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The gut microbiota is an emerging frontier in wildlife research and its importance to vertebrate health and physiology is becoming ever more apparent. Reptiles, in particular snakes, have not received the same attention given to other vertebrates and the composition of their wild gut microbiome remains understudied. The primary goal of this work was to describe the cloacal microbiota of two Colubrids, the Eastern Gartersnake (Thamnophis sirtalis sirtalis) and the Northern Watersnake (Nerodia sipedon sipedon), and if their cloacal microbiota differed as well as if it did between a wetland and upland population of the former species. We utilized next-generation sequencing of cloacal swabs—a non-destructive proxy for the gut microbiota. The cloacal microbiome of Eastern Gartersnakes (N = 9) was like those of other snakes being comprised of Proteobacteria, Bacteroidetes, and Firmicutes, while that of Northern Watersnakes (N = 6) was dominated by Tenericutes. Seven microbial operational taxonomic units (OTUs), all members of Proteobacteria, were shared among all individuals and were indicative of a core microbiome in Eastern Gartersnakes, but these OTUs were not particularly relevant to Northern Watersnakes. The latter had greater OTU richness than did Eastern Gartersnakes, and habitat did not have any apparent effect on the microbial community composition in Eastern Gartersnakes. Our findings suggest host taxonomy to be a determining factor in the cloacal microbiota of snakes and that Tenericutes are associated with aquatic habitats. This is the first report to examine the cloacal microbiome of these species and provides a useful foundation for future work to build upon.

Nitrogen (N) from anthropogenic sources has dramatically increased in terrestrial ecosystems globally. Although belowground microbial processes and events that release N into the atmosphere, such as fire, could support ecosystem resilience to eutrophication, little is known about how these factors might affect N loss following chronic fertilization, thus promoting ecosystem recovery. We studied how N pools, N-cycling potential rates and their affiliated microbial populations, and microbial community composition responded to the factorial effects of cessation of 30 years of chronic N fertilization and annual burning at a tallgrass prairie. Soil N availability in previously fertilized plots recovered by 86% (using never-fertilized control plots as a 100% recovery reference), while plant and microbial biomass did not change. Nitrification potential recovered (80%), and denitrification potential partially recovered (50%), in previously fertilized plots. There were differential responses among key groups of nitrifiers (archaea vs. bacteria) and denitrifiers (nosZ clade I vs. clade II from Anaeromyxobacter dehalogenans) to long-term N fertilization and cessation despite the whole microbial community composition not shifting significantly after fertilization ceased. Also, N-cycling potentials were consistently higher in unburned prairie. Together, results suggest that fire is a prominent mechanism for ecosystem N removal in annually burned prairie, while N-cycling microbes will have an important role in the absence of fire; however, the recovery to pre-fertilized condition, with or without fire, will take longer than 1 year. Overall, differential resilience of biotic populations and processes can potentially shape different outcomes of soil N loss and tallgrass prairie ecosystem recovery from long-term N fertilization.

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

Fire can impact terrestrial ecosystems by changing abiotic and biotic conditions. Short fire intervals maintain grasslands and communities adapted to frequent, low-severity fires. Shrub encroachment that follows longer fire intervals accumulates fuel and can increase fire severity. This patchily distributed biomass creates mosaics of burn severities in the landscape—pyrodiversity. Afforded by a scheduled burn of a watershed protected from fires for 27 years, we investigated effects of woody encroachment and burn severity on soil chemistry and soil-inhabiting bacteria and fungi. We compared soils before and after fire within the fire-protected, shrub-encroached watershed and soils in an adjacent, annually burned and non-encroached watershed. Organic matter and nutrients accumulated in the fire-protected watershed but responded less to woody encroachment within the encroached watershed. Bioavailable nitrogen and phosphorus and fungal and bacterial communities responded to high-severity burn regardless of encroachment. Low-severity fire effects on soil nutrients differed, increased bacterial but decreased fungal diversity and effects of woody encroachment within the encroached watershed were minimal. High-severity burns in the fire-protected watershed led to a novel soil system state distinct from non-encroached and encroached soil systems. We conclude that severe fires may open grassland restoration opportunities to manipulate soil chemistry and microbial communities in shrub-encroached habitats.

In grasslands, fire management and fertilization are established drivers of plant community change, but associated soil fungal responses are less well defined. We predicted that soil fungal communities would change seasonally, that decades of fire cessation and nitrogen (N) fertilization would alter fungal distributions, and that plant and fungal community change would be correlated. Surface soils were sampled monthly for 1 y from a 30-y fire by fertilization experiment to evaluate fungal community dynamics and assess correlation with plant community heterogeneity. ITS gene community composition was seasonally stable, excepting increased arbuscular mycorrhizal fungal summer abundance in the burned, fertilized treatment. Long-term treatments affected soil fungal and plant communities, with correlated heterogeneity patterns. Despite woody encroachment in the fire cessation treatment, soil fungal communities did not resemble those of forests. This study provides evidence supporting the strength of feedbacks between fungal and plant community change in response to long-term grassland fire and N management changes.

A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation history with extended dry periods, versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.

