James B Cotner

James B Cotner
University of Minnesota Twin Cities | UMN · Department of Ecology, Evolution and Behaviour

PhD

About

152
Publications
20,962
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9,884
Citations
Citations since 2017
28 Research Items
4288 Citations
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20172018201920202021202220230200400600
20172018201920202021202220230200400600

Publications

Publications (152)
Article
Full-text available
An oxygenated atmosphere changed life on Earth but it also provided a negative feedback to organic matter accumulation by increasing decomposition rates. Nonetheless, dissolved organic carbon (DOC) is a huge carbon pool (> 750 Pg) and it can accumulate to high concentrations (20–100 mg C L−1) in some freshwater aquatic systems, yet it is not clear...
Article
Biogeochemistry patterns in shallow lakes are influenced by both in-lake factors such as ecosystem state as well as watershed-level factors such as land use, but the relative importance of in-lake versus watershed factors is poorly known. This knowledge gap makes it difficult for lake mangers to prioritize efforts on watershed versus in-lake strate...
Article
Full-text available
Dissolved oxygen controls important processes in lakes, from chemical reactions to organism community structure and metabolism. In shallow lakes, small volumes allow for large fluctuations in dissolved oxygen concentrations, and the oxygen regime can greatly affect ecosystem‐scale processes. We used high frequency dissolved oxygen measurements to e...
Article
Where they are present in catchments, peatlands are a dominant source of dissolved organic matter (DOM) to surrounding waterways due, in part, to high production rates. Despite the preponderance of peatlands in northern latitudes and expected peatland vulnerability to climate change, little is known about peatland DOM degradation relative to a more...
Article
Full-text available
Stable isotopes 13 C and 15 N are often used in lake ecosystems to assess energy sources and trophic positions, respectively. However, d 13 C and d 15 N are also influenced by internal biogeochemical processes in epilimnetic and hypolimnetic habitats in lakes, but the extent to which biogeochemical processing mediates isotope values between these t...
Data
This data publication includes water chemistry data for samples from the S2 and S6 research catchments at the Marcell Experimental Forest (MEF) in Balsam Township, Itasca County, Minnesota. Data include weekly or more frequent samples of stream water collected from 2009 to 2011. Measurements were taken in upland runoff waters (both overland flow an...
Presentation
Background Heterotrophic bacteria are key biogeochemical regulators in freshwater systems. Bacteria are key drivers of both the decomposition and production of organic matter. In this way, bacteria link multiple biogeochemical cycles including carbon and phosphorus. To date, much of the work on dissolved organic matter transformations has been carb...
Presentation
Background Engaging undergraduates in research opportunities is imperative for cultivating a new generation of motivated scientists but offering these experiences to a large number of students in ecology is often challenging. Course-based undergraduate researcher experiences (CUREs) represent a powerful tool for scaling research experiences and red...
Poster
Full-text available
Engaging undergraduates in research opportunities is imperative for cultivating a new generation of motivated scientists but offering these experiences to a large number of students in the field of limnology is often challenging. Course-based undergraduate researcher experiences (CUREs) represent a powerful training tool for preparing future resear...
Preprint
Soils transform large amounts of organic matter as it passes from land to freshwater. Heterotrophic bacteria are key players in those transformations, yet their precise role in modifying this organic matter remains unclear. In particular, little is known about the role of microbes in controlling the nutrient stoichiometry of terrestrially derived o...
Preprint
Heterotrophic bacteria are key biogeochemical regulators in freshwater systems. Through both the decomposition and production of organic matter, bacteria link multiple biogeochemical cycles together. While there has been a significant amount of work on understanding the role of microbes in the aquatic carbon cycle, improving our understanding of th...
Presentation
Full-text available
Engaging undergraduates in research opportunities is imperative for cultivating a new generation of motivated scientists but offering these experiences to a large number of students in the field of limnology is often challenging. Course-based undergraduate researcher experiences (CUREs) represent a powerful training tool for preparing future resear...
Presentation
Full-text available
Freshwater systems are hotspots of biogeochemical processing having large impacts on the composition of nutrients and organic matter that passes through them. Biological processes are critical to sizes of these pools in that they are primarily responsible for both production and degradation of organic carbon and organic nutrients suck as dissolved...
