About

Dan Buckley is a Professor at the School of Integrative Plant Sciences within the Department of Microbiology at Cornell University. He holds a Ph.D. in Microbiology from Michigan State University, obtained in 2000, and a B.S. in Microbiology from the University of Rochester, earned in 1994. His research focuses on microbial ecology and genomics of soil, exploring the microbial communities and their functions within soil environments. As a faculty member, he is involved in leading research efforts in microbial ecology, contributing to the understanding of soil microbiomes and their roles in ecological processes.

Research topics

• Computer Science
• Biology
• Genetics
• Ecology
• Computational biology
• Artificial Intelligence
• Evolutionary biology
• Data Mining
• Machine Learning
• Environmental science
• Astronomy
• Organic chemistry
• Geology
• Library science
• Environmental chemistry
• Data science
• Oceanography
• World Wide Web
• Paleontology
• Soil science
• Botany
• Bioinformatics
• Biochemistry
• Chemistry

Selected publications

• Bacterial growth efficiency and population dynamics during community assembly on plant litter

  Research Square · 2025-11-11

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Dynamics of bacterial growth, and life-history tradeoffs, explain differences in soil carbon cycling due to land-use

  ISME Communications · 2025-01-01 · 2 citations

  articleOpen accessSenior author

  Abstract Soil contains a considerable fraction of Earth’s organic carbon. Bacterial growth and mortality drive the microbial carbon pump, influencing carbon use efficiency and necromass production, key determinants for organic carbon persistence in soils. However, bacterial growth dynamics in soil are poorly characterized. We used an internal standard approach to normalize 16S ribosomal RNA gene sequencing data allowing us to quantify growth dynamics for 30 days following plant litter input to soil. We show that clustering taxa into three groups optimized variation of bacterial growth parameters in situ. These three clusters differed significantly with respect to their lag time, growth rate, growth duration, and change in abundance due to growth (ΔNg) and mortality (ΔNd), matching predictions of Grime’s CSR life-history framework. In addition, we show a striking relationship between ΔNg and ΔNd, which reveals that growth in soil is tightly coupled to death. This result suggests a fitness paradox whereby some bacteria can optimize fitness in soil by minimizing mortality rather than maximizing growth. We hypothesized that land-use constrains microbial growth dynamics by favoring different life-history strategies and that these constraints control carbon mineralization. We show that life-history groups vary in prevalence with respect to land-use, and that bacterial growth dynamics correlated with carbon mineralization rate and net growth efficiency. Meadow soil supported more bacterial growth, greater mortality, and higher growth efficiency than agricultural soils, pointing toward more efficient conversion of plant litter into microbial necromass, which should promote long-term C stabilization.

  PublisherDOI

• Draft genomes of six <i>Streptomyces</i> species from a United States biogeography survey

  Microbiology Resource Announcements · 2025-12-08

  articleOpen accessSenior author

  ABSTRACT Streptomyces bacteria play key ecological and functional roles in terrestrial ecosystems. We surveyed soil samples across the continental United States, identifying six novel Streptomyces species. Here, we report the whole genome sequences of these strains and their predicted biosynthetic products, providing additional information for studying biological and chemical diversity in this ubiquitous species.

  PublisherDOI

• Decomposition causes short-term increases in functional molecular diversity of dissolved organic matter

  Nature Communications · 2025-12-10 · 1 citations

  articleOpen access

  The molecular diversity of dissolved organic matter (DOM) in soil depends on the stage of plant litter decomposition and microbial metabolism. Yet the contributions of catabolic and anabolic processes on DOM molecular diversity, and their consequences for organic carbon mineralization, remain unclear. To address this question, we used an 18O-H2O isotope-labelling approach to track microbial transformation of DOM during blue grama grass (Bouteloua gracilis) decomposition and determine how these processes alter molecular diversity. Here, we show that 18O-isotopically labeled compounds indicate that microbially produced DOM increases functional molecular diversity (recognizing compound dissimilarity) during early decomposition (days) but not at later stages (months). Furthermore, carbon mineralization from DOM is most strongly correlated with molecular weight, highlighting the role of chemical properties in regulating microbial decomposition. Our findings suggest that early microbial catabolic and anabolic metabolism enhances DOM molecular diversity, whereas later decomposition favors the accumulation of fewer, recycled microbial compounds. Microbial decomposition of plant litter initially increases the molecular diversity of dissolved organic matter, but prolonged microbial recycling diminishes this diversity, highlighting how microbial metabolism influences soil carbon turnover.