Colonization of gut microbiomes during early life can shape metabolism and immunity of adult animals. However, most data are derived from antibiotic-treated or germ-free laboratory mammals. Furthermore, few studies have explored how microbial colonization during critical windows influences a suite of other fitness-related traits in wild animals. This study tested whether hatching constitutes a critical developmental window for gut microbiome colonization in wild-caught amphibians and whether perturbations to gut microbiota at hatching shape fitness-related traits of larval growth, metabolism, metamorphosis and disease susceptibility. We sterilized wood frog eggs and then inoculated them with microbes from differing sources, including from another species (bullfrogs) that differ in disease resistance and life history. We measured development, growth and metabolic rates through metamorphosis among individuals from each microbial treatment. A separate group was exposed to an LD50 dose of ranavirus-an emerging disease-to test for microbiome effects on disease susceptibility. We also quantified rates of deformities to test for microbial treatment effects on overall health. Manipulation of microbiota on eggs altered the trajectory of gut microbiome communities across larval ontogeny, though disruption appeared to be transitory. While microbiome structure converged among the treatments by metamorphosis, the effects of disruption on host phenotypes persisted. Larvae inoculated with the bullfrog gut microbiota exhibited accelerated growth and development rates compared to controls. By contrast, sterilized larvae maintained in sterile water for several days after hatching exhibited greater disruption to their gut microbiota across ontogeny, as well as altered metabolism, more tail deformities, and were more likely to die when exposed to an LD50 dose of ranavirus compared to the other treatments. These results suggest perturbations to the microbiota during critical developmental windows can alter the trajectory of the gut microbiome, and have long-term effects on fitness-related traits in larval amphibians. These results suggest that explicit tests of how changes in the composition and abundance of the microbial community shape phenotypes across ontogeny in amphibians could shed light on host-microbe interactions in wildlife, as well as inform conservation efforts to mitigate emerging diseases.

Microbiota in streams drive many ecosystem functions, including whole-stream metabolism, nitrogen (N) cycling, and the production of basal resources that fuel stream food webs. Interactions...

Anthropogenic increases in nitrogen (N) and phosphorus (P) concentrations can strongly influence the structure and function of ecosystems. Even though lotic ecosystems receive cumulative inputs of nutrients applied to and deposited on land, no comprehensive assessment has quantified nutrient-enrichment effects within streams and rivers. We conducted a meta-analysis of published studies that experimentally increased concentrations of N and/or P in streams and rivers to examine how enrichment alters ecosystem structure (state: primary producer and consumer biomass and abundance) and function (rate: primary production, leaf breakdown rates, metabolism) at multiple trophic levels (primary producer, microbial heterotroph, primary and secondary consumers, and integrated ecosystem). Our synthesis included 184 studies, 885 experiments, and 3497 biotic responses to nutrient enrichment. We documented widespread increases in organismal biomass and abundance (mean response = +48%) and rates of ecosystem processes (+54%) to enrichment across multiple trophic levels, with no large differences in responses among trophic levels or between autotrophic or heterotrophic food-web pathways. Responses to nutrient enrichment varied with the nutrient added (N, P, or both) depending on rate versus state variable and experiment type, and were greater in flume and whole-stream experiments than in experiments using nutrient-diffusing substrata. Generally, nutrient-enrichment effects also increased with water temperature and light, and decreased under elevated ambient concentrations of inorganic N and/or P. Overall, increased concentrations of N and/or P altered multiple food-web pathways and trophic levels in lotic ecosystems. Our results indicate that preservation or restoration of biodiversity and ecosystem functions of streams and rivers requires management of nutrient inputs and consideration of multiple trophic pathways.

Nitrogen (N) availability is a driver of soil microbial diversity and function, and is affected by prescribed burning (N removal through volatilization) and fertilization (N addition). Because soil microbes control critical feedbacks to ecosystem function, it is important to understand the dynamics and responses of microbial populations under conditions of contrasting N availability. This study took place at a long-term field manipulation in which native tallgrass prairie was annually burned or not burned, and annually fertilized or not fertilized, in a factorial design, since 1986. Composite surface soil samples (0–15 cm) were collected monthly between November 2014 and December 2015 from replicate plots to evaluate event-based (post-fire, post-fertilization), seasonal, and long-term responses of soil microbial communities to management and environmental changes. Bacterial 16S rRNA gene and fungal ITS population sizes were estimated using qPCR, and bacterial community composition (BCC) was measured using Illumina MiSeq sequencing of 16S rRNA genes. We expected seasonal and event-based change in all parameters, and that total microbial population sizes and diversity would be lower in soils with higher N availability, due to greater competitive dominance of nitrophilic or copiotrophic taxa. Bacterial and fungal population sizes varied significantly by sampling month, in that bacterial populations were approximately 10× greater in summer (June–August), but did not change in response to management events or long-term treatments. In contrast, very few individual taxonomic groups displayed seasonal or event-based responses, and there was no significant whole-community turnover on weekly or monthly time-scales; instead, BCC was strongly impacted by both the long-term fire and fertilization treatments. Specifically, there were increases and decreases in putatively "copiotrophic" and "oligotrophic" prokaryotic Phyla in response to long-term N fertilization, which were significantly stronger and more predictable in soils following long-term fire suppression. These results reveal that while long-term grassland management changes BCC beyond the detected range of seasonal variability, total bacterial populations change coherently month-to-month, potentially due to significant plant inputs of labile carbon during the growing season. Furthermore, because prescribed burning reduces soil N availability, the interactive responses to fire suppression plus fertilization suggest that higher background levels of soil N availability may increase the magnitude of soil microbial sensitivity to N fertilization.

