Geology topics

Joseph M. Craine

Publications and source records attributed to Joseph M. Craine.

8 recordsLinked to original sources

USGS2026

Cost-efficient filtration and replication strategies match or exceed detection sensitivity for marine eDNA diversity at an intertidal site under a standardized laboratory workflow

Optimizing environmental DNA (eDNA) metabarcoding to maximize species detection while minimizing costs and effort remains a challenge, particularly in high-throughput workflows. In the marine intertidal zone off Point Conception, California, we compared eDNA richness accumulation between filtration approaches that differed in filter type and downstream processing, field and laboratory replicates, and independent and pooled polymerase chain reaction (PCR) replicates. Ten 10-cm 2 capsule filters and 10 5-cm 2 syringe disc filters were processed using a standardized laboratory workflow for 12S ribosomal ribonucleic acid (rRNA) (marine vertebrates) and 18S rRNA (metazoans and phytoplankton) metabarcoding, with 10 independent PCR replicates per filter. Because capsules generated larger lysate volumes than discs, the fixed extraction input volume under the standardized workflow resulted in less lysate being processed. A follow-up study pooled 10 PCR replicates for 12S rRNA. When comparing individual PCR replicates, individual filters, or all filters aggregated, discs detected greater marine vertebrate richness than capsules. Probabilistic models indicated that varying effective volume alone could produce similar richness accumulation patterns to those observed, though other filter characteristics were unaccounted for. Minimal differences in richness accumulation were detected between filters for 18S rRNA, and modeling indicated that this was not explained by higher initial copies of 18S rRNA. Meanwhile, vertebrate richness accumulation was similar when adding PCR replicates from the same sample or independent field samples across the short, relatively homogenous intertidal transect. Pooling PCR replicates had no detectable difference on richness compared to sequencing PCR replicates independently: a single pooled PCR replicate detected the same vertebrate richness as the sum of 10 independent PCR replicates. These results show that, under the standardized workflow and conditions tested here, eDNA programs may reduce costs and effort without detectable loss of richness by using filtration approaches aligned with extraction input and pooling technical replicates.

California↗

USGS2025

What is eDNA method standardization and why do we need it?

The rapid advancement of environmental DNA ( eDNA ) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

Metabarcoding and Metagenomics↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2023

Toward a national eDNA strategy for the United States

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next-generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

Environmental DNA↗

USGS2020

Global plant trait relationships extend to the climatic extremes of the tundra biome

The majority of variation in six traits critical to the growth, survival and reproduction of global plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.

Nature Communications↗

USGS2018

Identifying diet of a declining prairie grouse using DNA metabarcoding

Diets during critical brooding and winter periods likely influence the growth of Lesser Prairie-Chicken ( Tympanuchus pallidicinctus ) populations. During the brooding period, rapidly growing Lesser Prairie-Chicken chicks have high calorie demands and are restricted to foods within immediate surroundings. For adults and juveniles during cold winters, meeting thermoregulatory demands with available food items of limited nutrient content may be challenging. Our objective was to determine the primary animal and plant components of Lesser Prairie-Chicken diets among native prairie, cropland, and Conservation Reserve Program (CRP) fields in Kansas and Colorado, USA, during brooding and winter using a DNA metabarcoding approach. Lesser Prairie-Chicken fecal samples ( n = 314) were collected during summer 2014 and winter 2014–2015, DNA was extracted, amplified, and sequenced. A region of the cytochrome oxidase I (COI) gene was sequenced to determine the arthropod component of the diet, and a portion of the trn L intron region was used to determine the plant component. Relying on fecal DNA to quantify dietary composition, as opposed to traditional visual identification of gut contents, revealed a greater proportion of soft-bodied arthropods than previously recorded. Among 80 fecal samples for which threshold arthropod DNA reads were obtained, 35% of the sequences were most likely from Lepidoptera, 26% from Orthoptera, 14% from Araneae, 13% from Hemiptera, and 12% from other orders. Plant sequences from 137 fecal samples were composed of species similar to Ambrosia (27%), followed by species similar to Lactuca or Taraxacum (10%), Medicago (6%), and Triticum (5%). Forbs were the predominant (>50% of reads) plant food consumed during both brood rearing and winter. The importance both of native forbs and of a broad array of arthropods that rely on forbs suggests that disturbance regimes that promote forbs may be crucial in providing food for Lesser Prairie-Chickens in the northern portion of their distribution.

The Auk↗

USGS2017

Centennial-scale reductions in nitrogen availability in temperate forests of the United States

Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes on forest N cycling, we measured stable N isotopes in wood, a proxy for N supply relative to demand, on large spatial and temporal scales across the continental U.S.A. Here, we show that forest N availability has generally declined across much of the U.S. since at least 1850 C.E. with cool, wet forests demonstrating the greatest declines. Across sites, recent trajectories of N availability were independent of recent atmospheric N deposition rates, implying a minor role for modern N deposition on the trajectory of N status of North American forests. Our results demonstrate that current trends of global changes are likely to be consistent with forest oligotrophication into the foreseeable future, further constraining forest C fixation and potentially storage.

Scientific Reports↗

USGS2015

Convergence of soil nitrogen isotopes across global climate gradients

Quantifying global patterns of terrestrial nitrogen (N) cycling is central to predicting future patterns of primary productivity, carbon sequestration, nutrient fluxes to aquatic systems, and climate forcing. With limited direct measures of soil N cycling at the global scale, syntheses of the 15 N: 14 N ratio of soil organic matter across climate gradients provide key insights into understanding global patterns of N cycling. In synthesizing data from over 6000 soil samples, we show strong global relationships among soil N isotopes, mean annual temperature (MAT), mean annual precipitation (MAP), and the concentrations of organic carbon and clay in soil. In both hot ecosystems and dry ecosystems, soil organic matter was more enriched in 15 N than in corresponding cold ecosystems or wet ecosystems. Below a MAT of 9.8°C, soil δ 15 N was invariant with MAT. At the global scale, soil organic C concentrations also declined with increasing MAT and decreasing MAP. After standardizing for variation among mineral soils in soil C and clay concentrations, soil δ 15 N showed no consistent trends across global climate and latitudinal gradients. Our analyses could place new constraints on interpretations of patterns of ecosystem N cycling and global budgets of gaseous N loss.

Scientific Reports↗