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USGS2013

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

Florida↗

USGS2007

Toward a transport-based analysis of nutrient spiraling and uptake in streams

Nutrient addition experiments are designed to study the cycling of nutrients in stream ecosystems where hydrologic and nonhydrologic processes determine nutrient fate. Because of the importance of hydrologic processes in stream ecosystems, a conceptual model known as nutrient spiraling is frequently employed. A central part of the nutrient spiraling approach is the determination of uptake length ( S w ), the average distance traveled by dissolved nutrients in the water column before uptake. Although the nutrient spiraling concept has been an invaluable tool in stream ecology, the current practice of estimating uptake length from steady‐state nutrient data using linear regression (called here the “ S w approach”) presents a number of limitations. These limitations are identified by comparing the exponential S w equation with analytical solutions of a stream solute transport model. This comparison indicates that (1) S w is an aggregate measure of uptake that does not distinguish between main channel and storage zone processes, (2) S w is an integrated measure of numerous hydrologic and nonhydrologic processes—this process integration may lead to difficulties in interpretation when comparing estimates of S w , and (3) estimates of uptake velocity and areal uptake rate ( v f and U ) based on S w are not independent of system hydrology. Given these findings, a transport‐based approach to nutrient spiraling is presented for steady‐state and time‐series data sets. The transport‐based approach for time‐series data sets is suggested for future research on nutrient uptake as it provides a number of benefits, including the ability to (1) separately quantify main channel and storage zone uptake, (2) quantify specific hydrologic and nonhydrologic processes using various model parameters (process separation), (3) estimate uptake velocities and areal uptake rates that are independent of hydrologic effects, and (4) use shortterm, non‐plateau nutrient additions such that the effects of regeneration and mineralization are minimized. In summary, the transport‐based, time‐series approach provides a means of estimating traditional measures of nutrient uptake ( S w , v f , U ) while providing additional information on the location and magnitude of uptake (main channel versus storage zone). Application of the transport‐based approach to time‐series data from Green Creek, Antarctica, indicates that the bulk of nitrate uptake (~74% to 100%) occurred within the main channel where benthic uptake by algal mats is a likely process. Substantial uptake (~26%) also occurred in the storage zone of one reach, where uptake is attributed to the microbial community.

Limnology and Oceanography: Methods↗

USGS2006

Correlates of biological soil crust abundance across a continuum of spatial scales: Support for a hierarchical conceptual model

1. Desertification negatively impacts a large proportion of the global human population and > 30% of the terrestrial land surface. Better methods are needed to detect areas that are at risk of desertification and to ameliorate desertified areas. Biological soil crusts are an important soil lichen-moss-microbial community that can be used toward these goals, as (i) bioindicators of desertification damage and (ii) promoters of soil stability and fertility. 2. We identified environmental factors that correlate with soil crust occurrence on the landscape and might be manipulated to assist recovery of soil crusts in degraded areas. We conducted three studies on the Colorado Plateau, USA, to investigate the hypotheses that soil fertility [particularly phosphorus (P), manganese (Mn) and zinc (Zn)] and/or moisture limit soil crust lichens and mosses at four spatial scales. 3. In support of the soil fertility hypothesis, we found that lichen-moss crusts were positively correlated with several nutrients [Mn, Zn, potassium (K) and magnesium (Mg) were most consistent] at three of four spatial scales ranging from 3.5 cm2 in area to c. 800 km2. In contrast, P was negatively correlated with lichen-moss crusts at three scales. 4. Community composition varied with micro-aspect on ridges in the soil crust. Three micro-aspects [north-north-west (NNW), east-north-east (ENE) and TOP] supported greater lichen and moss cover than the warmer, windward and more xeric micro-aspects [west-south-west (WSW) and south-south-east (SSE)]. This pattern was poorly related to soil fertility; rather, it was consistent with the moisture limitation hypothesis. 5. Synthesis and application. Use of crusts as desertification bioindicators requires knowledge of a site's potential for crust cover in the absence of desertification. We present a multi-scale model of crust potential as a function of site properties. Future quantitative studies can use this model to guide sampling efforts. Also, our results suggest new directions in restoration research: enhancement of moisture residence time and fertilization with key nutrients (Mn, Zn, K and Mg). Re-establishment of soil crusts in desertified lands will help regain lost soil stability and fertility, and facilitate plant re-establishment. ?? 2006 British Ecological Society.