Microbial activity within the soil is critical for plant growth and development, and a major determinant of crop performance and yield. Claypan soils are characterized by a dense, impermeable subsoil that impedes root system development. Little is known about soil microbial properties in claypan soils or how microbial activity changes with depth in the soil profile. We explored how management practices mediate changes in soil microbial composition and potential enzyme activities with depth in a claypan soil. The soil microbial biomass and composition were examined through phospholipid fatty acid (PLFA) assay. We found that the soil organic carbon (SOC), microbial biomass, and oxidative enzyme activities declined with depth, while hydrolase activity increased in the upper layer of the claypan. Changes in soil management practices affected the degree of increase in hydrolase activity in subsoils, especially for N-acetyl-β- d -glucosaminidase. No accumulation of SOC in the claypan layer was observed. Contrary to our expectation, soil microbes deeper within the soil profile were phosphorus- and nitrogen-limited rather than carbon-limited. Vertical stratification of measured soil properties was found with an upper layer from 0 to 15 cm, an intermediate layer between 15 cm and approximately 30 cm, and the lowest layer of soils in the claypan below 30 cm. The interaction between clay content and changes in soil factors with depth resulted in an increased potential activity but unaltered microbial composition in the claypan layer.

Through litter and root inputs, plants modulate soil properties and the soil microbial communities around them. In turn, these changes in soil properties and microbial community composition can impact plant performance (i.e., plant-soil feedbacks). Many studies have focused on how plant-soil feedbacks affect plant performance and successional patterns, but studies on the impact of plant-soil feedbacks on ecosystem processes are rare. Our research focused on the potential of species-specific plant-soil feedbacks to affect rates of soil organic matter (SOM) decomposition. We conducted a “home vs. away” plant-soil feedback greenhouse experiment using two C3 grass species (Bromus inermis and Pascopyrum smithii) grown in C4 tallgrass prairie soil. We used a closed-circuit CO2 trapping method and isotopic analysis to differentiate between root-derived and SOM-derived CO2 production. Contrary to our predictions, plant-soil feedbacks on plant biomass were independent of the effects of plant-soil interactions on SOM-derived CO2 production, but we did detect a significant legacy of conditioning by B. inermis on subsequent total belowground respiration (i.e., total belowground respiration was higher in soils originally conditioned by B. inermis regardless of which plant species was currently growing in those soils). We attribute these results to the differential effects of these plant species on soil chemistry and soil microbes during the original conditioning phase. This is supported by the observation that differences in soil chemistry and bacterial community composition persisted in soils conditioned by different plant species throughout the entire experiment. Together these results suggest that plant-soil history is important for soil respiration and that differences in soil microbial communities induced by conditioning with different plant species may have lasting effects on ecosystem processes.

Managing landscapes to maintain climate refugia is likely the best strategy to promote persistence of temperature-sensitive species with limited dispersal capacity. Rare, cold-stenothermic taxa occupy mosaic mountain stream networks due largely to hydrological source heterogeneity. We collected environmental and biological data from alpine streams in the Teton Range, Wyoming representing runoff from snowpack (N=3), glaciers (N=4) and subterranean ice (N=4), every summer from 2015-2017. We quantified differences in habitat among the streams according to a glaciality index that included bed stability, suspended solids, temperature and conductivity, and by comparing annual water temperature profiles for each stream. We measured to what degree macroinvertebrate and diatom assemblages varied by stream type. Abiotic and biotic characteristics appeared to differ among sources. Notably, streams fed by subterranean ice (icy seeps) maintained extremely low (mean

Exploration of the importance of developmental windows for microbial colonization in diverse animal taxa, and tests of how these shape both animal microbiomes as well as host phenotypes promise to shed needed light on host-microbe interactions. The aims of this study were to explore how gut microbiota diversity of larval amphibians varies among species and across ontogeny, and to test if manipulation of gut colonization can reveal how microbiomes develop. We found that gut microbiomes differ among species and change across larval ontogeny, with distinctive differences between larvae, metamorphic animals, and juvenile frogs. Through applying a gnotobiotic protocol to eggs and cross-inoculating gut microbiomes between species, we demonstrated that microbiota can be transplanted among species and developmental stages. These results also demonstrated that microbial colonization at hatching is potentially formative for long term composition and function of amphibian gut microbiomes, suggesting that hatching may be a critical developmental window for colonization, similar to the effects of birth mode on human microbiomes. Specifically, our results suggest that either the egg jelly and/or capsules surrounding amphibian eggs are likely important sources for initial microbiome inoculation. Furthermore, we speculate these results suggest that vertical transmission may be important to amphibian microbiome establishment and development, as is common among many animal taxa. Taken together, our results suggest that explicit tests of how host developmental windows influence microbial colonization, and shape amphibian microbiomes across life stages promise to provide insight into the ecological and evolutionary dynamics of host-microbe interactions.

