Find research datasets worth reusing

openCC (other)Oct 2024View details →

Interviews with members of the HJA Community during the Lookout Fire, HJ Andrews Experimental Forest, 2023

This dataset records the interview instrument, analytical codebook, and summary of results for the 2023 Lookout Fire Qualitative Interviews. Data was collected in 2023 in Corvallis, Oregon, and over Zoom. Members of the H. J. Andrews Experimental Forest (HJA) community (e.g., university faculty and administrative professionals, agency scientists and personnel, students, alumni and emeritus from the aforementioned communities) were interviewed between September 26th and November 8th 2023. At the time, the fire had largely stopped growing (no significant runs occurred during the interview period), but the fire was not fully contained and the fire severity was not yet known by the community. Data collection is complete. The interview included questions about emotional reactions to the Lookout Fire, current and foreseen impacts to research at the HJA, social relationships and the fire, naturalness of the fire, and climate change, climate anxiety, and the fire. Interviews were semi-structured; while interviews were guided by the interview protocol, conversation was allowed to proceed organically. In total, 40 respondents were interviewed. Interviews were transcribed verbatim and analyzed inductively and deductively. A finalized codebook was developed iteratively; the included codebook are the final codes used to analyze the full dataset. Interview transcripts and other potentially identifying information is not available to protect respondent confidentiality and anonymity. This dataset summarizes the key interview results.

Herbaceous Community Composition in CRUI Land Use Project at Harvard Forest 1996

Patterns of vascular plant species richness were investigated in six land use legacy sites (2 formerly plowed, 2 formerly pastured, and 2 permanent woodlot) in Prospect Hill to test predictions about the effects of disturbance, light and soil resources, and forest floor environmental heterogeneity on community composition. The occurrence of vascular taxa was recorded in each of the 60 5 m x 5 m contiguous plots within the 30 m x 50 m permanently gridded study plot in each land use legacy site in June 1996. Identification was made to species in most cases. Woodlots showed higher average species richness at the site level (53) than either pastured (52 species) or plowed (49) sites. However woodlots also show greater spatial variation in richness at the 5 m x 5 m resolution than either the plowed or pastured sites (in that order) as represented by the range, standard deviation, and coefficient of variation. Seasonally-averaged light levels at 50 cm are approximately twice as high in the plowed and pastured sites as in the woodlots, but the woodlots show significantly greater soil organic matter, carbon, nitrogen and water-holding capacity than the post-agricultural sites. These results suggest that soil resources may be more important than light in fostering higher herbaceous stratum richness. However, woodlot richness is also affected by the presence of taxa that are slow to re-colonize heavily disturbed sites (e.g., Epigaea repens) and to distinctive microsites that are less common in the plowed or pastured sites in the Harvard Forest system (e.g., exposed boulders). The greater spatial variation in woodlot richness is strongly influenced by both substrate diversity and by scattered hemlock trees, which substantially depress the herb stratum in localized patches.

Bird Communities in Forest Openings at Harvard Forest 2014-2015

Currently, many of the most severely declining neotropical migrants in the northeastern United States are disturbance dependent, early-successional species. Much of their decline is attributed to loss of suitable habitat. Large clearcuts (>5.0 ha) are widely considered to be optimal habitat for most shrubland bird species. However, it is well documented that certain species are capable of breeding within significantly smaller patches of habitat (less than 2.0 ha), which are most commonly created through group selection harvest cuttings. The goal of this research is to determine habitat characteristics translatable to habitat value for shrubland birds for use in conservation programs to maximize biological value. This research will provide an assessment of the value of forest openings for shrubland birds, helping to define the suitability of forest canopy openings for specific bird species. This project will describe the conservation value of shrubland openings deemed too small to sustain full suites of specialist shrubland birds by providing threshold patch area values for individual species able to use these smaller patches.