  PublisherOA PDFDOI

• Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution in <i>Streptomyces</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-05

  preprintOpen accessSenior author

  Abstract The role of horizontal gene transfer (HGT) in shaping bacterial genomes is well recognized, but constraints on gene exchange and the degree to which these constraints shape genome evolution remain poorly described. In this study, we sought to determine whether geographic and phylogenetic distance constrains HGT within and between bacterial species. To address this question, we isolated strains ( n = 17) of two closely related bacterial species, Streptomyces griseus and Streptomyces pratensis from two ecologically similar sites. We identified homologous recombination events within the core genomes of these species (557 recent and 457 ancient) and determined that patterns of recombination were constrained primarily by phylogeny rather than geography. Notably, shell accessory genes were over three times more likely to be shared between the same species than with non-related geographical neighbors. The richness of secondary metabolite gene clusters is highly variable with an average of 35 – 55 clusters per genome, depending on clade membership. The majority of secondary metabolite gene clusters (60%) are found in all strains, indicating that they were present in the most recent common ancestor of S. griseus and pratensis . We conclude that most HGT in the core and accessory genome is phylogenetically constrained, while HGT of shell genes is more likely constrained by geography. This outcome indicates that the predominant mechanisms of HGT favor high phylogenetic relatedness, and that rapid gene acquisition and loss in the accessory genome could aid with adaptation to contemporary environmental conditions. Importance Horizontal gene transfer (HGT) is a vital ecological and evolutionary force in microbiology, but we still lack a precise understanding of how precisely HGT acts on the gene pool of a species or genus. While HGT can complicate phylogenetic analyses and assumptions of homology, its role in adaptation and acquiring secondary metabolites should not be overlooked. Microbial ecologists agree that the pangenome is a shifting collection of genes that can be influenced by both vertical inheritance and ecological factors. This study examines how the Streptomyces pangenome is shaped by these two forces and offers an important quantitative insight into how HGT shapes bacterial genome dynamics.

  PublisherOA PDFDOI

• Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution in <i>Streptomyces</i>

  Microbiology Spectrum · 2025-12-17 · 2 citations

  articleOpen accessSenior author

  ABSTRACT The role of horizontal gene transfer (HGT) in shaping bacterial genomes is well recognized, but constraints on gene exchange and the degree to which these constraints shape genome evolution remain poorly described. In this study, we sought to determine whether geographic and phylogenetic distance constrains HGT within and between bacterial species. To address this question, we isolated strains ( n = 17) of two closely related bacterial species, Streptomyces griseus and Streptomyces pratensis from two ecologically similar sites. We identified homologous recombination events within the core genomes of these species (557 recent and 457 ancient) and determined that patterns of recombination were constrained primarily by phylogeny rather than geography. Notably, shell accessory genes were over three times more likely to be shared between the same species than with non-related geographical neighbors. The richness of secondary metabolite gene clusters is highly variable with an average of 35–55 clusters per genome, depending on clade membership. The majority of secondary metabolite gene clusters (60%) are found in all strains, indicating that they were present in the most recent common ancestor of S. griseus and pratensis . We conclude that most HGT in the core and accessory genome is phylogenetically constrained, while HGT of shell genes is more likely influenced by geography. This outcome indicates that the predominant mechanisms of HGT favor high phylogenetic relatedness, and that rapid gene acquisition and loss in the accessory genome could aid with adaptation to contemporary environmental conditions. IMPORTANCE Horizontal gene transfer (HGT) is a vital ecological and evolutionary force in microbiology, but we still lack a precise understanding of how precisely HGT acts on the gene pool of a species or genus. While HGT can complicate phylogenetic analyses and assumptions of homology, its role in adaptation and acquiring secondary metabolites should not be overlooked. Microbial ecologists agree that the pangenome is a shifting collection of genes that can be influenced by both vertical inheritance and ecological factors. This study examines how the Streptomyces pangenome is shaped by these two forces and offers an important quantitative insight into how HGT shapes bacterial genome dynamics.