Alpine streams are threatened as meltwater sources diminish. We established baseline monitoring efforts of alpine streams in the Teton Range during 2015 by describing biotic and abiotic conditions of surface glacier and snowmelt streams. Our results indicated a third alpine stream type, icy seeps. Icy seeps are fed by subterranean ice melt, extremely cold but stable water temperature (summer mean 50 μS cm-1). In 2016, we documented several icy seeps in the Teton massif, and our data suggest that they have the potential to serve as climate refugia for organisms and processes associated with extremely cold meltwater, due to the subterranean ice sources being more insulated from atmospheric conditions than surface glaciers and snowpack. Our 2016 work focused on locating icy seeps and documenting physical conditions, invertebrates, diatoms, and microbes in these alpine streams. We are processing the biological data, but microbial assemblages in icy seeps are similar to those found in streams fed by dwindling surface glacier ice. We are preparing to submit a paper about the microbial patterns, including how they compare to alpine streams representing comparable hydrological sources in Glacier National Park. Featured photo by Nicole Y-C on Unsplash. https://unsplash.com/photos/9XixVlnUCbk

Closing nutrient loops in terrestrial and aquatic ecosystems is integral to achieve resource security in the food-energy-water (FEW) nexus. We performed multiyear (2005-2008), monthly sampling of instream dissolved inorganic nutrient concentrations (NH4-N, NO3-N, soluble reactive phosphorus-SRP) along a ∼ 300-km arid-land river (Rio Grande, NM) and generated nutrient budgets to investigate how the net source/sink behavior of wastewater and irrigated agriculture can be holistically managed to improve water quality and close nutrient loops. Treated wastewater on average contributed over 90% of the instream dissolved inorganic nutrients (101 kg/day NH4-N, 1097 kg/day NO3-N, 656 kg/day SRP). During growing seasons, the irrigation network downstream of wastewater outfalls retained on average 37% of NO3-N and 45% of SRP inputs, with maximum retention exceeding 60% and 80% of NO3-N and SRP inputs, respectively. Accurate quantification of NH4-N retention was hindered by low loading and high variability. Nutrient retention in the irrigation network and instream processes together limited downstream export during growing seasons, with total retention of 33-99% of NO3-N inputs and 45-99% of SRP inputs. From our synoptic analysis, we identify trade-offs associated with wastewater reuse for agriculture within the scope of the FEW nexus and propose strategies for closing nutrient loops in arid-land rivers.

Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within-stream (α) diversity was highest in groundwater-fed springs, lowest in glacier-fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type-the icy seep-that are fed by subterranean ice, exhibit cold temperatures (summer mean

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

The current and future direction of aquatic ecological research leans toward addressing questions that cover multiple scales and levels of complexity. Historically, the ability to do comparative aquatic research across large spatial and temporal scales has been impeded by a lack of comparable measurements, standard methods, and a well organized data management and retrieval system. The National Ecological Observatory Network (NEON) is the first continental-scale ecological observation system designed to collect and provide freely available data on the drivers and responses of ecological change. In this paper, we describe past and present attempts to work across multiple scales in aquatic ecology, and the potential use of NEON aquatics data and infrastructure by researchers to integrate and expand ecological research programs and address novel ecological questions.

Microbial diversity and function in intermittent rivers and ephemeral streams (IRES) are tightly linked to specific habitat availability and hydrological phases. The intensity and frequency of the different phases (especially drying and rewetting) affect community composition and key functions, mainly linked to biogeochemical processes. Resistance and resilience strategies are distinct among microorganism groups-bacteria, archaea, fungi, protozoans-and strongly depend on different types of microhabitat or refuge available. The biodiversity of prokaryotes in IRES is strongly affected by hydrology but microhabitat conditions and type of benthic substrate significantly affect their community composition. Fungi are very sensitive to drying but use several refuges, including the terrestrial habitat, and resistance strategies. Protozoans show a wide range of survival strategies and several species can resist harsh conditions such as anoxia in drying pools. Thus, they become especially relevant for ecosystem functions when other organisms are inhibited. This sensitivity causes "waves" of microbial functions and biodiversity to covary with hydrological phases, potentially affecting ecosystem functioning and higher trophic levels. Microbially mediated functions in IRES are perhaps the most critical to freshwater ecosystem services such as nitrogen and carbon cycling. Therefore, efforts to manage and restore IRES will depend on improved understanding of hydrological controls on microbial communities and functions across space and time. © 2017 Copyright

Technological advances in sequencing technologies and bioinformatics analysis tools now enable the generation of a metagenome from soil, although the ultimate goal of obtaining the entire complement of all genes of all organisms in a given sample of soil still lies in the future. The rich information obtained from a soil metagenome will undoubtedly provide new insights into the taxonomic and functional diversity of soil microorganisms; the question is whether it will also yield greater understanding of how C, N, and other nutrients cycle in soil. The purpose of this review is to describe the steps involved in producing a soil metagenome, including some of the potential pitfalls associated with its production and annotation. Possible solutions to some of these challenges are presented. Selected examples from published soil metagenomic studies are discussed, with an emphasis on clues that they have provided about biogeochemical cycling.

