Engineering topics

Kostka, Joel E.

Publications and source records attributed to Kostka, Joel E..

16 records

DOE OSTI2024

SPRUCE Root Tip and Ectomycorrhizal Fungi Colonization Measurements from Ingrowth Cores, 2017

This data set contains root tip and ectomycorrhizal fungi colonization measurements taken from ingrowth cores from the SPRUCE experiment (Hanson et al. 2017) that were deployed during the 2017 growing season (2017-06 to 2017-10-01). This study explored the relationship between warming treatments and fine-root growth. Increased fine-root growth may increase root exudates and accelerate turnover, representing an underlying mechanism for peat decomposition through priming, as exudates provide a labile carbon source to the microbial community. Roots of two tree species were studied: an evergreen conifer Picea mariana (black spruce) and a deciduous conifer Larix laricina (tamarack). Measurements include root tips counts and densities by tree species and the abundance of ectomycorrhizal colonization on root tips. This dataset contains one data file in comma separate (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

black spruce [Picea mariana]↗

DOE OSTI2024

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO 2 in northern peatlands

Warming and elevated CO 2 (eCO 2 ) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO 2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO 2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO 2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Shared governance in the plant holobiont and implications for one health

Abstract The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Climate warming and elevated CO 2 alter peatland soil carbon sources and stability

Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and elevated atmospheric CO 2 concentration (eCO 2 ) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO 2 increased plant-derived SOC compounds. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and eCO 2 . The decline in SOC compounds with warming and gains from new root-derived C under eCO 2 , suggest that warming and eCO 2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum -dominated bog

Abstract Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Song, Tianze (ORCID:0000000282060247)↗

DOE OSTI2023

Climate drivers alter nitrogen availability in surface peat and decouple N 2 fixation from CH 4 oxidation in the Sphagnum moss microbiome

Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N 2 -fixing (diazotrophic) and CH 4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. In this work, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO 2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH 4 , CO 2 ) and nitrogen (NH 4 -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO 2 . Under ambient CO 2 , warming increased plant-available NH 4 -N in surface peat, excess N accumulated in Sphagnum tissue, and N 2 fixation activity decreased. Elevated CO 2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO 2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N 2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO 2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

SPRUCE Sphagnum Phytobiome Responses to Whole Ecosystem Warming and Elevated Atmospheric CO2 in July, 2017-2021

This dataset reports the carbon (C) and nitrogen (N) isotopic composition of Sphagnum moss tissue collected from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Tissues were collected inside the SPRUCE experimental study plot, where air and peat warming are combined in whole-ecosystem warming treatments, from 2019-2021. Additionally, rates of nitrogen fixation and methane oxidation measured for Sphagnum from 2017, 2019, and 2021. Sphagnum tissue % water content was measured at all timepoints. This dataset was used to conduct analyses within Petro et al (2023). Sphagnum C and N concentrations and 13C and 15N isotopic natural abundance were determined for three replicate Sphagnum tissue samples collected from inside the SPRUCE enclosures in July 2019-2021. Elemental and isotope analyses were conducted at the University of Georgia – Center for Applied Isotope Studies (CAIS; https://cais.uga.edu/). Plant elemental analysis was performed by the micro-Dumas method, while isotopic natural abundance was measured by isotope ratio mass spectrometry. 13C natural abundance is expressed as the per mille (‰) deviation from the Pee Dee Belemnite standard (PDB) 13C:12C ratio (δ13C), while 15N natural abundance is expressed as the ‰ deviation from the N2 atmospheric 15N:14N ratio (δ15N). Rates of nitrogen fixation and methane oxidation were measured using serum bottle incubations performed with Sphagnum collected inside the SPRUCE enclosures in July 2017, 2019, and 2021. Rates were calculated according to the amount of 15N-N2 or 13C-CH4 (methane) incorporated into the Sphagnum tissue or incubation headspace over the 48-hour intion period. In 2017, incubations were performed in growth chambers set to the temperature of the experimental plots during Sphagnum sampling. In 2019 and 2021, the incubations were performed directly inside the experimental plots. The 13C and 15N isotopic natural abundance data and rate measurements presented in this dataset provide insight into the impacts of whole-ecosystem warming and elevated atmospheric carbon dioxide (CO2) on N and C cycling within the Sphagnum phytobiome. This dataset contains two data files in comma-separate values (*.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format. Additional datasets on NH4-N availability, porewater concentrations of CH4 and CO2, and Sphagnum groundcover within the SPRUCE experimental plots are available. These are outlined in the Related Datasets section in the user guide.

delta 13 carbon↗

DOE OSTI2023

SPRUCE Climate Warming and Elevated CO2 Rapidly Alter Peatland Soil Carbon Sources and Stability: Supporting Data

