Geology topics

Scott F. Jones

Publications and source records attributed to Scott F. Jones.

9 recordsLinked to original sources

USGS2025

Combining ecological and genomic diversity surveys to inform conservation and restoration of an endangered wetland plant, soft salty bird’s-beak (Chloropyron molle ssp. molle)

Emergent tidal wetlands are declining globally as a result of sea level rise and land use change. This habitat loss can keenly affect rare plant species within wetlands, and may require restoration to meet species recovery goals related to retaining populations throughout species' ranges. Soft salty bird’s-beak ( Chloropyron molle ssp. molle ) is a federally- and state-endangered hemi-parasitic plant that occurs at the upper marsh transition zone in the San Francisco Bay–Delta, California, USA. We combined field surveys to document habitat associations and trends in abundance with genomic surveys to understand patterns of genetic structure in this rare endemic. We found that C . molle ssp. molle persisted at nine previously occupied marsh sites, although four sites (Hill Slough, MOTCO East, Fagan Marsh, and Joice Island) were smaller in population size than when surveyed in the 1990s. Additionally, twelve sites contained plots with suitable but unoccupied habitat that could be further assessed for restoration. Genomic analysis of over 40,000 single-nucleotide polymorphisms (SNPs) and 253 individuals grouped C . molle ssp. molle into six to seven regional genetic clusters with isolation by distance, and confirmed that C . molle ssp. molle is genetically distinct from adjacent populations of its closest relative ( C . molle ssp. hispidum ). The western-most C . molle ssp. molle sites of Point Pinole and Fagan Marsh were the most genetically and geographically isolated and had the lowest genome-wide diversity. Heterozygosity in sets of genes associated with tidal elevation, salinity, and annual and summer precipitation varied independently across populations. Overall, these genomic patterns indicate that selecting donor sites with similar environmental conditions and utilizing composite seeding approaches from multiple sites could allow for local adaptation to a range of possible environmental conditions. This comprehensive survey of habitat and genomic patterns can allow for the development of restoration actions and build climate-adaptation planning to help prevent the loss of a rare plant.

California↗

USGS2025

Blue carbon stocks along the Pacific Coast of North America are mainly driven by local rather than regional factors

Coastal wetlands, including seagrass meadows, emergent marshes, mangroves, and temperate tidal swamps, can efficiently sequester and store large quantities of sediment organic carbon (SOC). However, SOC stocks may vary by ecosystem type and along environmental or climate gradients at different scales. Quantifying such variability is needed to improve blue carbon accounting, conservation effectiveness, and restoration planning. We analyzed SOC stocks in 1,284 sediment cores along >6,500 km of the Pacific coast of North America that included large environmental gradients and multiple ecosystem types. Tidal wetlands with woody vegetation (mangroves and swamps) had the highest mean stocks to 1 m depth (357 and 355 Mg ha −1 , respectively), 45% higher than marshes (245 Mg ha −1 ), and more than 500% higher than seagrass (68 Mg ha −1 ). Unvegetated tideflats, though not often considered a blue carbon ecosystem, had noteworthy stocks (148 Mg ha −1 ). Stocks increased with tidal elevation and with fine (<63 μm) sediment content in several ecosystems. Stocks also varied by dominant plant species within individual ecosystem types. At larger scales, marsh stocks were lowest in the Sonoran Desert region of Mexico, and swamp stocks differed among climate zones; otherwise stocks showed little correlation with ecoregion or latitude. More variability in SOC occurred among ecosystem types, and at smaller spatial scales (such as individual estuaries), than across regional climate gradients. These patterns can inform coastal conservation and restoration priorities across scales where preserving stored carbon and enhancing sequestration helps avert greenhouse gas emissions and maintains other vital ecosystem services.

Pacific Coast of North America↗

USGS2024

When and where can coastal wetland restoration increase carbon sequestration as a natural climate solution?