Organic horizons of old-growth Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] forests are colonized by ectomycorrhizal fungi, which can form large patches or mats. Respiration, N mineralization, chitinase activity, and amino sugar C and N turnover are higher in soils colonized by ectomycorrhizal mats. To test if microbial activity in mat soil is driven by decomposition of fungal biomass, we incubated mat and non-mat soil with ¹³C¹⁵N-labeled, chitin-enriched fungal cell wall material. Cell wall material was readily decomposed during 22-d incubations in both soils, and cell-wall-derived ¹³C and ¹⁵N were traced into mineralized pools, extractable organic pools, microbial biomass, and microbial phospholipid fatty acids (PLFAs). Basal microbial activity was higher in mat soils. Although total respiration was higher in mat soils with cell walls added, more cell wall C was mineralized in non-mat than mat soils; this was inferred to reflect greater preferential respiration of cell wall C over soil organic matter (SOM). Mineralization of N from cell wall material was low, with no difference between soils, and positive priming of N mineralization from SOM occurred after 3 wk. Both the proportion of cell wall N assimilated and N growth yield efficiency (GYE) were higher than for cell wall C. The relative abundance of fungi was higher in cell-wall-amended soils, and cell-wall-derived ¹³C was found in fungal and Gram-negative bacterial PLFAs. Cell wall C assimilation and C GYE were higher in mat soils, which could be linked to greater mineralization of SOM or to differential activity of select microbial taxonomic groups. Chitin-rich fungal cell wall material was utilized as both a microbial N and C source; N was predominantly assimilated and C was predominantly metabolized. It is possible that fungal necromass may contribute to N stabilization in these soils.

Enzyme activities in soil indicate the relative activities of microbes, which include bacteria, fungi, algae, and other organisms. Changes in soil management alter the composition and activity of soil microbes. Plants rely on soil microbes to break down soil nutrients, and make those nutrients available for plant growth. Symbiotic relationships between soil microbes and plants enhance plant growth and productivity. Alternatively, antagonistic relationships between the soil microbial community and plants limit plant production. Soil dwellers such as nematodes or disease-causing fungi such as Macrophomina phaseolina (the fungus responsible for charcoal rot) can be particularly deleterious to crop growth and yield. Changes in the soil microbial community impact crop performance through the synergistic or antagonistic relationships between crop plants and soil biological activity. Our research is designed to explore soil microbial activity, assess changes in the potential activities of hydrolytic and oxidative enzymes involved in nutrient acquisition in the soil, and determine their potential impact on the productive capacity of soil.

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of 13 C- and 15 N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of 15 N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.

Amino sugar dynamics represent an important but under-investigated component of the carbon (C) and nitrogen (N) cycles in old-growth Douglas-fir forest soils. Because fungal biomass is high in these soils, particularly in areas colonized by rhizomorphic ectomycorrhizal fungal mats, organic matter derived from chitinous cell wall material (or the monomeric building block of chitin, N-acetylglucosamine (NAG)) could be a significant source of C or N to the soil microbiota, and thus an important driver of microbial C and N processing. This paper reports the results of incubation experiments initiated to measure chitin degradation, NAG utilization, and the contribution of these substrates to soil respiration and N mineralization rates in mat-colonized and non-mat soil organic horizons. Amendments of chitin and NAG stimulated respiration, N mineralization, and biomass accumulation in mat and non-mat soils, and responses to NAG amendment were stronger than to chitin amendment. NAG-induced respiration was consistently two-fold higher in mat soils than non-mat soils, but induced N mineralization was similar between the two soil patch types. Assimilation of both C and N into microbial biomass was apparent, biomass C:N ratio decreased in all treatments, and microbial N use efficiency (treatment means 0.25 ± 0.06–0.50 ± 0.05) was greater than C use efficiency (treatment means 0.12 ± 0.04–0.32 ± 0.02). NAGase enzyme response was non-linear and showed the same pattern in chitin and NAG amendments. Responses to NAG and chitin amendment differed between mat and non-mat soils, indicating different mechanisms driving NAG and chitin utilization or differences in saprotrophic community composition between the two soil patch types. Net chitin and NAG processing rates were 0.08–3.4 times the basal respiration rates and 0.07–14 times the ambient net N mineralization rates, high enough for the turnover of total soil amino sugars to potentially occur in days to weeks. The results support the hypotheses that amino sugars are important microbial C and N sources and drivers of C and N cycling in these soils.

Ammonia-oxidizing bacteria and ammonia-oxidizing archaea are commonly found together in soils, yet the factors influencing their relative distribution and activity remain unclear. We examined archaeal and bacterial amoA gene distribution, and used a novel bioassay to assess archaeal and bacterial contributions to nitrification potentials in soils spanning a range of land uses (forest, pasture, cultivated and long-term fallowed cropland) along a 10 km transect. The assay, which quantifies the extent to which acetylene-inactivated soil nitrification potential recovers (RNP) in the presence of bacterial protein synthesis inhibitors, indicated a significant archaeal contribution to the nitrification potentials of the pasture and long-term fallowed soils. Archaeal amoA gene abundance did not vary significantly among the soils, but bacterial amoA gene abundance did, resulting in archaeal : bacterial amoA abundance ratios ranging from 1.1 ± 0.8 in cultivated soils to 396 ± 176 in pasture soils. Both archaeal and bacterial amoA gene compositions were heterogeneous across the landscape, but differed in their patterns of variability. Archaeal amoA gene distributions were distinct among each of the three main land-use types: forest, pasture and cropland soils. In contrast, bacterial amoA gene composition was distinct in forest and in cultivated cropland, while pasture and long-term fallowed cropland soils were similar. In both pasture and long-term fallowed cropland soils, one phylotype of Nitrosospira cluster 3a was highly abundant. This distinct bacterial amoA gene fingerprint correlated with significant contributions of archaea to RNP of both soils, despite differences in archaeal amoA gene composition between the pasture and fallowed soils. This observation suggests that the factors driving the development of ammonia-oxidizing bacteria community composition might influence the extent of archaeal contribution to soil nitrification.

