Publications by authors named "Zachary T Aanderud"

19 Publications

  • Page 1 of 1

Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance.

Environ Sci (Camb) 2021 ;9

Department of Civil & Environmental Engineering, Stanford University, Stanford, CA, USA.

SARS-CoV-2 RNA detection in wastewater is being rapidly developed and adopted as a public health monitoring tool worldwide. With wastewater surveillance programs being implemented across many different scales and by many different stakeholders, it is critical that data collected and shared are accompanied by an appropriate minimal amount of metainformation to enable meaningful interpretation and use of this new information source and intercomparison across datasets. While some databases are being developed for specific surveillance programs locally, regionally, nationally, and internationally, common globally-adopted data standards have not yet been established within the research community. Establishing such standards will require national and international consensus on what metainformation should accompany SARS-CoV-2 wastewater measurements. To establish a recommendation on minimum information to accompany reporting of SARS-CoV-2 occurrence in wastewater for the research community, the United States National Science Foundation (NSF) Research Coordination Network on Wastewater Surveillance for SARS-CoV-2 hosted a workshop in February 2021 with participants from academia, government agencies, private companies, wastewater utilities, public health laboratories, and research institutes. This report presents the primary two outcomes of the workshop: (i) a recommendation on the set of minimum meta-information that is needed to confidently interpret wastewater SARS-CoV-2 data, and (ii) insights from workshop discussions on how to improve standardization of data reporting.
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http://dx.doi.org/10.1039/d1ew00235jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459677PMC
January 2021

Phagotrophic Protists and Their Associates: Evidence for Preferential Grazing in an Abiotically Driven Soil Ecosystem.

Microorganisms 2021 Jul 21;9(8). Epub 2021 Jul 21.

Department of Biology, Brigham Young University, Provo, UT 84602, USA.

The complex relationship between ecosystem function and soil food web structure is governed by species interactions, many of which remain unmapped. Phagotrophic protists structure soil food webs by grazing the microbiome, yet their involvement in intraguild competition, susceptibility to predator diversity, and grazing preferences are only vaguely known. These species-dependent interactions are contextualized by adjacent biotic and abiotic processes, and thus obfuscated by typically high soil biodiversity. Such questions may be investigated in the McMurdo Dry Valleys (MDV) of Antarctica because the physical environment strongly filters biodiversity and simplifies the influence of abiotic factors. To detect the potential interactions in the MDV, we analyzed the co-occurrence among shotgun metagenome sequences for associations suggestive of intraguild competition, predation, and preferential grazing. In order to control for confounding abiotic drivers, we tested co-occurrence patterns against various climatic and edaphic factors. Non-random co-occurrence between phagotrophic protists and other soil fauna was biotically driven, but we found no support for competition or predation. However, protists predominately associated with Proteobacteria and avoided Actinobacteria, suggesting grazing preferences were modulated by bacterial cell-wall structure and growth rate. Our study provides a critical starting-point for mapping protist interactions in native soils and highlights key trends for future targeted molecular and culture-based approaches.
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http://dx.doi.org/10.3390/microorganisms9081555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8398437PMC
July 2021

Citizen science reveals unexpected solute patterns in semiarid river networks.

PLoS One 2021 19;16(8):e0255411. Epub 2021 Aug 19.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America.

Human modification of water and nutrient flows has resulted in widespread degradation of aquatic ecosystems. The resulting global water crisis causes millions of deaths and trillions of USD in economic damages annually. Semiarid regions have been disproportionately affected because of high relative water demand and pollution. Many proven water management strategies are not fully implemented, partially because of a lack of public engagement with freshwater ecosystems. In this context, we organized a large citizen science initiative to quantify nutrient status and cultivate connection in the semiarid watershed of Utah Lake (USA). Working with community members, we collected samples from ~200 locations throughout the 7,640 km2 watershed on a single day in the spring, summer, and fall of 2018. We calculated ecohydrological metrics for nutrients, major ions, and carbon. For most solutes, concentration and leverage (influence on flux) were highest in lowland reaches draining directly to the lake, coincident with urban and agricultural sources. Solute sources were relatively persistent through time for most parameters despite substantial hydrological variation. Carbon, nitrogen, and phosphorus species showed critical source area behavior, with 10-17% of the sites accounting for most of the flux. Unlike temperate watersheds, where spatial variability often decreases with watershed size, longitudinal variability showed an hourglass shape: high variability among headwaters, low variability in mid-order reaches, and high variability in tailwaters. This unexpected pattern was attributable to the distribution of human activity and hydrological complexity associated with return flows, losing river reaches, and diversions in the tailwaters. We conclude that participatory science has great potential to reveal ecohydrological patterns and rehabilitate individual and community relationships with local ecosystems. In this way, such projects represent an opportunity to both understand and improve water quality in diverse socioecological contexts.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255411PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8376020PMC
November 2021

Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds.

Sci Total Environ 2021 Jun 12;775:145790. Epub 2021 Feb 12.

Utah Department of Health, Division of Disease Control and Prevention, Bureau of Epidemiology, 288 N 1460 W, Salt Lake City, UT, USA.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19), is shed in feces and the viral ribonucleic acid (RNA) is detectable in wastewater. A nine-week wastewater epidemiology study of ten wastewater facilities, serving 39% of the state of Utah or 1.26 M individuals was conducted in April and May of 2020. COVID-19 cases were tabulated from within each sewershed boundary. RNA from SARS-CoV-2 was detectable in 61% of 126 wastewater samples. Urban sewersheds serving >100,000 individuals and tourist communities had higher detection frequencies. An outbreak of COVID-19 across two communities positively correlated with an increase in wastewater SARS-CoV-2 RNA, while a decline in COVID-19 cases preceded a decline in RNA. SARS-CoV-2 RNA followed a first order decay rate in wastewater, while 90% of the RNA was present in the liquid phase of the influent. Infiltration and inflow, virus decay and sewershed characteristics should be considered during correlation analysis of SAR-CoV-2 with COVID-19 cases. These results provide evidence of the utility of wastewater epidemiology to assist in public health responses to COVID-19.
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http://dx.doi.org/10.1016/j.scitotenv.2021.145790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7879159PMC
June 2021

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems.

Front Microbiol 2020 26;11:491425. Epub 2020 Nov 26.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States.

Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms' abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, United States) across three seasons. Of the 53 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.
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http://dx.doi.org/10.3389/fmicb.2020.491425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726219PMC
November 2020

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms.

Front Microbiol 2020 15;11:526545. Epub 2020 Oct 15.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States.

Bacteria in stream biofilms contribute to stream biogeochemical processes and are potentially sensitive to the substantial levels of pollution entering urban streams. To examine the effects of contaminants on stream biofilm bacteria , we exposed growing biofilms to experimental additions of nutrients [nitrogen (N), phosphorus (P), and iron (Fe)], pharmaceuticals (caffeine and diphenhydramine), nutrients plus pharmaceuticals, or no contaminants using contaminant exposure substrates (CES) in three catchments in northern Utah. We performed our study at montane and urban sites to examine the influence of existing pollution on biofilm response. We identified bacterial core communities (core) for each contaminant treatment at each land-use type (e.g., nutrient addition montane bacterial core, nutrient addition urban bacterial core, pharmaceutical addition montane bacterial core) by selecting all taxa found in at least 75% of the samples belonging to each specific grouping. Montane and urban land-use distinguished bacterial cores, while nutrients and pharmaceuticals had subtle, but nonetheless distinct effects. Nutrients enhanced the dominance of already abundant copiotrophs [i.e., Pseudomonadaceae (Gammaproteobacteria) and Comamonadaceae (Betaproteobacteria)] within bacterial cores at montane and urban sites. In contrast, pharmaceuticals fostered species-rich bacterial cores containing unique contaminant-degrading taxa within Pseudomonadaceae and Anaerolineaceae (Chloroflexi). Surprisingly, even at urban sites containing ambient pharmaceutical pollution, pharmaceutical additions increased bacterial core richness, specifically within DR-16 (Betaproteobacteria), WCHB1-32 (Bacteroidetes), and Leptotrichiaceae (Fusobacteria). Nutrients exerted greater selective force than pharmaceuticals in nutrient plus pharmaceutical addition treatments, creating bacterial cores more closely resembling those under nutrient rather than pharmaceutical addition, and promoting unique Oscillatoriales (Cyanobacteria) taxa in urban streams. Our results show that additions of N, P, and Fe intensified the dominance of already abundant copiotrophs, while additions of caffeine and diphenhydramine enabled unique taxa associated with contaminant degradation to participate in bacterial cores. Further, biofilm bacteria at urban sites remained sensitive to pharmaceuticals commonly present in waters, suggesting a dynamic interplay among pharmaceutical pollution, bacterial diversity, and contaminant degradation.
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http://dx.doi.org/10.3389/fmicb.2020.526545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593328PMC
October 2020