  PublisherDOI

• Strengthening farmer-led experiments through agronomic and causal inference frameworks

  2025-06-27

  preprintOpen access

  This study explores how scientists can support on-farm experiments using analytical methods that align with farmers’ endogenous learning processes. Four maize farmers across 10 site-years in New York participated in this study to evaluate the effectiveness of a nitrogen-fixing inoculant (NFI) applied with a reduced side-dress nitrogen rate. Farmers designed and implemented their own experiments using a range of layouts, including side-by-side comparisons and strip trials. Two analytical approaches were compared: a quantitative yield analysis using spatial regression, and a causal pathway analysis based on mechanistic steps informed by field sampling (e.g., qPCR detection of NFI organisms, nitrogen nutrition index, and yield). While yield data suggested positive or neutral treatment effects at all sites when simply comparing yield average, the spatial regression analysis and causal pathway analysis identified positive outcomes in only 7 or 4 of 10 site-years respectively, reflecting a more conservative interpretation of efficacy. Both methods provided consistent conclusions at 4 out of 10 site-years, demonstrating the contribution of metrics other than yield in the interpretation process. Findings suggest that simple causal diagrams can structure data collection and interpretation in ways aligned with farmers’ goals. Supporting farmer experiments with digital agronomy, mechanistic reasoning, and site-specific data enhances learning outcomes and scientific rigor without requiring formal replication. This work contributes to the development of collaborative, scalable methodologies that integrate farmer knowledge and scientific analysis in OFE.

  PublisherOA PDFDOI

• Long-term tillage regime structures bacterial carbon assimilation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-08

  preprintOpen accessSenior authorCorresponding

  Abstract Microbial growth dynamics are deterministic of the fate of carbon in soil, responsible for the transformation of new carbon inputs and their stabilization on soil surfaces. Bacterial life history strategies are predictive of C substrate assimilation and growth response. High disturbance management practices such as tillage alter microbial community structure but have a poorly described impact on life histories that are central to C metabolism. We conducted a DNA stable isotope probing experiment using soil from a long-term field experiment with a 42-year legacy of no-till or annual moldboard plowing. We predicted that divergent legacies of disturbance would result in bacterial communities with distinct life histories, altering C assimilation dynamics. We incubated soil from each tillage regime with 13 C-xylose and 13 C-cellulose, two substrates that are components of plant litter and which differ in bioavailability. We identified 730 bacterial taxa that incorporated the labeled substrates and tracked their abundance in bulk microcosm soil over a 30 day period. Carbon addition rapidly altered bacterial community structure and function, with tilled soils demonstrating lower mineralization rates of each substrate. Xylose-assimilating taxa exhibited significantly lagged growth in tilled soils relative to no-till. We also found a higher number and diversity of late (day 30) cellulose incorporators in no-till soil, suggesting that minimal disturbance resulted in a longer residence time of 13 C-cellulose in members of the bacterial community. We show that soil management practices shape the path of carbon through bacterial communities by altering dynamic growth responses and secondary incorporation of carbon. Highlights DNA SIP identified divergent carbon dynamics resulting from tillage legacies Xylose assimilation in plow-till soils was late and decoupled from mineralization Cellulose-C was assimilated later in no-till soils relative to plow-till Growth responses of incorporator taxa differ by tillage and explain mineralization

  PublisherOA PDFDOI

• Functional molecular diversity of dissolved organic matter explained by predicted genome size of soil microbial communities