Preprint
Full-text available
Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influ...
Article
The elemental content of microbial communities is dependent upon the physiology of constituent populations, yet ecological stoichiometry has made slow progress toward identifying predictors of how species and strains change the elemental content of their biomass in response to the stoichiometry of elements in resources. We asked whether the element...
Article
Full-text available
Two contemporary effects of humans on aquatic ecosystems are increasing temperatures and increasing nutrient concentrations from fertilizers. The response of organisms to these perturbations has important implications for ecosystem processes. We examined the effects of phosphorus (P) supply and temperature on organismal carbon, nitrogen and phospho...
Article
Full-text available
The canonical Redfield C:N:P ratio for algal biomass is often not achieved in inland waters due to higher C and N content and more variability when compared to the oceans. This has been attributed to much lower residence times and higher contributions of the watershed to the total organic matter pool of continental ecosystems. In this study we exam...
Article
The Laurentian Great Lakes are an invaluable natural and economic resource for two North American countries, but really the entire world. They are threatened by anthropogenic, climate and biotic stresses; and it is increasingly difficult to manage them due to the complexity of interactions among these different stressors. At the same time, funding...
Article
Full-text available
Elemental homeostasis has been largely characterized using three important elements that were part of the Redfield ratio (i.e., carbon: nitrogen: phosphorus). These efforts have revealed substantial diversity in homeostasis among taxonomic groups and even within populations. Understanding the evolutionary basis, and ecological consequences of such...
Poster
Full-text available
Large amounts of organic matter (OM) are transformed along the path from land to the oceans by heterotrophic bacteria. However, the controls on and mechanisms of microbial interactions with OM remain unclear. Recent shifts in thinking have promoted the idea that soil microbial processes are key to soil organic matter formation (SOM) and that most,...
Presentation
Full-text available
Many of the world’s most serious problems are tied to complex environmental issues. For example, the spread of vector-borne diseases will be influenced by a changing future climate. Availability of drinkable water to communities across the globe will be influenced by land use and development of technologies to improve water treatment. An informed c...
Article
The effects of resource stoichiometry and growth rate on the elemental composition of biomass have been examined in a wide variety of organisms, but the interaction among these effects is often overlooked. To determine how growth rate and resource imbalance affect bacterial carbon (C): nitrogen (N): phosphorus (P) stoichiometry and elemental conten...
Article
Ecological shifts in shallow lakes from clear-water macrophyte-dominated to turbid-water phytoplankton-dominated are generally thought of as rapid short-term transitions. Diatom remains in sediment records from shallow lakes in the Prairie Pothole Region of North America provide new evidence that the long-term ecological stability of these lakes is...
Article
Full-text available
In this study, we utilized Illumina next-generation sequencing of 16S rDNA to characterize the bacterial communities in water, sediments, and soils at four sites along the Mississippi River and Minnesota River, in Minnesota, in order to evaluate community exchanges between these habitats. Communities in water and sediment were hypothesized to show...
Article
Parasites that rely on trophic transmission can manipulate the behavior of an intermediate host to compromise the host's antipredator competence and increase the probability of reaching the next host. Selection for parasite manipulation is diminished when there is significant risk of host death to causes other than consumption by a suitable definit...
Article
Shallow lakes process large amounts of carbon (C) via gross primary production (GPP) and respiration (R), but C fluxes are highly variable among lakes. We used a two-prong approach to determine whether C fluxes differed between two alternative stable states observed in shallow lakes. First, we used a replicated whole-lake experiment where we manipu...
Article
Full-text available
In this study, we determined the frequency of antibiotic resistance genes (ARGs) in the Upper Mississippi River using a high-throughput, functional, metagenomic screening procedure. Fosmid libraries containing ∼10,000 clones were screened for resistance to ampicillin, cephalothin, kanamycin, and tetracycline. We hypothesized that nutrient concentra...