Mercury and dissolved organic matter dynamics during snowmelt runoff in a montane watershed, Provo River, Utah, USA.

Sci Total Environ 2020 Feb 23;704:135297. Epub 2019 Nov 23.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.

The mechanisms of Hg and dissolved organic matter (DOM) transport from watersheds to streams remain unclear, especially in snowmelt dominated montane systems. We characterized total Hg concentrations and DOM characteristics during snowmelt by weekly and/or monthly sampling at three locations in the upper Provo River, northern Utah, over two water years (2016 and 2017). Total Hg concentrations increased from <1 ng/L during baseflow to >7 ng/L during the snowmelt period (April-June), with decreasing concentrations from upstream to downstream. Filtered THg concentrations accounted for 65-75% of the unfiltered concentrations, suggesting that Hg is primarily transported in the dissolved phase. Annual THg loading in the upper Provo River was approximately 1 kg/yr, with ~90% of the flux occurring during the snowmelt period. Filtered THg concentrations were strongly correlated with in-situ fluorescence DOM (fDOM) measurements, allowing for the development of high-resolution proxy THg concentrations. Further, DOM characteristics, evaluated using excitation-emission matrices (EEMs) and parallel factor analysis (PARAFAC), identified the dominance of soil humic and fulvic acid fractions of DOM during runoff. Total Hg concentrations were low in snowpack but elevated in ephemeral streams during snowmelt runoff, indicating that Hg originated from shallow soil water rather than snow. Concentration-discharge relationships revealed clockwise hysteresis patterns, suggesting that Hg was flushed from soils on the rising limb of the hydrograph. Our results demonstrate that a majority of Hg transport occurs with a flux of DOM during the short snowmelt season as shallow soils are flushed by meltwater. The snowmelt-driven Hg pulse is a substantial source to downstream reservoirs and potentially contributes to a fish consumption advisory.
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http://dx.doi.org/10.1016/j.scitotenv.2019.135297DOI Listing
February 2020

Salt-Tolerant Halophyte Rhizosphere Bacteria Stimulate Growth of Alfalfa in Salty Soil.

Front Microbiol 2019 14;10:1849. Epub 2019 Aug 14.

Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States.

Halophytes are plants that are adapted to grow in saline soils, and have been widely studied for their physiological and molecular characteristics, but little is known about their associated microbiomes. Bacteria were isolated from the rhizosphere and as root endophytes of and , three native Utah halophytes. A total of 41 independent isolates were identified by 16S rRNA gene sequencing analysis. Isolates were tested for maximum salt tolerance, and some were able to grow in the presence of up to 4 M NaCl. Pigmentation, Gram stain characteristics, optimal temperature for growth, and biofilm formation of each isolate aided in species identification. Some variation in the bacterial population was observed in samples collected at different times of the year, while most of the genera were present regardless of the sampling time. , , and species were consistently isolated both from the soil and as endophytes from roots of all three plant species at all collection times. Non-culturable bacterial species were analyzed by Illumina DNA sequencing. The most commonly identified bacteria were from several phyla commonly found in soil or extreme environments: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gamma- and Delta-Proteobacteria. Isolates were tested for the ability to stimulate growth of alfalfa under saline conditions. This screening led to the identification of one and one isolate that, when used to inoculate young alfalfa seedlings, stimulate plant growth in the presence of 1% NaCl, a level that significantly inhibits growth of uninoculated plants. The same bacteria used in the inoculation were recovered from surface sterilized alfalfa roots, indicating the ability of the inoculum to become established as an endophyte. The results with these isolates have exciting promise for enhancing the growth of inoculated alfalfa in salty soil.
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http://dx.doi.org/10.3389/fmicb.2019.01849DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6702273PMC
August 2019

Corrigendum: Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages.

