About

Jaimie West is an Honorary Associate at the Department of Bacteriology within the College of Agricultural & Life Sciences at the University of Wisconsin-Madison. He is associated with the Anantharaman Lab and is located in the Microbial Sciences Building at Madison, WI. His contact information includes a phone number (608) 265-4307 and an email address jrwest@wisc.edu. The page indicates his role as part of the department's faculty, but does not provide specific details about his research focus, background, or key contributions.

Research topics

• Agronomy
• Biology
• Environmental science
• Chemistry
• Ecology
• Economics
• Soil science

Selected publications

• Quantifying the response of goldrush potato to nitrogen on sandy soil

  Agronomy Journal · 2026-05-01

  articleOpen access

  Abstract Optimizing nitrogen (N) application rate is essential for effective N management and requires an understanding of crop growth dynamics, nutrient partitioning, cultivar traits, and soil characteristics. The effects of seven in‐season N rates (37–391 kg N ha −1 ) on dry matter (DM) and N accumulation and partitioning at early‐ and late‐growth stages and tuber yield and quality of potato ( Solanum tuberosum L.) cv. Goldrush grown in the sandy soils of central Wisconsin were evaluated over three growing seasons. The objective was to identify optimal regression models to achieve a sustainable balance between maximizing marketable tuber yield and economic profitability. In‐season N applications improved total N uptake and tuber N concentration but reduced DM and N partitioning to tuber. Yield gains were most consistent between 277 and 295 kg N ha − 1 , with no additional benefit beyond this range. While the quadratic and linear‐plateau models best described total and marketable yield, respectively, model fits were similar, and critical N rates varied by <7%. Relative yield normalization improved model accuracy across years. These findings support model‐based, site‐ and cultivar‐specific N recommendations to improve N use efficiency and the need for broader, multi‐environment datasets to refine predictive models and ensure both agronomic performance and environmental sustainability in potato production systems.

  PublisherDOI

• Effects of disturbance on seasonal CO ₂ dynamics in two boreal forest sites underlain by permafrost

  ˜The œcryosphere · 2026-04-13

  articleOpen access

  Abstract. Permafrost regions in subarctic and arctic areas harbor substantial carbon reserves, which are becoming increasingly vulnerable to microbial decomposition as soils warm. As the seasonally thawed active layer deepens and anthropogenic disturbances escalate, accurately predicting carbon fluxes from disturbed environments underlain by permafrost requires a comprehensive understanding of soil respiration dynamics. This study investigated the impact of surface disturbance on seasonal soil biological properties in a boreal forest ecosystem near Fairbanks, Alaska. Further, we sought to identify the key environmental and geochemical factors influencing soil biology in the undisturbed and disturbed soils. Our results revealed a substantial rise in soil respiration at the disturbed boreal forest site, which exhibited a 14.4 % overall increase in CO2 efflux compared to the undisturbed site. This effect was most pronounced during the summer, when the increase in CO2 efflux peaked at 20 %. This heightened respiratory activity was directly linked to significantly warmer soil conditions, with the mean annual soil temperature at the disturbed site measuring 0.60±0.16 °C, in stark contrast to the sub-zero temperatures of -0.37±0.08°C at the undisturbed site. Furthermore, the disturbed site had 30 % higher bacterial community richness, 1 % higher total mean C and 0.03 % higher total mean N concentration levels, and 11.9 % higher pH values in the subsoil layer, as well as a 147 % deeper maximum active thaw depth, suggesting potential controls underlying the variation in CO2 efflux. Our research underscores the essential importance of considering the rise in carbon emissions from anthropogenically disturbed soils underlain by permafrost, which are frequently neglected in assessments of the carbon cycle. This study contributes to a deeper understanding of the complex interactions governing soil respiration in disturbed permafrost environments, ultimately informing more accurate predictions of carbon fluxes in these ecosystems.

  PublisherOA PDFDOI

• Antimicrobial resistance varies with warming in active layer soil and permafrost

