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USGS2008

Modelling invasion for a habitat generalist and a specialist plant species

Predicting suitable habitat and the potential distribution of invasive species is a high priority for resource managers and systems ecologists. Most models are designed to identify habitat characteristics that define the ecological niche of a species with little consideration to individual species' traits. We tested five commonly used modelling methods on two invasive plant species, the habitat generalist Bromus tectorum and habitat specialist Tamarix chinensis, to compare model performances, evaluate predictability, and relate results to distribution traits associated with each species. Most of the tested models performed similarly for each species; however, the generalist species proved to be more difficult to predict than the specialist species. The highest area under the receiver-operating characteristic curve values with independent validation data sets of B. tectorum and T. chinensis was 0.503 and 0.885, respectively. Similarly, a confusion matrix for B. tectorum had the highest overall accuracy of 55%, while the overall accuracy for T. chinensis was 85%. Models for the generalist species had varying performances, poor evaluations, and inconsistent results. This may be a result of a generalist's capability to persist in a wide range of environmental conditions that are not easily defined by the data, independent variables or model design. Models for the specialist species had consistently strong performances, high evaluations, and similar results among different model applications. This is likely a consequence of the specialist's requirement for explicit environmental resources and ecological barriers that are easily defined by predictive models. Although defining new invaders as generalist or specialist species can be challenging, model performances and evaluations may provide valuable information on a species' potential invasiveness.

Diversity and Distributions↗

USGS2008

Restoration ecology and invasive riparian plants: An introduction to the special section on Tamarix spp. in western North America

River systems around the world are subject to various perturbations, including the colonization and spread of non-native species in riparian zones. Riparian resource managers are commonly engaged in efforts to control problematic non-native species and restore native habitats. In western North America, small Eurasian trees or shrubs in the genus Tamarix occupy hundreds of thousands of hectares of riparian lands, and are the targets of substantial and costly control efforts and associated restoration activities. Still, significant information gaps exist regarding approaches used in control and restoration efforts and their effects on riparian ecosystems. In this special section of papers, eight articles address various aspects of control and restoration associated with Tamarix spp. These include articles focused on planning restoration and revegetation; a synthetic analysis of past restoration efforts; and several specific research endeavors examining plant responses, water use, and various wildlife responses (including birds, butterflies, and lizards). These articles represent important additions to the Tamarix spp. literature and contain many lessons and insights that should be transferable to other analogous situations in river systems globally.

Restoration Ecology↗

USGS2006

Plant phenology in a cloud forest on the island of Maui, Hawaii

We recorded the times of flowering, fruiting, and leafing for ten native canopy and subcanopy trees and shrubs (monthly from December 1994 through December 1997) in a montane cloud forest with relatively aseasonal rainfall on the island of Maui, Hawaii. These species represented the great majority of individual woody plants at the site. Flowers and fruits were available in the community year–round; however, all species exhibited annual patterns of flowering, and four species showed annual patterns of fruiting while the rest fruited in supra–annual patterns. Many species had protracted flowering or fruiting peaks, and some bore small numbers of flowers or fruit year-round. Most species flowered in a monthly peak mainly between May and August, corresponding to the period of greatest solar irradiance and marginally higher temperatures. Fruit ripening followed at varying intervals. In contrast, the heaviest flowering occurred between November and March, resulting from bloom of the dominant tree, Metrosideros polymorpha. At the highest elevations, Metrosideros flowering was heaviest during September, but peak flowering of lower elevation trees occurred in late fall and winter. Two forms of this species differed in their temporal and spatial patterns of flowering. For M. polymorpha var. polymorpha and var. incana , bloom peaked annually between November and January; however, for M. polymorpha var. glaberrima , flowering peaked from April through July, with an earlier secondary peak in January.