Ectomycorrhizal Community of Red Oak at Harvard Forest 2013

There is evidence that ectomycorrhizal Pezizales prevail on roots at woodland edges or habitats where trees are well spaced, and where there is minimal understory vegetation, soil pH is relatively high, and bare soil is a feature. This observation was repeated in a recent study of mitospores produced by these fungi, where they were found most often at woodland edges, road sides, the middle of paths, and lawns. A key feature that distinguishes Basidiomycota from Ascomycota is that the dikaryon necessary for sexual reproduction is generally formed early after spore germination in the former, but not until fruitbody formation in the latter. Our hypothesis is that the mitospores produced by ectomycorrhizal Pezizales act as spermatia, and that these spores are more effectively produced and dispersed from bare soil than from areas with a thick organic layer. Here we tested our hypothesis by comparing the community of ectomycorrhizal root fungi on red oak trees in Harvard Forest and the Arnold Arboretum.

Taxonomy and Biogeography of Nematode Communities at Harvard Forest 2014

Our overall goal is to describe and map nematode biodiversity in North America. Specifically we will concentrate on Criconematina, a suborder of plant parasitic, soil-dwelling nematodes. Criconematina, commonly referred to as ring-nematodes, are distributed globally associated with a wide range of hosts and habitats. In native grasslands and forests, they may constitute as much as 30% of the below-ground nematode community. Their abundance often approaches 500 individuals per 100cc of soil with as many as a dozen species recorded from a single habitat. Host associations may be broad, covering entire plant families, or they may specialize in feeding on a few closely related plant species. Several are known agronomic pest species, but the vast majority is known only from native habitats and responds negatively to soil disturbance. Due to their sensitivity to disturbance and associations with a range of plant species, some ecologists have suggested that ring nematodes could serve as a below-ground biological indicator of habitat quality. Before this application is possible taxonomic boundaries need to be evaluated and a reference database needs to be established.

Effects of Warming on Soil Microbial Communities at Harvard Forest 2011

As Earth’s climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.

Soil Microbial Community Effects on Quercus Rubra Seedling Survival at Harvard Forest 2016-2017

Feedbacks between plants and their soil microbial communities often drive negative density dependence in tropical forests, but their importance for tree demographics in temperate forests remains unclear. Additionally, the relative contribution of intraspecific seedling competition and soil pathogens to density-dependent patterns has rarely been assessed. We assessed how the soil microbial community influenced Quercus rubra seedling survival by growing seedlings in a greenhouse inoculated with soil collected from beneath conspecific and heterospecific mature trees. We found that seedlings grown with soil from beneath conspecific adults had a higher mortality rate than seedlings grown with soil from beneath heterospecific adults; therefore adult plant-soil feedbacks decrease seedling survival in Q. rubra.

openCC0Jan 2024View details →

Community and Ecosystem Impacts in Hemlock Removal Experiment at Harvard Forest 2003-2020

Hemlock decline in New England is caused by direct and indirect effects of invasion of the hemlock woolly adelgid. Direct damage from the insect is causing gradual mortality of hemlock, and widespread harvesting of hemlock in advance of mortality creates a contrasting disturbance. Although both processes affect thousands of acres of forest annually, we have only a limited understanding of their effects on forest ecosystem function and productivity and the nature of the subsequent forest community. We anticipate that harvesting will yield different consequences than gradual mortality from the insect. Therefore we have designed an experiment to simulate the impact of both in order to contrast them. To simulate some of the effects of the adelgid (e.g., progressive mortality, retention of the wood on the site) we are girdling all hemlocks in a hemlock-dominated stand. In the adjacent area we are conducting a commercial harvesting of hemlock. Results from both experimental treatments will be compared to the changes observed in forests that are being infested by the adelgid, and can also be included in integrated analyses of a suite of large experiments that form a core component of the Harvard Forest LTER program.

openCC (other)Aug 2025View details →

Bird and forest communities in a northern Michigan jack pine stand before and after logging, 2013-2018

This package contains data associated with documentation of breeding-season bird communities in a dry, jack pine and mixed red pine-jack pine forest in Marquette Co., MI. In addition to repeated surveys, 2014-2018, of bird presence in a network of 45 study plots, the package includes vegetation data collected on the same plots 2013-2017. At initiation of the study, the stand was >100 years old and had experienced little or no active management. During the study period, stands were thinned to reduce fire risk, and most jack pine were cut; three plots fell in a control area with no logging. Bird communities and vegetation were sampled repeatedly before and after management activities. Subsequent to the study period, a managed burn affected much of the study area.

