Paul Dijkstra

Paul Dijkstra
Northern Arizona University | NAU

About

191
Publications
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6,719
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Additional affiliations
January 2003 - December 2012
Northern Arizona University
January 1999 - December 2002
January 1999 - present
University of South Florida

Publications

Publications (191)
Article
Chinese milk vetch (Astragalus sinicus L) is a widely used leguminous green manure in paddy rice culture and has potential to replace or partly replace inorganic nitrogen (N) fertilizer. However, there is little quantitative information regarding replacing inorganic N with milk vetch on CH4 and N2O emissions. This study investigated the relationshi...
Article
Full-text available
Scope Biochemistry is an essential yet undervalued aspect of soil ecology, especially when analyzing soil C cycling. We assume, based on tradition, intuition or hope, that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns cause...
Article
Soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with oth...
Preprint
Full-text available
Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic bio...
Article
Full-text available
Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages—particularly short-range order minerals—affect both bacterial community composition and taxon-specific...
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Full-text available
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content, and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, fe...
Preprint
Full-text available
Genomic traits, such as genome size, GC content, codon usage, and amino acid content, shed insight into the evolutionary processes of bacteria and selective forces behind microbial community composition. Nutrient limitation has been shown to reduce bacterial genome size and influence nucleotide composition, yet little research has been conducted in...
Article
If you need access to this paper, use this personal link (https://authors.elsevier.com/a/1dvcb8g13Q0av) before Dec 3, 2021. ______________________________________________________________________________ Microbes decompose soil organic matter (SOM), yet it is unclear how substrate inputs (i.e., stoichiometry) directly mediate microbial activities an...
Article
Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-de...
Article
Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to degrade DMF. Aerobic remediation has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. H...
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Full-text available
The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates...
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Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the ri...
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Despite abounding evidence that leaf litter traits can predict decomposition rate, the way these traits influence trophic efficiency and element transfer to higher trophic levels is not resolved. Here, we used litter labeled with 13 C and 15 N stable isotopes to trace fluxes of litter C and N from four leaf types to freshwater invertebrate communit...
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Full-text available
Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural s...
Article
Full-text available
Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales , is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth...
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Full-text available
Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in par...
Preprint
Full-text available
Free-living bacteria in nutrient limited environments often exhibit small genomes which curb the cost of reproduction - a phenomenon known as genomic streamlining. Streamlining has been associated with a suite of traits such as reduced GC content, fewer 16S rRNA copies, and a lower abundance of regulatory genes, such as sigma (σ)-factors. Here, we...
Preprint
Full-text available
Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48 h laboratory incubation with an agricultura...
Preprint
Full-text available
Effective degradation of N,N -Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to be capable of degrading DMF. Aerobic remediation of DMF has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include m...
Preprint
Full-text available
Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-de...
Preprint
Full-text available
Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in par...
Article
Full-text available
The addition of glucose to soil has long been used to study the metabolic activity of microbes in soil; however, the response of the microbial ecophysiology remains poorly characterized. To address this, we sequenced the metagenomes and metatranscriptomes of glucose-amended soil microbial communities in a laboratory incubation.
Article
Microorganisms in soil assimilate, transform, and mineralize soil C to support growth. There are an estimated 2.6 × 1029 microbial cells containing 26 Pg C in soils worldwide. Consequently, quantifying microbial growth in soil is critical for determining the degree to which microorganisms contribute to the global C cycle. Measuring taxonspecific mi...
Article
Organic matter input to soils can accelerate the decomposition of native soil carbon (C), a process called the priming effect. Priming is ubiquitous and exhibits some consistent patterns, but a general explanation remains elusive, in part because of variation in the response across different ecosystems, and because of a diversity of proposed mechan...
Preprint
Full-text available