Microorganisms inhabiting stream sediments mediate biogeochemical processes of importance to both aquatic and terrestrial ecosystems. In deserts, the lateral margins of ephemeral stream channels (parafluvial sediments) are dried and rewetted, creating periodically wet conditions that typically enhance microbial activity. However, the influence of water content on microbial community composition and diversity in desert stream sediments is unclear. We sampled stream margins along gradients of wet to dry sediments, measuring geochemistry and bacterial 16S rRNA gene composition, at streams in both a cold (McMurdo Dry Valleys, Antarctica) and hot (Chihuahuan Desert, New Mexico, USA) desert. Across the gradients, sediment water content spanned a wide range (1.6-37.9% w/w), and conductivity was highly variable (12.3-1,380 μS cm(-2)). Bacterial diversity (at 97% sequence similarity) was high and variable, but did not differ significantly between the hot and cold desert and was not correlated with sediment water content. Instead, conductivity was most strongly related to diversity. Water content was strongly related to bacterial 16S rRNA gene community composition, though samples were distributed in wet and dry clusters rather than as assemblages shifting along a gradient. Phylogenetic analyses showed that many taxa from wet sediments at the hot and cold desert site were related to, respectively, halotolerant Gammaproteobacteria, and one family within the Sphingobacteriales (Bacteroidetes), while dry sediments at both sites contained a high proportion of taxa related to the Acidobacteria. These results suggest that bacterial diversity and composition in desert stream sediments is more strongly affected by hydrology and conductivity than temperature.

A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammoniaoxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 g/ml), whereas a combination of kanamycin plus gentamicin (800 g/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30°C and 40°C and without supplemental NH4 (

Agricultural and urban development alters nitrogen and other biogeochemical cycles in rivers worldwide. Because such biogeochemical processes cannot be measured empirically across whole river networks, simulation models are critical tools for understanding river-network biogeochemistry. However, limitations inherent in current models restrict our ability to simulate biogeochemical dynamics among diverse river networks. We illustrate these limitations using a river-network model to scale up in situ measures of nitrogen cycling in eight catchments spanning various geophysical and land-use conditions. Our model results provide evidence that catchment characteristics typically excluded from models may control river-network biogeochemistry. Based on our findings, we identify important components of a revised strategy for simulating biogeochemical dynamics in river networks, including approaches to modeling terrestrial-aquatic linkages, hydrologic exchanges between the channel, floodplain/riparian complex, and subsurface waters, and interactions between coupled biogeochemical cycles.

Canalization and incision are common morphological alterations associated with human land use that reduce hydrological/hydrodynamic linkages between surtace and ground waters in stream ecosystems. To explore the impacts of these anthropogenic changes on nutrient spiraling in streams, we measured the linkage between hyporheic and surface zones of reference and human-altered streams using 15 N-nitrate ( 15 NO 3 ― ) and bromide (Br ― ) tracer injection experiments. Experiments were conducted in 7 streams (3 reference, 3 agricultural and 1 urban) in Arizona and New Mexico, USA, over a 3 yr period during the Lotic Intersite Nitrogen eXperiment (LINX II). Groundwater wells (6―9 in each stream) were inserted to 30cm depth and multilevel samplers (MLS) were installed downstream from injection sites to measure inorganic nitrogen (N) and Br ― concentrations in hyporheic water. There was measurable surface water-ground water (SW-GW) connectivity, as indicated by Br ― concentrations in shallow alluvial ground water (0―30 cm depth) at all sites. SW-GW connectivity was higher in reference than in human-altered streams. Concentrations of NO 3 ― and NH 4 + in MLS cells (0―10, 10―20, and 20―30 cm below streambed) were inversely correlated, and 15 N-enrichment of both N species was measurable in groundwater wells. Hyporheic zones with lower surface-water infiltration had higher quantities of 15 NH 4 + than of 15 NO 3 ― . Whole stream uptake (k tot ; calculated during the LINX II experiments) was correlated with δ 15 NH 4 + in wells; i.e., high δ 15 NH 4 + in wells was associated with high stream uptake, and both whole stream NO 3 ― uptake and δ 15 NH 4 + were highest in the human-altered streams. The presence of enriched 15 NH 4 + in many of the wells within 24 h of injection suggested that dissimilatory nitrate reduction to ammonium (DNRA) was occurring in the hyporheic zone.