  Scientific Reports · 2026-04-14

  articleOpen access

  Although antimicrobial resistance is a contemporary public health concern, antimicrobial resistance genes (ARGs) have existed long before human use of antimicrobials, and recent attention has focused on whether permafrost thaw could release ARGs as the resistome shifts. We present a metagenomic analysis of permafrost samples from four sites in Alaska and Sweden, thawed under laboratory conditions. We used ABRicate, an alignment-based tool, and DeepARG, a deep learning tool, to identify ARGs, assessed their abundances under experimental thaw, measured taxonomic shifts, and examined metagenome-assembled genomes (MAGs) carrying ARGs. ARG abundance varied with depth, with some permafrost containing more ARGs than the seasonally thawed active layer. ARG abundance increased with soil carbon and decreased with pH across sites, suggesting site-specific influences. The majority of 164 high-quality MAGs contained ARGs, including 80 out of 105 species identified. This included bacteria from nine phyla, demonstrating widespread distribution across microbial taxa. Laboratory thaw experiments revealed that ARG abundances did not change significantly in two of the sites, but declined with thaw in the remaining two sites. Together, these findings demonstrate that ARGs are consistently present in permafrost microbiomes across multiple sites, but relative abundances generally do not increase during thaw. While ARGs that persist may pose potential risks, our results suggest that permafrost thaw may not substantially elevate environmental or public health risks.

  PublisherOA PDFDOI

• Supplementary material to "Effects of permafrost thaw on seasonal soil CO ₂ efflux dynamics in a boreal forest site"

  2025-04-15

  preprintOpen access
  PublisherDOI

• Complete genomic sequences of nine Bacillota isolated from Alaskan permafrost

  Microbiology Resource Announcements · 2025-08-15

  articleOpen access

  A total of nine Bacillota bacteria were isolated from Alaskan permafrost, and complete genomic sequences were obtained via hybrid assembly of long and short reads (Oxford Nanopore and Illumina paired-end sequencing, respectively). These genomes highlight the diversity of Arctic Bacillota and their potential applications in biotechnology.

  PublisherDOI

• Effects of permafrost thaw on seasonal soil CO ₂ efflux dynamics in a boreal forest site

  2025-04-15

  preprintOpen access

  Abstract. Permafrost regions in subarctic and arctic areas harbor substantial carbon reserves, which are becoming increasingly vulnerable to microbial decomposition as soils warm. As the seasonally thawed active layer deepens and anthropogenic disturbances escalate, accurately predicting carbon fluxes from thawed permafrost requires a comprehensive understanding of soil respiration dynamics. This study aimed to investigate the impact of disturbance on soil respiration rates and identify the key environmental and geochemical factors influencing these processes in a boreal forest ecosystem near Fairbanks, Alaska. The disturbed site demonstrated an increase in mean annual soil temperatures, recorded at 0.60 ± 0.16 °C, along with a 14.4 % rise in mean annual microbial activity, which peaked at 20 % during the summer, in contrast to the undisturbed site, which had a mean annual temperature of -0.37 ± 0.08 °C. Furthermore, bacterial and fungal community composition differed significantly between the two sites, suggesting a potential mechanism underlying the variation in CO2 efflux. Our research underscores the essential importance of considering the rise in carbon emissions from anthropogenically disturbed soils in permafrost areas, which are frequently neglected in assessments of the carbon cycle. This study contributes to a deeper understanding of the complex interactions governing soil respiration in thawing permafrost, ultimately informing more accurate predictions of carbon fluxes in these ecosystems.

  PublisherOA PDFDOI

• Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal

  Soil Biology and Biochemistry · 2023-09-19 · 31 citations

  article1st authorCorresponding
  PublisherDOI

• Earthworm co-invasion by Amynthas tokioensis and Amynthas agrestis affects soil microaggregate bacterial communities

  Applied Soil Ecology · 2023-12-08 · 5 citations

  articleOpen access1st authorCorresponding

  Earthworms restructure the soil environment through burrowing, consumption, and casting behaviors. Though non-native European Lumbricid earthworms are well-studied in North American soils, the Asian pheretimoid Amynthas tokioensis and Amynthas agrestis earthworms exhibit distinct ecological patterns that alter invaded habitats. In particular, the combination of disruptive bioturbation with earthworm-driven aggregate formation may affect soil structure, C protection, and microbial community assembly processes, such as dispersal and selection. We aimed to determine the effects of A. tokioensis and A. agrestis co-invasions in woodlands in Madison, WI, U.S. on soil bacterial communities and edaphic characteristics. Using 16S rRNA gene sequencing, we found that the activity of these Amynthas species earthworms significantly affected bacterial community composition, however, sites demonstrated different responses in compositional dissimilarity (i.e., beta diversity), and the relative influences of homogenizing community assembly processes (i.e., homogeneous selection and homogenizing dispersal). Overall, inconclusive support for the hypothesized homogenization of bacterial community composition driven by homogenizing community assembly processes indicates that the effects of A. tokioensis and A. agrestis pressure in these systems represent a departure from previously established soil disturbance paradigms. Instead, we conclude that aggregate formation via A. tokioensis and A. agrestis casting activity does not consistently impose a strong selective filter on soil bacterial communities, nor does the heightened earthworm activity necessarily act to meaningfully homogenize soil communities via dispersal. Overall increases in soil C and N under A. tokioensis and A. agrestis activity support previous work indicating enhanced decomposition and incorporation of soil litter, but future work could focus on long-term fate of microaggregate-protected C.