Front Microbiol 2019 12;10:391. Epub 2019 Mar 12.

Evolutionary Ecology Laboratories, and Monte L. Bean Museum, Department of Biology, Brigham Young University, Provo, UT, United States.

[This corrects the article DOI: 10.3389/fmicb.2018.01401.].
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http://dx.doi.org/10.3389/fmicb.2019.00391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423447PMC
March 2019

Sediment potentially controls in-lake phosphorus cycling and harmful cyanobacteria in shallow, eutrophic Utah Lake.

PLoS One 2019 14;14(2):e0212238. Epub 2019 Feb 14.

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States of America.

Lakes worldwide are impacted by eutrophication and harmful algal or cyanobacteria blooms (HABs) due to excessive nutrients, including legacy P released from sediments in shallow lakes. Utah Lake (northern Utah, USA) is a shallow lake with urban development primarily on the east side of the watershed, providing an opportunity to evaluate HABs in relation to a gradient of legacy sediment P. In this study, we investigated sediment composition and P concentrations in sediment, pore water, and the water column in relation to blooms of harmful cyanobacteria species. Sediments on the east side of the lake had P concentrations up to 1710 mg/kg, corresponding to elevated P concentrations in pore water (up to 10.8 mg/L) and overlying water column (up to 1.7 mg/L). Sediment P concentrations were positively correlated with Fe2O3, CaO, and organic matter abundance, and inversely correlated with SiO2, demonstrating the importance of sediment composition for P sorption and mineral precipitation. Although the sediment contained <3% Fe2O3 by weight, approximately half of the sediment P was associated with redox-sensitive Fe oxide/hydroxide minerals that could be released to the water column under reducing conditions. Cyanobacteria cell counts indicate that blooms of Aphanizomenon flos-aquae and Dolichospermum flosaquae species tend to occur on the east side of Utah Lake, corresponding to areas with elevated P concentrations in the sediment, pore water, and water column. Our findings suggest that shallow lake eutrophication may be a function of P in legacy sediments that contribute to observed HABs in specific locations of shallow lakes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212238PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375609PMC
November 2019

Use of auto-germ to model germination timing in the sagebrush-steppe.

Ecol Evol 2018 Dec 14;8(23):11533-11542. Epub 2018 Nov 14.

Department of Plant and Wildlife Sciences Brigham Young University Provo Utah.

Germination timing has a strong influence on direct seeding efforts, and therefore is a closely tracked demographic stage in a wide variety of wildland and agricultural settings. Predictive seed germination models, based on soil moisture and temperature data in the seed zone are an efficient method of estimating germination timing. We utilized Visual Basic for Applications (VBA) to create Auto-Germ, which is an Excel workbook that allows a user to estimate field germination timing based on wet-thermal accumulation models and field temperature and soil moisture data. To demonstrate the capabilities of Auto-Germ, we calculated various germination indices and modeled germination timing for 11 different species, across 6 years, and 10 -steppe sites in the Great Basin of North America to identify the planting date required for 50% or more of the simulated population to germinate in spring (1 March or later), which is when conditions are predicted to be more conducive for plant establishment. Both between and within the species, germination models indicated that there was high temporal and spatial variability in the planting date required for spring germination to occur. However, some general trends were identified, with species falling roughly into three categories, where seeds could be planted on average in either fall ( ssp.  and ), early winter (, , , and ), or mid-winter (, , and ) and still not run the risk of germination during winter. These predictions made through Auto-Germ demonstrate that fall may not be an optimal time period for sowing seeds for most non-dormant species if the desired goal is to have seeds germinate in spring.
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http://dx.doi.org/10.1002/ece3.4591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303710PMC
December 2018

Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages.

Front Microbiol 2018 3;9:1401. Epub 2018 Jul 3.