Journal of Applied Ecology↗

USGS2020

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution↗

USGS2007

Integrated geoscience studies in the Greater Yellowstone Area - Volcanic, tectonic, and hydrothermal processes in the Yellowstone geoecosystem

Yellowstone National Park, rimmed by a crescent of older mountainous terrain, has at its core the Quaternary Yellowstone Plateau, an undulating landscape shaped by forces of volcanism, tectonism, and later glaciation. Its spectacular hydrothermal systems cap this landscape. From 1997 through 2003, the United States Geological Survey Mineral Resources Program conducted a multidisciplinary project of Yellowstone National Park entitled Integrated Geoscience Studies of the Greater Yellowstone Area, building on a 130-year foundation of extensive field studies (including the Hayden survey of 1871, the Hague surveys of the 1880s through 1896, the studies of Iddings, Allen, and Day during the 1920s, and NASA-supported studies starting in the 1970s—now summarized in USGS Professional Paper 729 A through G) in this geologically dynamic terrain. The project applied a broad range of scientific disciplines and state-of-the-art technologies targeted to improve stewardship of the unique natural resources of Yellowstone and enable the National Park Service to effectively manage resources, protect park visitors from geologic hazards, and better educate the public on geologic processes and resources. This project combined a variety of data sets in characterizing the surficial and subsurface chemistry, mineralogy, geology, geophysics, and hydrothermal systems in various parts of the park. The sixteen chapters presented herein in USGS Professional Paper 1717, Integrated Geoscience Studies in the Greater Yellowstone Area—Volcanic, Tectonic, and Hydrothermal Processes in the Yellowstone Geoecosystem , can be divided into four major topical areas: (1) geologic studies, (2) Yellowstone Lake studies, (3) geochemical studies, and (4) geophysical studies. The geologic studies include a paper by Ken Pierce and others on the influence of the Yellowstone hotspot on landscape formation, the ecological effects of the hotspot, and the human experience and human geography of the greater Yellowstone ecosystem as influenced by the Yellowstone hotspot. Another paper by Paul Carrara describes the recent movement of a large landslide block dated by tree-ring analyses in the Tower Falls area. The section under Yellowstone Lake studies begins with a classic paper by J. David Love and others on ancestral Lake Yellowstone. Other papers in this section include results and interpretation of the high-resolution bathymetric, seismic reflection, and submersible studies by Lisa Morgan and others. Ken Pierce and others describe results from their studies of shorelines along Yellowstone Lake and their interpretation of inflation-deflation cycles, tilting, and faulting in the Yellowstone caldera. The influence of sublacustrine hydrothermal vent fluids on the geochemistry of Yellowstone Lake is described by Laurie Balistrieri and others. In Pat Shanks and others’ chapter, hydrothermal reactions, stable-isotope systematics, sinter deposition, and spire formation are related to the geochemistry of sublacustrine hydrothermal deposits in Yellowstone Lake. The geochemical studies section considers park-wide geochemical systems in Yellowstone National Park. In Bob Rye and Alfred Truesdell’s paper, the question of recharge to the deep thermal reservoir underlying the geysers and hot springs of Yellowstone National Park is discussed. Irving Friedman and Dan Norton report on the chloride flux emissions from Yellowstone in their paper questioning whether Yellowstone is losing its steam. Wildlife issues as addressed by examining trace-element and stable-isotope geochemistry are discussed in a chapter by Maurice Chaffee and others. In another chapter by Chaffee and others, natural and anthropogenic anomalies and their potential impact on the environment using geochemistry is reported. Pam Gemery-Hill and others present geochemical data for selected rivers, lake waters, hydrothermal vents, and subaerial geysers for the time interval of 1996–2004. The life cycle of gold deposits near the northeast corner of the park is discussed by Brad Van Gosen. Under the geophysical studies segment, Ray Kokaly and others use AVIRIS (Airborne Visible and Infrared Spectroscopy) data to map vegetation cover and microbial communities in Yellowstone National Park. Eric Livo and others report their results using AVIRIS data on hydrothermally altered rock and hot-spring deposits. In his final paper following a half century of scientific research, Irving Friedman presents data on monitoring changes in geothermal activity at Norris Geyser Basin using satellite telemetry. These papers summarize a near-decade-long effort by the USGS from the late 1990s to mid-2000s. In 2001, the USGS in cooperation with the National Park Service (Yellowstone National Park) and the University of Utah established the Yellowstone Volcano Observatory, the 5th volcano observatory in the United States.

Professional Paper↗

USGS2025

Scaling from microsite to landscape to resolve litter decomposition dynamics in globally extensive drylands