openCC (other)Jan 2026View details →

Hubbard Brook Experimental Forest: Soil Fungal Communities, 2021-2023

Sporocarp (fungal fruiting body) observational data and fungal eDNA data extracted from soil samples collected primarily by Farrar Ransom in the summers of 2021, 2022, and 2023. Also included: detailed site metadata, soil moisture measurements, sample processing metadata, and R code used in publication analysis. Data are still being uploaded as of January 2026. The majority of these data were collected in study plots established around 2016 by Dr. Elizabeth Studer for her dissertation work. This factorial study design consists of approximately 60 plots on two hydropedological soil types beneath four canopy tree species. The four tree species we considered were white ash (Fraxinus americana), sugar maple (Acer saccharum), American beech (Fagus grandifolia), and yellow birch (Betula alleghaniensis). Some of these plots are now part of the ongoing Ash Protection Experiment. The following data tables and other entities were used in the analysis for the publication: Unique soil fungal communities are associated with disappearing ash trees in a northern temperate hardwood forest. Site_Metadata; eDNA_Abun_Table; eDNA_Taxa_Metadata; eDNA_Extraction_Metadata; iNext_Format_eDNA; Sporocarp_Count_Table; Sporocarp_Prop_Table; Soil_Moisture_Measurements; PCR_Plate_Gel_Photos; FR_DADA2_PlusFilter_CodePub; FR_eDNA_CodePub; FR_Sporocarp_CodePub; These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.

Linking Community Dynamics and Ecosystem Function at Harvard Forest 1996-2000

Human activities are effecting profound changes in the structure and function of natural ecosystems. A comprehensive understanding of current ecosystem dynamics and future responses to global change requires an integrated investigation of ecological processes at many levels of organization. My thesis research addressed this goal by examining interactions between community- and ecosystem-level dynamics in mixed conifer broad-leaved forests in eastern North America. I addressed the nature of canopy-seedling feedbacks in mixed forests by relating seedling regeneration patterns in contrasting stand types to understory conditions (EXPERIMENT 1), and by directly manipulating resource availability to separate the individual effects of particular resources (EXPERIMENT 2). To investigate how nitrogen deposition will influence future forest composition, I examined the impact of increased nitrogen availability on regeneration of both coniferous and broad-leaved tree species under both closed canopy (EXPERIMENT 3) and simulated gap (EXPERIMENT 4) conditions. Future changes in forest composition might then influence whole-ecosystem productivity. I used two scaling approaches (leaf-level aggregation, EXPERIMENT 5; whole-tree sap flow, EXPERIMENT 6), I examined how the dominant coniferous and broad-leaved species in mixed temperate forests differed in their contributions to canopy-level photosynthesis.

openCC0Mar 2025View details →

Tree-Associated Fungal and Bacterial Communities at Harvard Forest 2021

Cities are investing in tree-planting initiatives to protect their citizens from climate change-related heat and pollution exposure, yet Boston’s street trees are growing nearly four times as fast and dying twice as young as Massachusetts’ rural forest trees. Our research aims to characterize the belowground variables and microbial community composition that might explain the differences in growth and mortality rates observed between urban and rural trees. In 2021, soil, leaf, and root samples were taken from 25 trees in Harvard Forest to use as a rural comparison to Boston’s street trees and trees in other forests along an urban-to-rural gradient from Boston into Western Massachusetts. At each tree, three 12” deep, 2.4-centimeter radius soil cores were taken within the drip line, and soil cores were divided into the top 6” and lower 6” of soil. Fine roots were picked from each soil core. Six leaf samples were taken from the mid-canopy of each tree, where possible. Soil variables including temperature, moisture, percent organic matter, soluble nitrogen availability, bulk density, and root biomass were measured. Thus far, we have found that urban trees have fewer roots than Harvard Forest trees (F1,252) = 10.88, p = 0.0011), and that urban trees establish more root biomass deeper into the soil than Harvard Forest trees (p = 4.84e-5).