Water is a limiting factor for life in the McMurdo Dry Valleys (MDV), Antarctica. The active layer (seasonally thawed soil overlying permafrost) accommodates dynamic hydrological and biological processes for 10–16 weeks per year. Wetted margins (visually wetted areas with high moisture content) adjacent to lakes and streams are potential locations of great importance in the MDV because of the regular presence of liquid water, compared with the rest of the landscape where liquid water is rare. At 11 plots (four adjacent to lakes, seven adjacent to streams), soil particle size distribution, soil electrical conductivity, soil water content and isotopic signature, width of the wetted margin, and active layer thaw depth were characterised to determine how these gradients influence physicochemical properties that determine microbial habitat and biogeochemical cycling. Sediments were generally coarse-grained in wetted margins adjacent to both lakes and streams. Wetted margins ranged from 1·04 to 11·01 m in average length and were found to be longer at lakeside sites than streamside. Average thaw depths ranged from 0·12 to 0·85 m, and were found to be deepest under lake margins. Lake margins also had much higher soil electrical conductivity, steeper topographic gradients, but more gradual soil moisture gradients than stream margins. Patterns of soil water δ18O and δD distribution indicate capillary action and evaporation from wetted margins; margin pore waters generally demonstrated isotopic enrichment with distance from the shore, indicating evaporation of soil water. Lake margin pore waters were significantly more negative in DXS (DXS = δD-8δ18O) than streamside pore waters, indicating a longer history of evaporation there. Differences between lake and stream margins can be explained by the more consistent availability of water to lake margins than stream margins. Differences in margin characteristics between lakes and streams have important consequences for the microbial habitat of these margins and their functional role in biogeochemical cycling at these terrestrial–aquatic interfaces. Copyright © 2009 John Wiley & Sons, Ltd.

In desert ecosystems, microbial activity and associated nutrient cycles are driven primarily by water availability and secondarily by nutrient availability. This is especially apparent in the extremely low productivity cold deserts of the McMurdo Dry Valleys, Antarctica. In this region, sediments near streams and lakes provide the seasonally wet conditions necessary for microbial activity and nutrient cycling and thus transfer energy to higher organisms. However, aside from a few studies of soil respiration, rates of microbial activity throughout the region remain unexplored. We measured extracellular enzyme activity potentials (alkaline phosphatase, leucine-aminopeptidase, beta-glucosidase, phenol oxidase, and peroxidase) in soils adjacent to lakes and streams, expecting activity to be primarily related to soil water content, as well as time of season and organic matter supply. Phosphatase and beta-glucosidase activities were higher in shoreline than upland soils; however, potential rates were not correlated with soil water content. Instead, soil organic matter, salinity, and pH were the best predictors of microbial activity. Microbial nutrient limitation metrics estimated from extracellular enzyme activity were correlated with pH and salinity and exhibited similar patterns to previously published trends in soil P and N content. Compared to other terrestrial ecosystems, organic matter specific rates for leucine-aminopeptidase and oxidative enzyme activities were high, typical of alkaline desert soils. Phosphatase activity was close to the global mean whereas beta-glucosidase activity was extremely low, which may reflect the lack of vascular plant derived organic matter in the Dry Valleys. In this cold desert ecosystem, water availability promotes microbial activity, and microbial nutrient cycling potentials are related to soil geochemistry.

Extracellular enzymes are the proximate agents of organic matter decomposition and measures of these activities can be used as indicators of microbial nutrient demand. We conducted a global-scale meta-analysis of the seven-most widely measured soil enzyme activities, using data from 40 ecosystems. The activities of b-1,4-glucosidase, cellobiohydrolase, b-1,4-N-acetylglucosaminidase and phosphatase g )1 soil increased with organic matter concentration; leucine aminopeptidase, phenol oxidase and peroxidase activities showed no relationship. All activities were significantly related to soil pH. Specific activities, i.e. activity g )1 soil organic matter, also varied in relation to soil pH for all enzymes. Relationships with mean annual temperature (MAT) and precipitation (MAP) were generally weak. For hydrolases, ratios of specific C, N and P acquisition activities converged on 1 : 1 : 1 but across ecosystems, the ratio of C : P acquisition was inversely related to MAP and MAT while the ratio of C : N acquisition increased with MAP. Oxidative activities were more variable than hydrolytic activities and increased with soil pH. Our analyses indicate that the enzymatic potential for hydrolyzing the labile components of soil organic matter is tied to substrate availability, soil pH and the stoichiometry of microbial nutrient demand. The enzymatic potential for oxidizing the recalcitrant fractions of soil organic material, which is a proximate control on soil organic matter accumulation, is most strongly related to soil pH. These trends provide insight into the biogeochemical processes that create global patterns in ecological stoichiometry and organic matter storage.