Hawai'i↗

USGS2014

Assessment of endocrine-disrupting chemicals attenuation in a coastal plain stream prior to wastewater treatment plant closure

The U.S. Geological Survey is conducting a combined pre/post-closure assessment at a long-term wastewater treatment plant (WWTP) site at Fort Gordon near Augusta, Georgia. Here, we assess select endocrine-active chemicals and benthic macroinvertebrate community structure prior to closure of the WWTP. Substantial downstream transport and limited instream attenuation of endocrine-disrupting chemicals (EDCs) was observed in Spirit Creek over a 2.2-km stream segment downstream of the WWTP outfall. A modest decline (less than 20% in all cases) in surface water detections was observed with increasing distance downstream of the WWTP and attributed to partitioning to the sediment. Estrogens detected in surface water in this study included estrone (E1), 17β-estradiol (E2), and estriol (E3). The 5 ng/l and higher mean estrogen concentrations observed in downstream locations indicated that the potential for endocrine disruption was substantial. Concentrations of alkylphenol ethoxylate (APE) metabolite EDCs also remained statistically elevated above levels observed at the upstream control site. Wastewater-derived pharmaceutical and APE metabolites were detected in the outflow of Spirit Lake, indicating the potential for EDC transport to aquatic ecosystems downstream of Fort Gordon. The results indicate substantial EDC occurrence, downstream transport, and persistence under continuous supply conditions and provide a baseline for a rare evaluation of ecosystem response to WWTP closure.

Georgia↗

USGS2024

Trends in plant cover derived from vegetation plot data using ordinal zero-augmented beta regression

Questions Plant cover values in vegetation plot data are bounded between 0 and 1, and cover is typically recorded in discrete classes with non-equal intervals. Consequently, cover data are skewed and heteroskedastic, which hampers the application of conventional regression methods. Recently developed ordinal beta regression models consider these statistical difficulties. Our primary question is whether we can detect species trends in vegetation plot time series data with this modelling approach. A second question is whether trends in cover have additional value compared to trends in occurrence, which are easier to assess for practitioners. Location The Netherlands, Western Europe. Methods We used vegetation plot data collected from 10,000 fixed plots which were surveyed once every four years during 1999–2022. We used the ordinal zero-augmented beta regression (OZAB) model, a hierarchical model consisting of a logistic regression for presence and an ordinal beta regression for cover. We adapted the OZAB model for longitudinal data and produced estimates of cover and occurrence for each four-year period. Thereafter we assessed trends in cover and in occurrence across all periods. Results We found evidence of a trend in cover in 318 out of the 721 species (44%) with sufficient data. Most species showed similar directional trends in occurrence and percent cover. No trend in occurrence was detected for 64 species that had evidence of a trend in cover. Declining species had stronger relative changes in cover than in occurrence. Conclusions Our model enables researchers to detect trends in cover using longitudinal vegetation plot data. Cover trends often corroborated trends in occurrence, but we also regularly found trends in cover even in the absence of evidence for trends in occurrence. Our approach thus contributes to a more complete picture of (changes in) vegetation composition based on large monitoring data sets.

Journal of Vegetation Science↗

USGS2015

A plant toxin mediated mechanism for the lag in snowshoe hare population recovery following cyclic declines

A necessary condition for a snowshoe hare population to cycle is reduced reproduction after the population declines. But the cause of a cyclic snowshoe hare population's reduced reproduction during the low phase of the cycle, when predator density collapses, is not completely understood. We propose that moderate-severe browsing by snowshoe hares upon preferred winter-foods could increase the toxicity of some of the hare's best winter-foods during the following hare low, with the result being a decline in hare nutrition that could reduce hare reproduction. We used a combination of modeling and experiments to explore this hypothesis. Using the shrub birch Betula glandulosa as the plant of interest, the model predicted that browsing by hares during a hare cycle peak, by increasing the toxicity B. glandulosa twigs during the following hare low, could cause a hare population to cycle. The model's assumptions were verified with assays of dammarane triterpenes in segments of B. glandulosa twigs and captive hare feeding experiments conducted in Alaska during February and March 1986. The model's predictions were tested with estimates of hare density and measurements of B. glandulosa twig growth made at Kluane, Yukon from 1988–2008. The empirical tests supported the model's predictions. Thus, we have concluded that a browsing-caused increase in twig toxicity that occurs during the hare cycle's low phase could reduce hare reproduction during the low phase of the hare cycle.