This data set reports a suite of complementary biogeochemical analyses of peat samples from the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment. Results were collected using quantitative molecular analysis of bulk soil carbon to assess the stability of soil organic carbon following whole-ecosystem warming and exposure to elevated carbon dioxide concentrations (eCO2). Targeted soil organic carbon components include solvent-extractable compounds (alkanoic acids, alkanols, alkanes, steroids, and terpenoids), ester-bound hydrolysable biopolymers (cutin and suberin markers), lignin phenols, and pyrogenic carbon. Bulk peat samples were analysed by Soxhlet extraction and solid phase separation for solvent-extractable compounds, alkaline hydrolysis to extract hydrolysable biopolymers, copper (II) oxide oxidation to extract lignin phenols and benzene polycarboxylic acids (BPCAs) as an approximation of pyrogenic carbon. Samples were analysed by gas chromatography (GC) equipped with a flame ionization detector (GC-FID) and compound identification was performed on GC coupled to mass selective detector (MS) for solvent-extractable compounds, ester-bound hydrolysable biopolymers and lignin phenols, and high-performance liquid chromatograph (HPLC) for pyrogenic carbon. Results are presented in Ofiti et al. (accepted). The experimental work was conducted on samples collected in August 2018 at the SPRUCE climate manipulation experiment in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). Samples were collected and later analysed in a 10 cm increments over 0 to 50 cm depth and 25 cm intervals from 50 to 75 cm. Samples were analyzed for lignin phenols over 0 to 30 cm depth. This data set contains one file in comma separate (*.csv) format. This dataset contains data used to produce: Ofiti, N.O.E., Schmidt, M.W.I., Abiven, S., Hanson, P.J., Iversen, C.M., Wilson, R.M., Kostka, J.E., Wiesenberg, G.L.B., Malhotra, A. 2023. Climate warming and elevated CO2 rapidly alter peatland soil carbon sources and stability. Nat Commun 14, 7533. https://doi.org/10.1038/s41467-023-43410-z.

SPRUCE experiment, Marcell Experimental Forest, so↗

DOE OSTI2022

Expansion of the global RNA virome reveals diverse clades of bacteriophages

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe

We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially warmed, and geothermally warmed conditions across Europe. These data will enable further research regarding the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning of northern peatland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Compositional stability of peat in ecosystem-scale warming mesocosms

Peatlands historically have acted as a C sink because C-fixation rates exceeded the rate of heterotrophic decomposition. Under future warmer conditions predicted for higher latitudes, however, that balance may shift towards higher rates of heterotrophic respiration leading to the release of previously stored C as CO 2 and CH 4 . The Spruce and Peatlands Response Under Changing Environments (SPRUCE) experiment is designed to test the response of peatlands to climate forcing using a series of warmed enclosures in combination with peat below-ground heating from 0 to +9°C above ambient conditions. This experimental design allowed a test of chemical changes occurring within peatland soils following five years of warming. We analyzed samples in the uppermost 2m of peat using Fourier Transform Infrared Spectroscopy (FT-IR) to quantify the relative abundance of carbohydrate and aromatic compounds in the peat. The peat soils were subjected to deep peat heating (DPH) beginning in June of 2014 followed by whole ecosystem warming (WEW) in August of 2015. We found that the relative amounts of labile and recalcitrant chemical compound groups across the full peat depth interval did not significantly change after five years of exposure to warming. This appears the case even though previous studies have shown that net C losses and loss of bulk peat mass to be instability over that time period. Results suggest that the current store of carbon in peatlands are largely compositionally stable leading to no changes the in the ratio of chemical moieties on the initial four-year timescale of this experiment.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Radiocarbon Analyses Quantify Peat Carbon Losses With Increasing Temperature in a Whole Ecosystem Warming Experiment

Abstract Climate warming is expected to accelerate peatland degradation and release rates of carbon dioxide (CO 2 ) and methane (CH 4 ). Spruce and Peatlands Responses Under Changing Environments is an ecosystem‐scale climate manipulation experiment, designed to examine peatland ecosystem response to climate forcings. We examined whether heating up to +9 °C to 3 m‐deep in a peat bog over a 7‐year period led to higher C turnover and CO 2 and CH 4 emissions, by measuring 14 C of solid peat, dissolved organic carbon (DOC), CH 4 , and dissolved CO 2 (DIC). DOC, a major substrate for heterotrophic respiration, increased significantly with warming. There was no 7‐year trend in the DI 14 C of the ambient plots which remained similar to their DO 14 C. At +6.75 °C and +9 °C, the 14 C of DIC, a product of microbial respiration, initially resembled ambient plots but became more depleted over 7 years of warming. We attributed the shifts in DI 14 C to the increasing importance of solid phase peat as a substrate for microbial respiration and quantified this shift via the radiocarbon mass balance. The mass‐balance model revealed increases in peat‐supported respiration of the catotelm depths in heated plots over time and relative to ambient enclosures, from a baseline of 20%–25% in ambient enclosures, to 35%–40% in the heated plots. We find that warming stimulates microorganisms to respire ancient peat C, deposited under prior climate (cooler) conditions. This apparent destabilization of the large peat C reservoir has implications for peatland‐climate feedbacks especially if the balance of the peatland is tipped from net C sink to C source.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2013

Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)−10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup −1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

Psychrophile↗