Summary 1 Aridland ecosystems cover about one-third of terrestrial environments globally, yet the extent to which models of carbon (C) and nitrogen (N) cycling, developed largely from studies of mesic ecosystems, apply to aridland systems remains unclear. 2 Within aridland ecosystems, C and N dynamics are often described by a pulse-reserve model in which episodic precipitation events stimulate biological activity that generate reserves of biomass, propagules and organic matter that prime the ecosystem to respond rapidly to subsequent precipitation events. 3 The role of microbial C and N processing within the pulse-reserve paradigm has not received much study. We present evidence suggesting that fungi play a critical and underappreciated role in aridland soils, including efficient decomposition of recalcitrant C compounds, N-transformations such as nitrification, and nutrient storage and translocation of C and N between plants and biotic soil crusts. While fungi may perform some of these functions in other ecosystems, this ‘fungal loop’ assumes particular importance in the N cycle in aridlands because water availability imposes even greater restrictions on bacterial activity and physicochemical processes limit accumulation of soil organic matter (SOM). 4 We incorporate these findings into a Threshold-Delay Nutrient Dynamics (TDND) model for aridland ecosystems in which plant responses to pulsed precipitation events are mediated by a fungal loop that links C and N cycling, net primary production (NPP) and decomposition in aridland soils. 5 Synthesis. Arid ecosystems are highly sensitive to global environmental change including N deposition and altered precipitation patterns; yet, models from mesic ecosystems do not adequately apply to aridland environments. Our ‘fungal loop’ N cycle model integrates spatial structure with pulse dynamics and extends the pulse-reserve paradigm to include the key role of microbial processes in aridland ecosystem dynamics.

Polar deserts are characterized by limited water availability across much of the terrestrial landscape. In the McMurdo Dry Valleys, Antarctica, soil active layers are wetted only briefly after infrequent snowfall ( −1 ). Adjacent to glacial meltwater streams and lakes, however, sediments and soils appear visibly wetted throughout the summer. We hypothesized that this apparent wicking of water from aquatic environments is controlled by capillary action determined by the physical properties of near-shore sediments including slope, particle size distribution, and depth to permafrost. We performed synoptic sampling of near-shore sediments around two lakes in Taylor Valley, East Antarctica. We measured the water content, active layer depth, particle size distribution, and topography to determine the relative importance of shore slope, pore size distribution, and depth of the active layer on the spatial dimension of wetted hydrologic margins. The horizontal dimension (distance from the lake edge) of wetted margins ( H W ) and slopes ranged from 1.1 to 32.9 m and 1 to 61% and active layer depth ranged from 5.5 to >120 cm. Our results indicate that particle size distributions of near-shore sediments are homogeneous; slope had a greater effect on the dimensions of wetted margins, explaining 73% of the variance in H W . These findings show that the spatial dimensions of wetted zones are controlled by a suite of physical parameters that may be easily measured using remotely sensed data and a limited number of samples. Such information is useful for constraining landscape-scale models of nutrient redistribution because intermittently wetted soils are zones of enhanced biogeochemical transformation and transport in desert ecosystems.

The effects of global N enrichment on soil processes in grassland ecosystems have received relatively little study. We assessed microbial community response to experimental increases in N availability by measuring extracellular enzyme activity (EEA) in soils from three grasslands with contrasting edaphic and climatic characteristics: a semiarid grassland at the Sevilleta National Wildlife Refuge, New Mexico, USA (SEV), and mesic grasslands at Konza Prairie, Kansas, USA (KNZ) and Ukulinga Research Farm, KwaZulu-Natal, South Africa (SAF). We hypothesized that, with N enrichment, soil microbial communities would increase C and P acquisition activity, decrease N acquisition activity, and reduce oxidative enzyme production (leading to recalcitrant soil organic matter [SOM] accumulation), and that the magnitude of response would decrease with soil age (due to higher stabilization of enzyme pools and P limitation of response). Cellulolytic activities followed the pattern predicted, increasing 35-52% in the youngest soil (SEV), 10-14% in the intermediate soil (KNZ) and remaining constant in the oldest soil (SAF). The magnitude of phosphatase response did not vary among sites. N acquisition activity response was driven by the enzyme closest to its pH optimum in each soil: i.e., leucine aminopeptidase in alkaline soil, beta-N-acetylglucosaminidase in acidic soil. Oxidative enzyme activity varied widely across ecosystems, but did not decrease with N amendment at any site. Likewise, SOM and %C pools did not respond to N enrichment. Between-site variation in both soil properties and EEA exceeded any treatment response, and a large portion of EEA variability (leucine aminopeptidase and oxidative enzymes), 68% as shown by principal components analysis, was strongly related to soil pH (r = 0.91, P0.001). In these grassland ecosystems, soil microbial responses appear constrained by a molecular-scale (pH) edaphic factor, making potential breakdown rates of SOM resistant to N enrichment.

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of the hundreds of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream organic matter compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors.

In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

Nutrient spiraling in theory and application provides a framework for comparing nutrient retention efficiency of urban streams to relatively unaltered streams. Previous research indicated that streams of the southwestern USA deserts are highly retentive of N because of N limitation, high productivity, and high channel complexity (in particular, extensive transient storage associated with the hyporheic zone). Most southwestern urban streams have extensively modified channels and experience N loading from urban runoff and inputs of NO3−-contaminated groundwater. Therefore, we predicted southwestern urban streams are neither N-limited nor retentive. For some urban streams, however, restoration efforts reestablish flow in long-dry channels, create nonstructural flood-management solutions, and design riparian areas as a public recreation amenity. These human modifications may, in part, restore N retention functions if channel complexity and heterogeneity are as important to N retention efficiency as be...