Evolutionary Ecology Laboratories, and Monte L. Bean Museum, Department of Biology, Brigham Young University, Provo, UT, United States.

Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH and NO, and P as NaPO) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After 6 years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant [e.g., nitrite oxidizing species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium]. Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.
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http://dx.doi.org/10.3389/fmicb.2018.01401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037766PMC
July 2018

Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes.

Front Microbiol 2016 9;7:853. Epub 2016 Jun 9.

Department of Microbiology and Molecular Biology, Brigham Young University Provo, UT, USA.

Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.
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http://dx.doi.org/10.3389/fmicb.2016.00853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899617PMC
July 2016

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity.

Front Microbiol 2015 30;6:24. Epub 2015 Jan 30.

Department of Biology, Indiana University Bloomington, IN, USA.

Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H(18) 2O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69-74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5-20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.
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http://dx.doi.org/10.3389/fmicb.2015.00024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311709PMC
February 2015

Altered snowfall and soil disturbance influence the early life stage transitions and recruitment of a native and invasive grass in a cold desert.

Oecologia 2015 Feb 25;177(2):595-606. Epub 2014 Dec 25.

Department of Plant Sciences, University of California, Davis, Davis, 95616, CA, USA,

Climate change effects on plants are expected to be primarily mediated through early life stage transitions. Snowfall variability, in particular, may have profound impacts on seedling recruitment, structuring plant populations and communities, especially in mid-latitude systems. These water-limited and frequently invaded environments experience tremendous variation in snowfall, and species in these systems must contend with harsh winter conditions and frequent disturbance. In this study, we examined the mechanisms driving the effects of snowpack depth and soil disturbance on the germination, emergence, and establishment of the native Pseudoroegnaria spicata and the invasive Bromus tectorum, two grass species that are widely distributed across the cold deserts of North America. The absence of snow in winter exposed seeds to an increased frequency and intensity of freeze-thaw cycles and greater fungal pathogen infection. A shallower snowpack promoted the formation of a frozen surface crust, reducing the emergence of both species (more so for P. spicata). Conversely, a deeper snowpack recharged the soil and improved seedling establishment of both species by creating higher and more stable levels of soil moisture availability following spring thaw. Across several snow treatments, experimental disturbance served to decrease the cumulative survival of both species. Furthermore, we observed that, regardless of snowpack treatment, most seed mortality (70-80%) occurred between seed germination and seedling emergence (November-March), suggesting that other wintertime factors or just winter conditions in general limited survival. Our results suggest that snowpack variation and legacy effects of the snowpack influence emergence and establishment but might not facilitate invasion of cold deserts.
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http://dx.doi.org/10.1007/s00442-014-3180-7DOI Listing
February 2015

Rapid adjustment of leaf angle explains how the desert moss, Syntrichia caninervis, copes with multiple resource limitations during rehydration.

Funct Plant Biol 2014 Feb;41(2):168-177

Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.

Although the desert moss Syntrichia caninervis Mitt. is extremely desiccation tolerant, it still requires water and photosynthates for growth. The ecological significance of the leaf angle in maintaining a balance between water and light availability is critical to its survival. Active leaf repositioning balances water and light availability following rehydration. S. caninervis can adjust leaf angles from a steep (84-69°) to a stable level at 30° within 7s after rehydration, obtaining maximum net photosynthetic gain at a shoot relative water content of ~60%. Leaf morphological characters, (leaf hair points, surface papillae and costal anatomy) and ultrastructural changes (chloroplast reordering and loss of lipid reserves as shown by changes in osmiophilic globules) were linked to rapid leaf spreading, water gain and sunlight reflectivity of leaves during rehydration. The high 377.20±91.69 (cm2g-1) surface area to mass ratio was a major factor in facilitating the rapid response to rewetting. Hyaline cells of the leaf base absorbed water, swelled and forced the leaf away from the stem as soon as rehydration commenced. Loss of leaf hair points retards leaf angle adjustment during rehydration.
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http://dx.doi.org/10.1071/FP13054DOI Listing
February 2014

Mapping the niche space of soil microorganisms using taxonomy and traits.