Coastal wetlands are hotspots of carbon sequestration, and their conservation and restoration can help to mitigate climate change. However, there remains uncertainty on when and where coastal wetland restoration can most effectively act as a Natural Climate Solution (NCS). Here, we synthesize current understanding to illustrate the requirements for coastal wetland restoration to benefit climate, and discuss potential paths forward that address key uncertainties impeding implementation. To be effective as NCS, coastal wetland restoration projects will accrue climate cooling benefits that would not occur without management action (additionality), will be implementable (feasibility), and will persist over management-relevant timeframes (permanence). Several issues add uncertainty to understanding if these minimum requirements are met. First, coastal wetlands serve as both a landscape source and sink of carbon for other habitats, increasing uncertainty in additionality. Second, coastal wetlands can potentially migrate outside of project footprints as they respond to sea-level rise, increasing uncertainty in permanence. To address these first two issues, a system-wide approach may be necessary, rather than basing cooling benefits only on changes that occur within project boundaries. Third, the need for NCS to function over management-relevant decadal timescales means methane responses may be necessary to include in coastal wetland restoration planning and monitoring. Finally, there is uncertainty on how much data is required to justify restoration action. We summarize the minimum data required to make a decision on whether there is a net cooling benefit from a management action, noting that these data are more readily available than the data required to quantify the magnitude of cooling benefits for carbon crediting purposes. By reducing uncertainty, coastal wetland restoration can be implemented at the scale required to significantly contribute to addressing the current climate crisis.

Coastal Futures↗

USGS2024

Bay Miwok evening primrose: A new subspecies of Oenothera deltoides (Onagraceae) endemic to California

California contains exceptional biodiversity in geography and plant life, including numerous endemic species, some of which are cryptic. The Oenothera deltoides Torr. & Frém. species complex represents a prime example of cryptic diversity. Here, we recognize a new subspecies of Oenothera deltoides , O. deltoides subsp. julpunensis S.F.Jones, subsp. nov., that is a local endemic of windblown sand deposits on the eastern Antioch Dunes sand sheet in the San Francisco Bay-Delta region of California, USA. With the goal of providing clarity to managers of listed species and better understanding of California's diverse flora, we addressed the puzzle of O. deltoides in the region by combining range-wide field surveys with modern genomic tools. We describe the proposed subspecies, its ecology and distribution, and discuss its conservation. As a somewhat cryptic local endemic with small population size and disappearing habitat, the proposed subspecies would benefit from conservation and management to persist as a member of the California flora.

California↗

USGS2023

Stress gradients structure spatial variability in coastal tidal marsh plant composition and diversity in a major Pacific coast estuary

Understanding the drivers of variability in plant diversity from local to landscape spatial scales is a challenge in ecological systems. Environmental gradients exist at several spatial scales and can be nested hierarchically, influencing patterns of plant diversity in complex ways. As plant community dynamics influence ecosystem function, understanding the drivers of plant community variability across space is paramount for predicting potential shifts in ecosystem function from global change. Determining the scales at which stress gradients influence vegetation composition is crucial to inform management and restoration of tidal marshes for specific functions. Here, we analyzed vegetation community composition in 51 tidal marshes from the San Francisco Bay Estuary, California, USA. We used model-based compositional analysis and rank abundance curves to quantify environmental (elevation/tidal frame position, distance to channel, and channel salinity) and species trait (species form, wetland indicator status, and native status) influences on plant community variability at the marsh site and estuary scales. While environmental impacts on plant diversity varied by species and their relationships to each other, overall impacts increased in strength from marsh to estuary scales. Relative species abundance was important in structuring these tidal marsh communities even with the limited species pools dominated by a few species. Rank abundance curves revealed different community structures by region with higher species evenness at plots higher in the tidal frame and adjacent to freshwater channels. By identifying interactions (species–species, species–environment, and environment–trait) at multiple scales (local, landscape), we begin to understand how variability measurements could be interpreted for conservation and land management decisions.

California↗

USGS2020

Soil moisture product validation good practices protocol, version 1.0

The Global Climate Observing System (GCOS) included soil moisture in the list of Essential Climate Variables (ECVs) to express its important role in Earth’s water, energy and carbon cycle. Soil moisture has a major impact on agriculture, land surface hydrology, weather, and climate forecasting. This document is a community-based effort to provide recommendations on good practices for the validation of global to regional soil moisture products. Definitions are given and metrics to adequately describe the quality of soil moisture products are presented. Spaceborne active and passive microwave sensors are listed with their characteristics, and the typical soil moisture retrieval methods are explained, including dielectric mixing models and optical methods. Spatial scaling, root zone soil moisture estimation, and operational implementations are addressed, as these issues continue to gain more and more importance. Standard and advanced in situ measurement techniques are described as well as sensor calibration, spatial representativity, sampling strategies, and the benefit of airborne campaigns.The community has agreed upon the utilization of the International Soil Moisture Network (ISMN) as the main online repository for in situ soil moisture measurements. Different validation methods such as ground-based validation, satellite product intercomparison, and time series analyses are presented. We provide strategies to evaluate the long-term quality of soil moisture products, and give advice on how to handle typical temporal and spatial-scale mismatches and how to effectively report validation results. Moreover, the benefit of blind tests is discussed to gain objective validation results. We encourage data providers, scientists and practitioners to use this Soil Moisture Product Validation Good Practices Protocol to provide, analyze, and improve high quality Earth Observation results.