  PublisherDOI

• Physical Disturbances to Soil Homogenize Bacterial Communities via Dispersal and Selection within Microaggregate Fractions

  2023-02-25

  preprintOpen access1st authorCorresponding

  <p>Soil aggregation physically protects soil organic matter and promotes soil carbon persistence through microaggregate formation and organo-mineral associations, in concert with soil microbial community activity. Soil aggregates are sensitive to physical disturbances due to management, bioturbation, and intrinsic factors like root growth and freeze-thaw cycles, all of which affect soil microhabitat conditions, resource availability, and microbial interactions. Using 16S rRNA gene sequencing, we explored how tillage in agricultural systems and <em>Amynthas</em> spp. earthworm bioturbation in woodland systems affected the bacterial community composition of different soil microaggregate fractions (free in the soil vs. occluded within macroaggregates) isolated via wet sieving. We then inferred ecological community assembly processes using phylogenetic distance and community dissimilarity metrics in a null-modelling approach. Our results suggest that mixing disturbances homogenized bacterial communities, as quantified by increased compositional similarity across both within-plot and between-plot scales. Findings also indicate increased influences of homogenizing dispersal and homogeneous selection. Contrary to our hypothesis, we did not find major distinctions between the communities of the free and occluded microaggregate fractions. In the agricultural tillage system, this suggests that soil microaggregates may shift between these operationally defined fractions following crop senescence and seasonal changes. In the woodland bioturbation system, microaggregate results reflect biogenic aggregate formation, which is distinct from the pedogenic aggregate processes that may differentiate the free and occluded microaggregate pools. This study improves our understanding of microbial community responses to soil disturbance, and thus the potential mechanisms through which physical disturbances affect soil carbon persistence.</p>

  PublisherDOI

• Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-03-10 · 5 citations

  preprintOpen access1st authorCorresponding

  Abstract Soil aggregation physically protects soil organic matter and promotes soil carbon persistence through microaggregate formation and organo-mineral associations. Tillage is a ubiquitous disturbance to arable soil that disrupts aggregation, thus affecting microbial resource availability, soil microhabitat conditions, and microbial interactions. We investigated how tillage affects bacterial community composition of soil microaggregate fractions (53–250 µm), specifically the free microaggregate fraction in bulk soil, and the occluded microaggregate fraction from within macroaggregates, using two long-term tillage vs. no-tillage experiments in southern WI, U.S., that represent two different silt loam soils (Alfisol and Mollisol). We applied 16S rRNA gene amplicon sequencing to characterize the effects of tillage on microaggregate bacterial communities by relating compositional changes and ecological community assembly patterns to various tillage-driven changes in the soil environment, including aggregate size distribution and carbon content. Tillage homogenized soil bacterial communities, as quantified by increased compositional similarity at both within-plot and between-plot scales, and community assembly was increasingly influenced by homogenizing dispersal with tillage. We did not identify major distinctions between bacterial communities of the free and occluded microaggregate fractions, thus highlighting how soil microaggregates readily shift between these operationally defined fractions in temperate annual cropping systems, where the soil environment is subject to drastic seasonal changes that are exacerbated by tillage. With this study, we improve our understanding of the microbial response to soil disturbance, and thus the potential mechanisms through which disturbances like tillage affect soil carbon persistence. Highlights Tillage homogenized soil bacterial communities, within and between plots Homogenizing dispersal drove community assembly under tillage Free and occluded microaggregate fractions hosted similar communities

  PublisherOA PDFDOI

Frequent coauthors

• Thea Whitman

  University of Wisconsin–Madison

  8 shared

• Matthew D. Ruark

  University of Wisconsin–Madison

  4 shared

• Joseph G. Lauer

  University of Wisconsin–Madison

  2 shared

• Paula Pinheiro Sanhes

  Pemaquid Oyster Company (United States)

  2 shared

• Mônica Mariana Jorge Fratoni

  Pemaquid Oyster Company (United States)

  2 shared

• Bradley M. Herrick

  University of Wisconsin–Madison

  2 shared

• Eli Carlos de Oliveira

  2 shared

• André Prechlak Barbosa

  2 shared

Labs

• Kaçar LabPI

Education

• PhD, Department of Soil Science

  University of Wisconsin-Madison

  2023

• MS, Department of Soil Science

  University of Wisconsin Madison

  2013