Article
Full-text available
Bacteria are central to the cycling of carbon (C), nitrogen (N) and phosphorus (P) in every ecosystem, yet our understanding of how tightly these cycles are coupled to bacterial biomass composition is based upon data from only a few species. Bacteria are commonly assumed to have high P content, low biomass C:P and N:P ratios, and inflexible stoichi...
Article
Full-text available
It is frequently presumed that heterotrophic bacteria from aquatic environments have low carbon (C) content, high phosphorus (P) content, and maintain homeostasis at low C:P in their biomass. Dissolved and particulate organic matter from primary producers in terrestrial and aquatic environments typically has high C:P ratios, suggesting that heterot...
Article
A major episodic sediment resuspension event (25-yr high), which was triggered by atmospheric and water column instability in an El Nino year, temporarily altered the dynamics of autotrophy and heterotrophy in Lake Michigan. Resuspended sediments, rich in organic and inorganic nutrients, especially phosphorus, stimulated heterotrophic production de...
Article
Full-text available
For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or...
Article
Several studies have noted a disparity between the stoichiometric regulation of bacterial assemblages and populations. In response to phosphorus availability, assemblages of bacteria often exhibit greater flexibility in their biomass carbon (C) to phosphorus (P) ratios (C:P) than axenic populations, some of which are homeostatic. We hypothesized th...
Article
Variable hydrology of rivers strongly affects biophysical factors that influence primary production and population densities, thereby affecting the relative influence of bottom-up and top-down processes in trophic networks. Many tropical floodplain rivers have sustained seasonal flood pulses driven by precipitation patterns of the Intertropical Con...
Article
Photochemical and bacterial degradation are important pathways to carbon mineralization and can be coupled in dissolved organic matter (DOM) decomposition. However, details of several mechanisms of the coupled photochemical and biological processing of DOM remain too poorly understood to achieve accurate predictions of the impact of these processes...
Article
Full-text available
Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequenci...
Conference Paper
Background/Question/Methods Because many freshwater ecosystems are small, quantifying carbon cycling in wetlands is vital in understanding their role in regional carbon cycling. Wetlands in the Prairie Pothole Region (PPR) of North America exist in either a clear-water state dominated by submerged macrophytes, or a turbid-water state dominated by...
Article
Full-text available
Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high...
Article
Full-text available
The capacity of a lake to remove reactive nitrogen (N) through denitrification has important implications both for the lake and for downstream ecosystems. In large oligotropic lakes such as Lake Superior, where nitrate (NO3−) concentrations have increased steadily over the past century, deep oxygen penetration into sediments may limit the denitrifi...
Article
Full-text available
In September 2011, we investigated the distribution and composition of dissolved and particulate phosphorus (P) pools throughout Lake Superior, a large P-limited freshwater ecosystem. Average seston particulate P (PP) concentrations in the deep chlorophyll maximum (DCM; 85 ± 28 nmol L-1) were significantly greater than in the epilimnion (63 ± 22 nm...
Poster
Background/Question/Methods Inland waters have been shown to be important players in the global carbon cycle, particularly by transforming carbon as it moves from terrestrial ecosystems to the ocean. Despite our increased understanding about the role of inland waters in processing organic carbon, the magnitude and quality of terrestrial carbon inpu...
Article
A next-generation, Illumina-based sequencing approach was used to characterize the bacterial community at ten sites along the Upper Mississippi River to evaluate shifts in the community potentially resulting from upstream inputs and land use changes. Furthermore, methodological parameters including filter size, sample volume, and sample reproducibi...
Conference Paper
Background/Question/Methods Imbalance between the chemical composition of organisms and that of their resources is central to consumer-resource ecology and is the foundation of ecological stoichiometry. The stoichiometry of populations and individuals has been examined for a diverse suite of organisms, but comparatively few studies have examined...
Chapter
This chapter explores how cultural values, beliefs, and traditions affect the fluxes of phosphorus in the biosphere. It examines three human-culture interactions with phosphorus biogeochemistry: (a) genetically engineered organisms, (b) human diet, and (c) management of human excreta. It looks into how individual and societal perspectives on geneti...
Conference Paper
Background/Question/Methods Ecosystem metabolism, or the balance between gross primary production and respiration, has rarely (if at all) been compared within environments exhibiting alternative stable states. Shallow lakes typically exist in two alternative states that differ by their dominating primary producers: a clear-water, submerged macroph...