Ecology 2012 Aug;93(8):1867-79

W.K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, Michigan 49060, USA.

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.
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http://dx.doi.org/10.1890/11-1745.1DOI Listing
August 2012

Validation of heavy-water stable isotope probing for the characterization of rapidly responding soil bacteria.

Appl Environ Microbiol 2011 Jul 6;77(13):4589-96. Epub 2011 May 6.

W. K. Kellogg Biological Station, Department of Microbiology & Molecular Genetics, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI 49060, USA.

Rapid responses of bacteria to sudden changes in their environment can have important implications for the structure and function of microbial communities. In this study, we used heavy-water stable isotope probing (H2(18)O-SIP) to identify bacteria that respond to soil rewetting. First, we conducted experiments to address uncertainties regarding the H2(18)O-SIP method. Using liquid chromatography-mass spectroscopy (LC-MS), we determined that oxygen from H2(18)O was incorporated into all structural components of DNA. Although this incorporation was uneven, we could effectively separate 18O-labeled and unlabeled DNAs derived from laboratory cultures and environmental samples that were incubated with H2(18)O. We found no evidence for ex vivo exchange of oxygen atoms between DNA and extracellular H2O, suggesting that 18O incorporation into DNA is relatively stable. Furthermore, the rate of 18O incorporation into bacterial DNA was high (within 48 to 72 h), coinciding with pulses of CO2 generated from soil rewetting. Second, we examined shifts in the bacterial composition of grassland soils following rewetting, using H2(18)O-SIP and bar-coded pyrosequencing of 16S rRNA genes. For some groups of soil bacteria, we observed coherent responses at a relatively course taxonomic resolution. Following rewetting, the relative recovery of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria increased, while the relative recovery of Chloroflexi and Deltaproteobacteria decreased. Together, our results suggest that H2(18)O-SIP is effective at identifying metabolically active bacteria that influence soil carbon dynamics. Our results contribute to the ecological classification of soil bacteria while providing insight into some of the functional traits that influence the structure and function of microbial communities under dynamic soil moisture regimes.
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http://dx.doi.org/10.1128/AEM.02735-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127692PMC
July 2011

Contribution of relative growth rate to root foraging by annual and perennial grasses from California oak woodlands.

Oecologia 2003 Aug 15;136(3):424-30. Epub 2003 May 15.

Land, Air and Water Resources Department, University of California, One Shields Avenue, Davis, CA 95616, USA.

Plants forage for nutrients by increasing their root length density (RLD) in nutrient-rich soil microsites through root morphological changes resulting in increased root biomass density (RBD), specific root length (SRL), or branching frequency (BF). It is commonly accepted that fast-growing species will forage more than slow-growing species. However, foraging responses may be due solely to differences in relative growth rates (RGR). There is little evidence, after the effects of RGR are removed, that the fast versus slow foraging theory is correct. In a pot study, we evaluated foraging of four grass species that differed in RGR: one fast-growing annual species, Bromus diandrus, two intermediate-growing species, annual Bromus hordeaceus and perennial Elymus glaucus, and one slow-growing perennial species, Nassella pulchra. We harvested plants either at a common time (plants varied in size) or at a common leaf number (plants similar size, surrogate for common biomass). By evaluating species at a common time, RGR influenced foraging. Conversely, by evaluating species at a common leaf number, foraging could be evaluated independent of RGR. When RGR was allowed to contribute to foraging (common time harvest), foraging and RGR were positively correlated. B. diandrus (fast RGR) foraged to a greater extent than did E. glaucus (intermediate RGR) and N. pulchra (slow RGR). E. glaucus (intermediate RGR) foraged to a greater extent than N. pulchra (slow RGR). Root growth within nutrient-rich microsites was due to significant increases in RBD, not to modifications of SRL or BF. However, when RGR was not allowed to influence foraging (common leaf number harvest), none of the four species significantly enhanced RLD in nutrient-rich compared to control microsites. This suggests that RGR strongly influenced the ability of these grass species to forage and also supports the need to evaluate plastic root traits independent of RGR.
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http://dx.doi.org/10.1007/s00442-003-1275-7DOI Listing
August 2003
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