  Soil Biology and Biochemistry · 2025-07-29 · 11 citations

  article
  PublisherDOI

• Long term tillage regime alters bacterial assimilation of xylose and cellulose

  Applied and Environmental Microbiology · 2025-08-06 · 1 citations

  articleOpen accessSenior author

  ABSTRACT Microbial growth dynamics determine carbon fate in soil by transforming carbon inputs into microbial products available for stabilization on soil surfaces. Management practices such as tillage disturb microbial communities and promote C loss, but the degree to which tillage alters bacterial metabolism of soil C remains poorly described. We conducted a multi-substrate DNA stable isotope probing experiment using soil from a long-term field experiment with a 42-year legacy of either no-till or annual moldboard plowing. We predicted that this land use history would alter C assimilation dynamics due to differences in bacterial growth responses. We incubated soil from each tillage regime with 13 C-xylose and 13 C-cellulose, substrates that differ in bioavailability and which favor different bacterial life history strategies in soil. We identified 730 13 C-labeled bacterial taxa and tracked their abundance in bulk soil over a 30 day period. Carbon addition to soil rapidly altered bacterial community structure and function. 13 C-labeling dynamics differed substantially between tilled and no-till soils with respect to both xylose and cellulose. Bacterial xylose metabolism in tilled soils exhibited substantial lag relative to no-till soils, and this lag corresponded with lower mineralization rates for xylose. In addition, bacterial cellulose metabolism was mediated primarily by specialist taxa in no-till soils, while dual incorporators dominated tilled soils. Differences in carbon assimilation corresponded to lower cellulose mineralization rates and cumulative cellulose mineralization in tilled soils. We show that soil management practices shape the path of carbon through bacterial communities by altering dynamic growth responses associated with bacterial life history strategies. IMPORTANCE We applied DNA stable isotope probing in a microcosm experiment to understand the role of soil management (till vs no-till) in shaping bacterial carbon cycling. Our hypothesis was that a legacy of disturbance through tillage would exert a selective influence on bacterial growth dynamics, thereby altering bacterial processing of added carbon substrates. We found that lagged growth in tilled soil resulted in delayed bacterial assimilation of xylose and a streamlined, single carbon “channel” characterized by the co-metabolism of xylose and cellulose. In no-till soil, temporally distinct bacterial assimilation of xylose and cellulose by separate carbon “channels” was associated with higher carbon mineralization rates and total mineralization relative to tilled soil. Our findings indicate that soil management practices altered the growth dynamics of active carbon cycling bacteria. Lagged growth associated with a history of disturbance resulted in reduced carbon mineralization.

  PublisherDOI

Recent grants

• MSB: Single Cell Ecology - Developing a new paradigm for the Microbial Diversity course of the Marine Biological Laboratory, Woods Hole, MA

  NSF · $205k · 2009–2013

• Resolving systematic uncertainty in Streptomyces by interpreting their evolution and biogeography through the prism of horizontal gene exchange

  NSF · $676k · 2011–2016

• CAREER: Targeted Environmental Genomics: Stable Isotope Probing of Non-cultivated Diazotrophs in Soil

  NSF · $686k · 2005–2012

• Phylogenetic niche conservatism as a driver of microbial diversification and biogeography

  NSF · $749k · 2015–2021

Frequent coauthors

• Roland C. Wilhelm

  Purdue University West Lafayette

  54 shared

• Charles Pepe‐Ranney

  Cornell University

  38 shared

• Mary Lipton

  Environmental Molecular Sciences Laboratory

  21 shared

• Samuel E. Barnett

  Michigan State University

  21 shared

• Pamela Weisenhorn

  Argonne National Laboratory

  21 shared

• Johannes Lehmann

  20 shared

• Nicholas D. Youngblut

  19 shared

• Chantal Koechli

  Cornell University

  16 shared

Labs

• Buckley LabPI

Education

• PhD/Microbiology, Microbiology

  Michigan State University

  2000

• BS/Microbiology, Microbiology

  University of Rochester

  1994