Poster
Full-text available
Background/Question/Methods Preceding European settlement of North America, earthworms were not present in the hardwood forests on the continent. Since then, invasive earthworms have rapidly spread across many forest systems throughout the United States. In Minnesota alone, at least fifteen invasive species have been introduced so far. By consuming...
Poster
Background/Question/Methods Terrestrial inputs of organic matter are a major subsidy of nutrients and energy to many aquatic systems. Inland waters act as “active pipes” that connect terrestrial systems to the ocean and not only transport organic materials but also transform them along the way. Despite this integrative nature, a majority of researc...
Poster
Full-text available
Background/Question/Methods Terrigenous carbon inputs often account for greater than 50% of the dissolved organic carbon (DOC) in natural aquatic ecosystems. In fact, recent estimates suggest that the DOC pool in some systems may be over 90% terrestrial in origin. As such, understanding the linkages between terrestrial and aquatic ecosystems is imp...
Conference Paper
Background/Question/Methods Dissolved organic carbon (DOC) is the largest pool of reduced carbon for most lakes. Shallow lakes are important in C cycling but it is uncertain if they function as sources or sinks in the carbon cycle and even less is understood about DOC dynamics in this context. We have been investigating DOC burial in lake sedimen...
Conference Paper
Background/Question/Methods Lakes represent less than 1% of the aquatic surface area of the Earth, yet are extremely important to carbon processing owing to their close proximity to terrestrial ecosystems and high rates of productivity. Global estimates indicate that nearly 3 Pg of terrestrial carbon are processed by freshwater aquatic systems an...
Conference Paper
Background/Question/Methods Shallow lakes tend to exist in one of two ecological extremes, either a clear-water macrophyte dominated state, or a turbid-water phytoplankton dominated state. These states have been described theoretically through the concept of alternative stable states and stability landscapes. Our study focuses on a suite of shall...
Conference Paper
Background/Question/Methods Shallow lakes can be subject to two ecological extremes; a clear-water, macrophyte-dominated or turbid, algal-dominated state. The drivers of ecological instability that promote the success of these end-member states can overlap and interact making management of these ecosystems frustrating. Direct links between landsc...
Conference Paper
Background/Question/Methods Shallow lakes have the potential to sequester large amounts of organic carbon in their sediment and play a disproportionately large role in the global carbon cycle. However, the sequestration rates in these lakes are highly variable. The consumption of detritus by detritivorous fish and aquatic invertebrates may reduce...
Presentation
Full-text available
Background/Question/Methods Integrated Science Education Outreach (InSciEd Out) started in 2009 as a partnership between the Mayo Clinic, Winona State University, and Rochester Public Schools in Minnesota to achieve the shared vision of excellence in scientific education. This program relies on developing partnerships between cutting-edge scientist...
Article
Full-text available
Current models and observations indicate that bacterial respiration should increase and growth efficiency (BGE) should decrease with increasing temperatures. However, these models and observations are mostly derived from data collected in temperate regions, and the tropics are under-represented. The aim of this work was to compare bacterial metabol...
Data
The rate of organic carbon (OC) burial in inland waters is an important flux in the global C-cycle. Here we provide methodological improvements that offer a rapid and accurate assessment of modern OC burial rates in lakes from a single surface-sediment sample. Using a 93 lake dataset of reliably dated sediment cores (OC burial of 9 to 318 g m(-2) y...
Conference Paper
Background/Question/Methods Shallow lakes have the potential to sequester large amounts of organic carbon in their sediment and play a disproportionately large role in the global carbon cycle. However, the sequestration rates in these lakes are highly variable. The consumption of detritus by detritivorous fish and aquatic invertebrates may reduce...
Conference Paper
Background/Question/Methods Shallow lakes play an important role in the global carbon cycle, and can bury substantial quantities of organic carbon in their sediments. However, sedimentation rates vary greatly among shallow lakes and the factors controlling these rates are poorly known. Variability in sedimentation rates could be partially due to...