Chinese milk vetch (Astragalus sinicus L., vetch), a leguminous winter cover crop, has been widely adopted by farmers in southern China to boost yield of the succeeding rice crop. However, the effects of vetch on rice grain yield and nitrogen (N) use efficiency have not yet been well studied in the intensive double-cropped rice cropping systems. To...
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Full-text available
Organisms influence ecosystems, from element cycling to disturbance regimes, to trophic interactions and to energy partitioning. Microorganisms are part of this influence, and understanding their ecology in nature requires studying the traits of these organisms quantitatively in their natural habitats—a challenging task, but one which new approache...
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Relationships between microbial genes and performance are often evaluated in the laboratory in pure cultures, with little validation in nature. Here, we show that genomic traits related to laboratory measurements of maximum growth potential failed to predict the growth rates of bacteria in unamended soil, but successfully predicted growth responses...
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Leaf litter provides an important nutrient subsidy to headwater streams, but little is known about how tree genetics influences energy pathways from litter to higher trophic levels. Despite the charge to quantify carbon
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Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologist...
Article
Soil contains the largest terrestrial pool of carbon (C), but how this pool will be affected by global change remains unknown. Warmer temperatures generally increase soil respiration, while additional C inputs from plants to soil can increase or decrease soil C decomposition rates through a phenomenon known as priming. Priming occurs when soil orga...
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Full-text available
Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influenc...
Article
15 N isotope tracer Added nitrogen interaction Mineralization and immobilization ⁠ 15 N labeled fertilizer Plant-soil interaction Rhizosphere priming ABSTRACT Fertilizer inputs affect plant uptake of native soil nitrogen (N), yet the underlying mechanisms remain elusive. To increase mechanistic insight into this phenomenon, we evaluated the effect...
Article
Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field...
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Full-text available
Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more com...
Article
Invasive, non-native plant species can alter soil microbial communities in ways that contribute to their persistence. While most studies emphasize mycorrhizal fungi, invasive plants also may influence communities of dark septate fungi (DSF), which are common root endophytes that can function like mycorrhizas. We tested the hypothesis that a widespr...
Article
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Preprint
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Preprint
Full-text available
Bacteria grow and transform elements at different rates, yet quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to Stable Isotope Probing (SIP) that enables determining...
Article
Full-text available
Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced...
Article
Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in...
Article
Full-text available
Leaf litter decomposition plays a major role in nutrient dynamics in forested streams. The chemical composition of litter affects its processing by microorganisms, which obtain nutrients from litter and from the water column. The balance of these fluxes is not well known, because they occur simultaneously and thus are difficult to quantify separate...
Article
Full-text available
Rising temperatures are expected to reduce global soil carbon (C) stocks, driving a positive feedback to climate change1-3. However, the mechanisms underlying this prediction are not well understood, including how temperature affects microbial enzyme kinetics, growth efficiency (MGE), and turnover4,5. Here, in a laboratory study, we show that micro...
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Full-text available
Rising atmospheric CO2 concentrations could alter the nitrogen (N) content of ecosystems by changing N inputs and N losses, but responses vary in field experiments, possibly because multiple mechanisms are at play. We measured N fixation and N losses in a subtropical oak woodland exposed to 11 yr of elevated atmospheric CO2 concentrations. We also...
Article
Tillage practices and straw management can affect soil microbial activities with consequences for soil organic carbon (C) dynamics. Microorganisms metabolize soil organic C and in doing so gain energy and building blocks for biosynthesis, and release CO2 to the atmosphere. Insight into the response of microbial metabolic processes and C use efficie...
Article
We present a significant relationship between the natural abundance isotopic composition of ecosystem pools and the abundance of a microbial gene. Natural abundance N-15 of soils and soil DNA were analysed and compared with archaeal ammonia oxidizer abundance along an elevation gradient in northern Arizona and along a substrate age gradient in Hawa...
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Full-text available
Isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) are core membrane lipids of many archaea that enhance the integrity of cytoplasmic membranes in extreme environments. We examined the iGDGT profiles and corresponding aqueous geochemistry in 40 hot spring sediment and microbial mat samples from the U.S. Great Basin with temperatures rangin...