Report↗

USGS2019

Restoration affects sexual reproductive capacity in a salt marsh

Plant sexual reproduction is an important driver of plant community maintenance, dispersal, and recovery from disturbance. Despite this, sexual reproduction in habitats dominated by clonally spreading perennial species, such as salt marshes, is often ignored. Communities dominated by long-lived perennial species can still depend on sexual reproduction for recolonizing large disturbed patches or for establishing in new patches, such as restored sites. We investigated the influence of restoration and elevation on flowering phenology, potential seed and seedling production, and insect flower damage of the dominant salt marsh grass, Spartina alterniflora , in reference and restored marshes in southeastern Louisiana, USA. We additionally tested whether elevation gradients or soil parameters could explain differences in sexual reproduction between sites. We demonstrate that sediment-slurry amendment restoration may not affect flowering phenology or insect flower damage at ecologically relevant levels, but that restoration activity increases sexual reproductive output at the patch scale. Restoration activity affected reproductive dynamics more often than changes in elevation alone. Restoration of subsiding salt marsh habitat by altering the soil environment may increase sexual reproductive capacity of these wetlands.

Louisiana↗

USGS2018

Flooding alters plant-mediated carbon cycling independently of elevated atmospheric CO2 concentrations

Plant‐mediated processes determine carbon (C) cycling and storage in many ecosystems; how plant‐associated processes may be altered by climate‐induced changes in environmental drivers is therefore an essential question for understanding global C cycling. In this study, we hypothesize that environmental alterations associated with near‐term climate change can exert strong control on plant‐associated ecosystem C cycling and that investigations along an extended hydrologic gradient may give mechanistic insight into C cycling. We utilize a mesocosm approach to investigate the response of plant, soil, and gaseous C cycling to changing hydrologic regimes and elevated atmospheric carbon dioxide (CO 2) concentrations expected by 2100 in a coastal salt marsh in Louisiana, USA. Although elevated CO 2 had no significant effects on C cycling, we demonstrate that greater average flooding depth stimulated C exchange, with higher rates of labile C decomposition, plant CO 2 assimilation, and soil C respiration. Greater average flooding depth also significantly decreased the soil C pool and marginally increased the aboveground biomass C pool, leading to net losses in total C stocks. Further, flooding depths along an extended hydrologic gradient garnered insight into decomposition mechanisms that was not apparent from other data. In C‐4 dominated salt marshes, sea‐level rise will likely overwhelm effects of elevated CO 2 with climate change. Deeper flooding associated with sea‐level rise may decrease long‐term soil C pools and quicken C exchange between soil and atmosphere, thereby threatening net C storage in salt marsh habitats. Manipulative studies will be indispensable for understanding biogeochemical cycling under future conditions.

Journal of Geophysical Research: Biogeosciences↗

USGS2016

Tidal saline wetland regeneration of sentinel vegetation types in the Northern Gulf of Mexico: An overview

Tidal saline wetlands in the Northern Gulf of Mexico (NGoM) are dynamic and frequently disturbed systems that provide myriad ecosystem services. For these services to be sustained, dominant macrophytes must continuously recolonize and establish after disturbance. Macrophytes accomplish this regeneration through combinations of vegetative propagation and sexual reproduction, the relative importance of which varies by species. Concurrently, tidal saline wetland systems experience both anthropogenic and natural hydrologic alterations, such as levee construction, sea-level rise, storm impacts, and restoration activities. These hydrologic alterations can affect the success of plant regeneration, leading to large-scale, variable changes in ecosystem structure and function. This review describes the specific regeneration requirements of four dominant coastal wetland macrophytes along the NGoM ( Spartina alterniflora , Avicennia germinans , Juncus roemerianus , and Batis maritima ) and compares them with current hydrologic alterations to provide insights into potential future changes in dominant ecosystem structure and function and to highlight knowledge gaps in the current literature that need to be addressed.

Gulf of Mexico↗