Wolfgang Wanek

MANGROVE ISOTOPIC (δ15N AND δ13C) FRACTIONATION ACROSS A NITROGEN VS. PHOSPHORUS LIMITATION GRADIENT

Mangrove islands in Belize are characterized by a unique switching from nitrogen (N) to phosphorus (P) limitation to tree growth from shoreline to interior. Fertilization has previously shown that Rhizophora mangle (red mangrove) fringe trees (5–6 m tall) growing along the shoreline are N limited; dwarf trees (≤1.5 m tall) in the forest interior are P limited; and transition trees (2–4 m tall) are co-limited by both N and P. Growth patterns paralleled a landward decrease in soil flushing by tides and an increase in bioavailable N, but P availability remained consistently low across the gradient. Stable isotopic composition was measured in R. mangle leaves to aid in explaining this nutrient switching pattern and growth variation. Along control transects, leaf δ15N decreased from +0.10‰ (fringe) to −5.38‰ (dwarf). The δ15N of N-fertilized trees also varied spatially, but the values were consistently more negative (by ∼3‰) compared to control trees. Spatial variation in δ15N values disappeared when the trees were fertilized with P, and values averaged +0.12‰, similar to that in control fringe trees. Neither variation in source inputs nor microbial fractionation could fully account for the observed patterns in δ15N. The results instead suggest that the lower δ15N values in transition and dwarf control trees were due to plant fractionation as a consequence of slower growth and lower N demand. P fertilization increased N demand and decreased fractionation. Although leaf δ13C was unaffected by fertilization, values increased from fringe (−28.6‰) to transition (−27.9‰) to dwarf (−26.4‰) zones, indicating spatial variation in environmental stresses affecting stomatal conductance or carboxylation. The results thus suggest an interaction of external supply, internal demand, and plant ability to acquire nutrients under different hydro-edaphic conditions that vary across this tree-height gradient. The findings not only aid in understanding mangrove discrimination of nitrogen and carbon isotopes, but also have implications for identifying nutrient loading and other stress conditions in coastal systems dominated by mangroves.

Long-Term Change in the Nitrogen Cycle of Tropical Forests

The ratio of stable isotopes in leaves and wood reveals an increase in nitrogen availability in Panamanian and Thai tropical forests. Deposition of reactive nitrogen (N) from human activities has large effects on temperate forests where low natural N availability limits productivity but is not known to affect tropical forests where natural N availability is often much greater. Leaf N and the ratio of N isotopes (δ15N) increased substantially in a moist forest in Panama between ~1968 and 2007, as did tree-ring δ15N in a dry forest in Thailand over the past century. A decade of fertilization of a nearby Panamanian forest with N caused similar increases in leaf N and δ15N. Therefore, our results indicate regional increases in N availability due to anthropogenic N deposition. Atmospheric nitrogen dioxide measurements and increased emissions of anthropogenic reactive N over tropical land areas suggest that these changes are widespread in tropical forests.

The effect of resource quantity and resource stoichiometry on microbial carbon‐use‐efficiency

The carbon-use-efficiency (CUE) of microorganisms is an important parameter in determining ecosystem-level carbon (C) cycling; however, little is known about how variance in resources affects microbial CUE. To elucidate how resource quantity and resource stoichiometry affect microbial CUE, we cultured four microorganisms - two fungi (Aspergillus nidulans and Trichoderma harzianum) and two bacteria (Pectobacterium carotovorum and Verrucomicrobium spinosum) - under 12 unique C, nitrogen (N) and phosphorus (P) ratios. Whereas the CUE of A. nidulans was strongly affected by C, bacterial CUE was more strongly affected by mineral nutrients (N and P). Specifically, CUE in P. carotovorum was positively correlated with P, while CUE of V. spinosum primarily depended on N. This resulted in a positive relationship between fungal CUE and resource C : nutrient stoichiometry and a negative relationship between bacterial CUE and resource C : nutrient stoichiometry. The difference in the direction of the relationship between CUE and C : nutrient for fungi vs. bacteria was consistent with differences in biomass stoichiometry and suggested that fungi have a higher C demand than bacteria. These results suggest that the links between biomass stoichiometry, resource demand and CUE may provide a mechanism for commonly observed temporal and spatial patterns in microbial community structure and function in natural habitats.

Heterotrophic microbial communities use ancient carbon following glacial retreat.

When glaciers retreat they expose barren substrates that become colonized by organisms, beginning the process of primary succession. Recent studies reveal that heterotrophic microbial communities occur in newly exposed glacial substrates before autotrophic succession begins. This raises questions about how heterotrophic microbial communities function in the absence of carbon inputs from autotrophs. We measured patterns of soil organic matter development and changes in microbial community composition and carbon use along a 150-year chronosequence of a retreating glacier in the Austrian Alps. We found that soil microbial communities of recently deglaciated terrain differed markedly from those of later successional stages, being of lower biomass and higher abundance of bacteria relative to fungi. Moreover, we found that these initial microbial communities used ancient and recalcitrant carbon as an energy source, along with modern carbon. Only after more than 50 years of organic matter accumulation did the soil microbial community change to one supported primarily by modern carbon, most likely from recent plant production. Our findings suggest the existence of an initial stage of heterotrophic microbial community development that precedes autotrophic community assembly and is sustained, in part, by ancient carbon.

Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea

Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell−1 h−1 and nitrification rates of 2.6±0.5 fmol NO2− cell−1 h−1 were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In 15N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting.

Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources

Terrestrial microbial decomposer communities thrive on a wide range of organic matter types that rarely ever meet their elemental demands. In this review we synthesize the current state-of-the-art of microbial adaptations to resource stoichiometry, in order to gain a deeper understanding of the interactions between heterotrophic microbial communities and their chemical environment. The stoichiometric imbalance between microbial communities and their organic substrates generally decreases from wood to leaf litter and further to topsoil and subsoil organic matter. Microbial communities can respond to these imbalances in four ways: first, they adapt their biomass composition toward their resource in a non-homeostatic behavior. Such changes are, however, only moderate, and occur mainly because of changes in microbial community structure and less so due to cellular storage of elements in excess. Second, microbial communities can mobilize resources that meet their elemental demand by producing specific extracellular enzymes, which, in turn, is restricted by the C and N requirement for enzyme production itself. Third, microbes can regulate their element use efficiencies (ratio of element invested in growth over total element uptake), such that they release elements in excess depending on their demand (e.g., respiration and N mineralization). Fourth, diazotrophic bacteria and saprotrophic fungi may trigger the input of external N and P to decomposer communities. Theoretical considerations show that adjustments in element use efficiencies may be the most important mechanism by which microbes regulate their biomass stoichiometry. This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.

The application of ecological stoichiometry to plant–microbial–soil organic matter transformations

Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of h...

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota–AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.

Nitrogen-15 natural abundance in a montane cloud forest canopy as an indicator of nitrogen cycling and epiphyte nutrition

Nutrients obtained by epiphytes may either be of atmospheric origin or from organic matter in the canopy, which decomposes to form canopy soil on large branches. We hypothesised that the N supply for epiphytes on small branches was lower, and a larger proportion provided by rainwater, than for epiphytes rooting in canopy soil. We tested this by measuring the N concentration and isotopic composition in terrestrial and canopy soil and in various canopy compartments of a Costa Rican cloud forest. In general, epiphytes on small branches without canopy soil had lower N foliar concentrations and δ15N signals than plants rooted in canopy soil, suggesting that the former receive a higher proportion of N directly from the rain. Epiphytes on small branches also had less negative δ13C values, indicating more frequent water stress. Epiphytes had lower δ15N values (–3.9±2.3‰) than ground-rooted trees (–1.1±1.6‰), and canopy soil had lower values (0.7±1.2‰) than terrestrial soil (3.8±0.7‰). Assuming that the isotopic effect of terrestrial and canopy soil organic matter formation is similar, our findings support earlier results showing that canopy soil is derived mainly from epiphytes, with only minor inputs from host tree matter. Thus, the epiphyte N cycle appears to be largely detached from the tree-soil cycle. Epiphylls on leaves of understorey shrubs had higher δ15N signals than cryptogams in the upper canopy, as a result of either 15N accumulation in throughfall or increased N2 fixation. The correlation between epiphyll and understorey host leaf δ15N suggests some exchange of N between epiphylls and host leaves. Differences between epiphyte groups also appear to be related to uptake of N through mycorrhizas or N2 fixation. Thus, the source and quantity of N supply is highly variable, depending on the systematic group and canopy position.

Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing

The animal and human intestinal mucosa secretes an assortment of compounds to establish a physical barrier between the host tissue and intestinal contents, a separation that is vital for health. Some pathogenic microorganisms as well as members of the commensal intestinal microbiota have been shown to be able to break down these secreted compounds. Our understanding of host-compound degradation by the commensal microbiota has been limited to knowledge about simplified model systems because of the difficulty in studying the complex intestinal ecosystem in vivo. In this study, we introduce an approach that overcomes previous technical limitations and allows us to observe which microbial cells in the intestine use host-derived compounds. We added stable isotope-labeled threonine i.v. to mice and combined fluorescence in situ hybridization with high-resolution secondary ion mass spectrometry imaging to characterize utilization of host proteins by individual bacterial cells. We show that two bacterial species, Bacteroides acidifaciens and Akkermansia muciniphila, are important host-protein foragers in vivo. Using gnotobiotic mice we show that microbiota composition determines the magnitude and pattern of foraging by these organisms, demonstrating that a complex microbiota is necessary in order for this niche to be fully exploited. These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research.