1. Decomposition controls the release of carbon and nutrients from decaying plant litter into soils or the atmosphere. In most biomes decomposition rates can be accurately predicted with simple mathematical models, but these models have long under-predicted decomposition in globally- extensive drylands. 2. We posit that the exposed surface conditions characteristic of drylands makes litter decomposition uniquely subject to microsite-specific environmental controls and spatially-variable microbial communities. As such, decomposition in dryland ecosystems – which are characterized by extremes in temporal heterogeneity of climate conditions and spatial heterogeneity of vegetation cover with corresponding microclimate variability – is a prime example of a macrosystems process that can be addressed by merging field data with new predictive models operating across a hierarchical continuum of spatial scales and process resolutions. 3. A macrosystems approach offers promise to reconcile model-measurement discrepancies by integrating observations and experiments across multiple scales, from microsites (e.g., shrub sub-canopy or intercanopy) to regions (e.g., across a 100s of km2 study site with complex topography, precipitation, and temperature) and ultimately to a continental perspective (e.g., North American drylands). 4. Recent developments in technology and data availability position the scientific community to integrate lab, field, modeling, and remote sensing approaches across a hierarchical range of scales to capture the spatiotemporal distribution of litter and environmental conditions needed to predict decay dynamics at the micro-to-macroscale. This multi-scale approach promises a path forward to resolving a longstanding disconnect between measured and modeled data in dryland litter decomposition. 5. Dryland litter decomposition presents an excellent case study for resolving spatially and temporally complex biogeochemical dynamics through a hierarchical, multidisciplinary macrosystems approach. 6. We focus on dryland litter decomposition, but the hierarchical, multidisciplinary macrosystems approach we outline shows great potential for resolving other spatially and temporally complex biogeochemical processes across a wide range of ecosystems.

Functional Ecology↗

USGS2022

Deconstructing the microbial necromass continuum to inform soil carbon sequestration

Microbial necromass is a large, dynamic and persistent component of soil organic carbon, the dominant terrestrial carbon pool. Quantification of necromass carbon stocks and its susceptibility to global change is becoming standard practice in soil carbon research. However, the typical proxies used for necromass carbon do not reveal the dynamic nature of necromass carbon flows and transformations within soil that ultimately determine necromass persistence. In this review, we define and deconstruct four stages of the necromass continuum: production, recycling, stabilization and destabilization. Current understanding of necromass dynamics is described for each continuum stage. We highlight recent advances, methodological limitations and knowledge gaps which need to be addressed to determine necromass pool sizes and transformations. We discuss the dominant controls on necromass process rates and aspects of soil microscale structure including biofilms and food web interactions. The relative importance of each stage of the continuum is then compared in contrasting ecosystems and for climate change drivers. From the perspective of the continuum, we draw three conclusions to inform future research. First, controls on necromass persistence are more clearly defined when viewed through the lens of the continuum; second, destabilization is the least understood stage of the continuum with recycling also poorly evidenced outside of a few ecosystems; and third, the response of necromass process rates to climate change is unresolved for most continuum stages and ecosystems. Future mechanistic research focused on the role of biotic and abiotic soil microscale structure in determining necromass process rates and the relative importance of organo–mineral and organo–organo interactions can inform necromass persistence in different climate change scenarios. Our review demonstrates that deconstructing the necromass continuum is key to predicting the vulnerability and persistence of necromass carbon in a changing world.

Functional Ecology↗

USGS2020

Modest residual effects of short-term warming, altered hydration, and biocrust successional state on dryland soil heterotrophic carbon and nitrogen cycling

Biological soil crusts (biocrusts) on the Colorado Plateau may fuel carbon (C) and nitrogen (N) cycling of soil heterotrophic organisms throughout the region. Late successional moss and lichen biocrusts, in particular, can increase soil C and N availability, but some data suggest these biocrust types will be replaced by early successional cyanobacterial biocrusts as the region undergoes warming and aridification. In this study, we evaluated the short-term interactive effects of biocrust successional state and elevated temperature on soil heterotrophic C and N cycling (specifically, soil respiration, N 2 O emissions, microbial biomass C and N, and soluble C and N). We collected soils following an 87-day greenhouse mesocosm experiment where the soils had been topped with different biocrust successional states (moss-dominated, cyanobacteria-dominated, or no biocrust) and had experienced different temperatures (ambient and warmed), under an artificial precipitation regime. Following this pre-incubation mesocosm phase, the soils were assessed using a short-term (2-day) laboratory incubation to determine the cumulative effect of the elevated temperature and altered biocrust successional state on the temperature sensitivity of soil heterotrophic C and N cycling. We found that there were interactive effects of biocrust successional state and exposure to warmer temperatures during the mesocosm phase under greenhouse conditions on the rate and temperature sensitivity of soil heterotrophic C and N cycling in laboratory incubations. Soils collected from beneath late successional biocrusts exhibited higher C and N cycling rates than those from beneath early successional crusts, while warming reduced both the magnitude and the temperature sensitivity of C and N cycling. The inhibiting effect of warming, was most evident in soils from beneath late successional biocrusts, which, during the mesocosm phase, also exhibited the greatest reductions in gross primary production and respiration in response to the warming treatment. Taken together, these data suggest that an overall effect of climate warming may be increasing resource limitation of the soil heterotrophic C and N cycles in the region, which may magnify alterations associated with the changes in biocrust community structure documented in previous studies. Overall, results from this study suggest that soil heterotrophic biogeochemical cycling is affected by interactions between temperature and the biocrust community that lives atop the mineral soil, with important implications for C and N cycling into the future.

Nevada↗