Stream Subsurface Flowpaths and Macroinvertebrate Communities at Harvard Forest 2004

Headwater streams and wetlands with a combination of surface and subsurface flows are common features of many upland-forested watersheds. Unlike headwater stream reaches with continuous surface flow, the hydrology and ecology of subsurface stream reaches are poorly studied and not factored into existing wetland legislation. We assessed subsurface habitats and associated biota in a 435-m reach of a first-order, intermittent stream draining a riparian zone dominated by eastern hemlock (Tsuga canadensis) in north central Massachusetts. Stream flow was found only in subsurface flowpaths beneath large boulders and surface root mats over approximately 70% of the total stream length at summer base flow. Temperature, specific conductivity, dissolved oxygen, and dissolved organic carbon concentrations of subsurface water were similar to surface water. Macroinvertebrates were found in subsurface habitats but at a lower abundance and richness per unit area compared to surface habitats. Collectors such as Chironomidae, Polycentropodidae, and Ephemerellidae were generally the most abundant families in both surface and subsurface habitats. Our findings indicate that in some glaciated watersheds, intermittent streams with no visual evidence of surface flow may contain subsurface flowpaths with water chemistry and biota comparable to coupled perennial surface flow reaches. The prevalence and importance of subsurface habitats in some headwater streams may warrant review or revision of existing state and local regulatory definitions of intermittent and headwater streams.

Structure of Ant Communities in Declining Hemlock Stands at Harvard Forest 2003

In biomass and ecological dominance, ants are the most important invertebrate taxon in terrestrial ecosystems and they can alter significantly fundamental processes and dynamics of soil ecosystems. Relative to deciduous stands, hemlock stands are depauperate in ant species that are linked to differences in rates of soil turnover and nutrient mineralization between these forest types. In both hemlock and deciduous stands, we will document ant species richness and abundance; assess their role in soil nutrient cycling; determine temporal trajectories of ant community assembly as hemlock declines following woolly adelgid infestation, and is subsequently replaced by birch; and discover how these trajectories influence nutrient availability during this transition. For more details see: Ellison, A. M., J. Chen, D. Dz, C. Kammerer-Burnham, and M. Lau. 2005. Changes in ant community structure and composition associated with hemlock decline in New England. Pages 280-289 in B. Onken and R. Reardon, editors. Proceedings of the 3rd Symposium on Hemlock Woolly Adelgid in the Eastern United States. US Department of Agriculgure - US Forest Service - Forest Health Technology Enterprise Team, Morgantown, West Virginia.

openCC (other)May 2025View details →

SBC LTER: Reef: Seasonal Kelp Forest Community Dynamics: biomass of kelp forest species, ongoing since 2008

These data represent values of biomass density for more than 200 species of macroalgae, invertebrates and fish measured in fixed plots at five reefs as part of SBCLTER's seasonal kelp forest monitoring program to track long-term patterns in species abundance and diversity. Taxon-specific relationships between size and mass were applied to field measurements of species abundance to estimate biomass density of each species. The five reefs (Arroyo Quemada 34°28.048’N, 120°07.031’W; Carpinteria 34°23.474’N, 119°32.510’W; Isla Vista 34°23.275’N, 119°32.792’W; Mohawk 34°23.649’N, 119°43.762’W; and Naples 34° 25.342’N, 119° 57.102’W) ranged in depth from 5.8 m to 8.9 m (MLLW) and were chosen to represent a range of physical and biological characteristics known to influence subtidal macroalgal assemblages in the region.

openCC (other)May 2025View details →

SBC LTER: Reef: Seasonal Kelp Forest Community Dynamics: Taxon-specific seasonal net primary production (NPP) for macroalgae