Yukon↗

USGS2022

Assessing population genomic structure and polyploidy: A crucial step for native plant restoration

Establishing an effective restoration program requires baseline genetic information to make sound decisions for seed increase and transfer. For many plants this information is lacking, especially among native forbs that are critical for pollinator health. Erigeron speciosus is a widespread, perennial forb occupying montane environments in the western United States and Canada. This species is important in fostering pollinator diversity. Our study examines the population genetic patterns across the species range using reduced-representation sequencing and surveys for genome duplication using flow cytometry and cytology. These genomic tools provide critical information for seed increase and seed transfer, necessary for restoration programs. Population genetic differentiation ( F ST ) average was 0.13 and ranged from 0.05 to 0.24 among 23 collection sites. Model-based Bayesian clustering supported a model with collection sites grouped into two populations, occupying distinct geographic regions of this species range. A genetic distance-based neighbor-joining tree also supported this division. Flow cytometry of 53 samples from 17 populations had 2C values that ranged from 1.7 to 3.6 pg with a mean 2C value of 2.3 pg. Putative triploids were found in two individuals from one collection site. The spatial distribution of genetic structure supports regionally based taxonomic descriptions of two varieties: speciosus in the North and macranthus in the South. This assessment of genetic structure and genome duplication describes an effective approach in developing baseline genetic information for restoration species, especially those species that may harbor complex taxonomy and polyploidy.

Colorado, Idaho, Montana, Oregon, South Dakota, Ut↗

USGS2007

A virus in a fungus in a plant: Three-way symbiosis required for thermal tolerance

A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. We characterized a virus from this fungus that is involved in the mutualistic interaction. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.

Science↗

USGS2011

Productivity is a poor predictor of plant species richness

For more than 30 years, the relationship between net primary productivity and species richness has generated intense debate in ecology about the processes regulating local diversity. The original view, which is still widely accepted, holds that the relationship is hump-shaped, with richness first rising and then declining with increasing productivity. Although recent meta-analyses questioned the generality of hump-shaped patterns, these syntheses have been criticized for failing to account for methodological differences among studies. We addressed such concerns by conducting standardized sampling in 48 herbaceous-dominated plant communities on five continents. We found no clear relationship between productivity and fine-scale (meters −2 ) richness within sites, within regions, or across the globe. Ecologists should focus on fresh, mechanistic approaches to understanding the multivariate links between productivity and richness.

Science↗

USGS2011

Comment on "Changes in climatic water balance drive downhill shifts in plant species' optimum elevations"

Crimmins et al . (Reports, 21 January 2011, p. 324) attributed an apparent downward elevational shift of California plant species to a precipitation-induced decline in climatic water deficit. We show that the authors miscalculated deficit, that the apparent decline in species’ elevations is likely a consequence of geographic biases, and that unlike temperature changes, precipitation changes should not be expected to cause coordinated directional shifts in species’ elevations.

California↗

USGS1968

Middle Pennsylvanian plant fossils: Problematic occurrence in the Bronx

A possible glacial boulder of undeformed and unmetamorphosed siltstone containing Middle Pennsylvanian plant fossils was recovered from the Bronx. The rock cannot be explained by known geologic relations and suggests the possibility of undetected outliers of Pennsylvanian rocks in the Hudson valley.

New York↗

USGS2017

Plant diversity increases with the strength of negative density dependence at the global scale

Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics. Our study reveals fundamental differences in the nature of local-scale biotic interactions that contribute to the maintenance of species diversity across temperate and tropical communities.

Science↗

USGS2013

Nutrient cycling, connectivity, and free-floating plant abundance in backwater lakes of the Upper Mississippi River

River eutrophication may cause the formation of dense surface mats of free floating plants (FFP; e.g., duckweeds and filamentous algae) which may adversely affect the ecosystem. We investigated associations among hydraulic connectivity to the channel, nutrient cycling, FFP, submersed aquatic vegetation (SAV), and dissolved oxygen concentration (DO) in ten backwater lakes of the Upper Mississippi River (UMR) that varied in connectivity to the channel. Greater connectivity was associated with higher water column nitrate (NO3-N) concentration, higher rates of sediment phosphorus (P) release, and higher rates of NO3-N flux to the sediments. Rates of sediment P and N (as NH4-N) release were similar to those of eutrophic lakes. Water column nutrient concentrations were high, and FFP tissue was nutrient rich suggesting that the eutrophic condition of the UMR often facilitated abundant FFP. However, tissue nutrient concentrations, and the associations between FFP biomass and water column nutrient concentrations, suggested that nutrients constrained FFP abundance at some sites. FFP abundance was positively associated with SAV abundance and negatively associated with dissolved oxygen concentration. These results illustrate important connections among hydraulic connectivity, nutrient cycling, FFP, SAV, and DO in the backwaters of a large, floodplain river.