Conference Paper
Background/Question/Methods Eutrophication of freshwater ecosystems continues to be a major issue, and nonpoint sources of nutrients are particularly difficult to quantify and alleviate. Agricultural activities can be a major source of nutrients for lakes and could be especially influential on shallow lakes in the prairie region of North America...
Article
We collected two sediment cores and modern submerged aquatic plants and phytoplankton from two sub-basins of Lake Christina, a large shallow lake in west-central Minnesota, and used stable isotopic and elemental proxies from sedimentary organic matter to explore questions about the pre- and post-settlement ecology of the lake. The two morphological...
Article
A multiyear field study was undertaken on Lake Superior to investigate singlet oxygen ((1)O(2)) photoproduction. Specifically, trends within the lake were examined, along with an assessment of whether correlations existed between chromophoric dissolved organic matter (CDOM) characteristics and (1)O(2) production rates and quantum yields. Quantum yi...
Article
We examined heterotrophic bacterial nutrient limitation at four sites in Florida Bay, U. S. in summer 1994 and winter 1995. Bacterial growth and biomass production in this system were most limited by inorganic phosphorus (P) in the eastern and southern regions of the bay. Nutrient additions stimulated productivity and biomass accumulation mostly in...
Article
Full-text available
Prokaryotic heterotrophs (hereafter, bacteria) represent a large proportion of global biomass, and therefore bacterial biomass stoichiometry likely exerts control on global phosphorus (P), carbon (C), and nitrogen cycling and primary productivity. In this study we grew recently isolated freshwater heterotrophic bacteria across an ecologically relev...
Article
Full-text available
Wolfe-Simon et al. (Research Articles, 3 June 2011, p. 1163; published online 2 December 2010) reported that the bacterial strain GFAJ-1 can grow by using arsenic (As) instead of phosphorus (P), noting that the P content in bacteria grown in +As/–P culture medium was far below the quantity needed to support growth. However, low P content is a commo...
Article
Full-text available
Although aquatic bacteria are assumed to be nutrient-rich, they out-compete other foodweb osmotrophs for nitrogen (N) and phosphorus (P) an apparent contradiction to resource ratio theory. This paradox could be resolved if aquatic bacteria were demonstrated to be nutrient-poor relative other portions of the planktonic food web. In a survey of >120...
Conference Paper
Shallow lakes can exist in two alternative stable regimes: a clear-water regime dominated by macrophytes with little phytoplankton abundance, or a turbid-water regime where conditions are the opposite. There is a need for more historical studies of shallow lakes as these systems constitute a critical habitat for waterfowl across a large region of t...
Conference Paper
Research on peatland catchments at the Marcell Experimental Forest in northern Minnesota, USA demonstrates the importance of dissolved organic matter (DOM) as a control on ecosystem processes. DOM is linked to biogeochemical cycles, especially in areas of the landscape where upland soils interface with organic soils of peatlands. At those interface...
Article
Dissolved organic matter (DOM) is a significant (>700 Pg) global C pool. Transport of terrestrial DOM to the inland waters and coastal zones represents the largest flux of reduced C from land to water (215 Tg yr(-1)) (Meybeck, M. Am. J. Sci. 1983, 282, 401-450). Oxidation of DOM by interdependent photochemical and biochemical processes largely cont...
Article
Full-text available
We explore the role of lakes in carbon cycling and global climate, examine the mechanisms influencing carbon pools and transformations in lakes, and discuss how the metabolism of carbon in the inland waters is likely to change in response to climate. Furthermore, we project changes as global climate change in the abundance and spatial distribution...
Article
Phosphorus (P) routinely limits microbial growth in freshwater ecosystems. The growth rate hypothesis (GRH) relates growth to biomass P content mechanistically through changes in ribosomal ribonucleic acid (rRNA). Although the GRH has been shown in cultured bacteria, less well understood is how GRH relationships are affected by interactions with en...
Article
Singlet oxygen (1O2) is a reactive oxygen species produced by dissolved organic matter (DOM) in sunlit waters. While the production of 1O2 by DOM has been studied, little is known on interactions between 1O2 and DOM. The central objective of this work was to quantify the rate constants of reaction and quenching of 1O2 with Suwannee River and Pony L...
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