This dataset provides estimates of seasonal net primary production (NPP) for all taxa of macroalgae sampled in fixed plots of the SBC LTER's seasonal kelp forest monitoring sites. The five reefs (Arroyo Quemada 34°28.048’N, 120°07.031’W; Carpinteria 34°23.474’N, 119°32.510’W; Isla Vista 34°23.275’N, 119°32.792’W; Mohawk 34°23.649’N, 119°43.762’W; and Naples 34° 25.342’N, 119° 57.102’W) ranged in depth from 5.8 m to 8.9 m (MLLW) and were chosen to represent a range of physical and biological characteristics known to influence subtidal macroalgal assemblages in the region. NPP of understory taxa was calculated using field measurements of irradiance and biomass (derived from abundance) and laboratory estimates of taxon-specific photosynthetic parameters. NPP for the giant kelp, Macrocystis pyrifera, was calculated using linear relationships between frond density in a given season and average NPP for that season.

openCC (other)Jul 2021View details →

SBC LTER: Reef: Kelp Forest Community Dynamics: Fish abundance (Reformatted to the ecocomDP Design Pattern)

This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/17/35. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The two tables in this data package include: 1) The annual benthic fish community survey which was conducted on 11 reefs once a year around late July or early August; and 2) The monthly fish survey which was conducted once a month at a subset of the sites (3 of the annual sites) The time period of data collection for the annual benthic fish community survey varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE (Transect1), and MOHK (Transect 1) in 2002. The Transect 2 and 3 at ABUR were discontinued in June 2006. See Method

openCC (other)Oct 2022View details →

Western columbine genetics across HJ Andrews Experimental Forest meadow communities

Woody plant encroachment is diminishing meadow and grassland habitat on a global scale. Increased woody cover influences local conditions such as light/shade environments, local soil characteristics, understory plant community structure, and disturbance regimes. Woody encroachment may also affect landscape-scale biological processes, such as herbaceous plant population structure, through reducing the total cover and continuity of open habitat and eroding mutualistic interactions, such as plant-pollinator interaction networks. A major concern is that habitat fragmentation will have a cascading effect if one or more mutualistic partners is adversely affected. For example, if pollinators are sensitive to disturbance, fragmentation may reduce rates of gene flow among sub-populations of plants, which is predicted to decrease effective population sizes and diminish adaptive potential (i.e. the capacity to respond to selective pressures through the evolution of genetically-based and heritable traits). Alpine meadows of the Cascade Mountains, which support diverse wildflower and pollinator communities, have shrunk dramatically over the last century as a result of forest encroachment. We posited that, as meadows become smaller and less connected, pollinators may abandon the smallest meadows and focus foraging efforts on the largest, most connected meadows with the most resources. This could expedite the decline and ultimate collapse of meadow communities through reducing adaptive potential across sub-populations of plants. We focus on a plant-pollinator interaction between a common, nectar-producing plant, Aquilegia formosa (western columbine), and rufous hummingbird (Selasphorus rufus) pollinators in four montane meadow complexes in the H.J. Andrews experimental forest, Oregon, USA (HJA). Using hummingbird movement data from SA028 (see H.J. Andrews project database), we first ask whether further forest encroachment in the HJA may alter hummingbird movement patterns among me

openCC (other)Oct 2025View details →

SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of bottom substrate and sand depth

These data describe the percent cover of eight bottom substrate types as determined by a uniform point contact method. The type of bottom substrate is recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Percent cover of each substrate type on a transect is estimated as the proportion of the 80 points contacted by that substrate type x 100. In cases where the substrate type is sand, the depth of the sand is measured. These data are part of the SBC LTER’s time series observations of kelp forest dynamics, which began in 2000 and was designed to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset include nine reef sites along the mainland coast of the Santa Barbara Channel and two on the north side of Santa Cruz Island. These 11 sites were chosen to reflect the wide range of oceanographic conditions present in the Channel and proximity to sources of terrestrial runoff. Data are collected at each site once per year in summer and this dataset is updated annually. The time period of data collection varied among the 11 reef sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The two tables in this data package include: 1) The percent cover of eight bottom substrate types; and 2) the sand depth of each sampling point (sand depth = 0 if substrate type ≠sand).