Upper Mississippi River↗

USGS2010

Bat guano virome: Predominance of dietary viruses from insects and plants plus novel mammalian viruses

Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identified using metagenomics in the guano of bats from California and Texas. A total of 34% and 58% of 390,000 sequence reads from bat guano in California and Texas, respectively, were related to eukaryotic viruses , and the largest proportion of those infect insects , reflecting the diet of these insectivorous bats, including members of the viral families Dicistroviridae, Iflaviridae, Tetraviridae, and Nodaviridae and the subfamily Densovirinae. The second largest proportion of virus -related sequences infects plants and fungi, likely reflecting the diet of ingested insects , including members of the viral families Luteoviridae, Secoviridae, Tymoviridae, and Partitiviridae and the genus Sobemovirus. Bat guano viruses related to those infecting mammals comprised the third largest group, including members of the viral families Parvoviridae, Circoviridae, Picornaviridae, Adenoviridae, Poxviridae, Astroviridae, and Coronaviridae. No close relative of known human viral pathogens was identified in these bat populations. Phylogenetic analysis was used to clarify the relationship to known viral taxa of novel sequences detected in bat guano samples, showing that some guano viral sequences fall outside existing taxonomic groups. This initial characterization of the bat guano virome , the first metagenomic analysis of viruses in wild mammals using second-generation sequencing, therefore showed the presence of previously unidentified viral species, genera, and possibly families. Viral metagenomics is a useful tool for genetically characterizing viruses present in animals with the known capability of direct or indirect viral zoonosis to humans.

Journal of Virology↗

USGS2002

Palynology and palynostratigraphy of the Hell Creek Formation in North Dakota: A microfossil record of plants at the end of Cretaceous time

The Hell Creek Formation of North Dakota preserves a rich and varied palynoflora including pollen, spores, and algal cysts; this palynoflora provides insight into the nature of plant life in the region in late Maastrichtian time. This palynological record supplements extensive data from the same ancient vegetation preserved in the megafloral record, and it provides background biostratigraphic data necessary to determine the nature of the Cretaceous-Tertiary (K-T) boundary event. This study of the Hell Creek palynoflora is based upon occurrences of palynomorphs in 71 samples from 20 measured sections in Bowman and Slope Counties, southwestern North Dakota . The palynoflora documented includes 115 or more palynomorph species, 98 of which are described. Three new genera are proposed, three new species are described, and five new nomenclatural combinations are made. The new taxa are Palaeoisoetes gen. nov., Styxpollenites gen. nov., Tschudypollis gen. nov., Aquilapollenites marmarthensis sp. nov., Osmundacidites stanleyi sp. nov., Styxpollenites calamitas sp. nov., Polyatriopollenites levis (Stanley 1965) comb. nov., Palaeoisoetes subengelmannii (Elsik 1968) comb. nov., Triporopollenites triplicatus (Anderson 1960) comb. nov., Tschudypollis retusus (Anderson 1960) comb. nov., and Tschudypollis thalmannii (Anderson 1960) comb. nov. The palynofloral taxa include 67 angiosperms, eight gymnosperms, 19 pteridophytes, and three bryophytes. Of these, 33 are regarded as characteristically uppermost Cretaceous taxa (K taxa). A few of the K taxa do not range all the way to the K-T boundary. Extinction of the Hell Creek palynoflora at the K-T boundary is ∼30%. The Hell Creek Formation is within theWodehouseia spinata Assemblage Zone.

North Dakota↗

USGS1975

Phoma herbarum , a fungal plant saprophyte, as a fish pathogen

Phoma herbarum , a fungal plant saprophyte, was isolated from diseased hatchery-reared coho salmon ( Oncorhynchus kisutch ), chinook salmon ( O . tshawytscha ), and rainbow trout ( Salmo gairdneri ). The disease was observed at 10 national fish hatcheries in Washington and Oregon, but the low incidence of experimental infections indicate that it is only weakly contagious. Histopathological examination suggests that the air bladder is one of the primary organs infected. The visceral organs are also affected in both natural and experimental infections.

Journal of the Fisheries Research Board of Canada↗

USGS2023

Compost, plants and endophytes versus metal contamination: Choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula , and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Environmental Microbiome↗

USGS1980

Plant stress detection by remote measurement of fluorescence

Chlorophyll fluorescence of mature lemon trees was measured with a Fraunhofer line discriminator (FLD). An increase in fluorescence was correlated with plant water stress as measured by stomatal resistance and twig water potential.

Applied Optics↗