation in a Juniperus monosperma woodland of northern Arizona 7 years after a major mortality event. Five major findings resulted: (1) there was a positive afterlife effect on understory plants, in which vegetation under dead junipers contained almost double the amount of cover; (2) the competitive effect on understory plants was exemplified by a 1.3 times greater cover and 1.6 additional species in open areas compared to under living junipers; (3) plant community composition significantly differed by aspect and condition; (4) the highly invasive cheatgrass (Bromus tectorum) was 1.5 times greater under dead junipers compared to live junipers; and (5) litter depth and light availability were negatively and positively correlated with plant cover, respectively, but weakly correlated with afterlife effects. Our results indicate that mortality events can promote changes in understory vegetation through afterlife effects. In ecosystems where foundation species suffer high rates of mortality, changes in plant population dynamics and ecosystem function may promote an altered trajectory in community composition with the potential to increase the presence of invasive species. Continued species die-offs associated with climate change-induced drought may contribute to an increased occurrence and legacy of afterlife effects.