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USGS2026

Using quantitative polymerase chain reaction to assess phytoplankton and indicate eutrophication in freshwater rivers: A multiyear nationwide study across the United States

Phytoplankton are essential primary producers in fresh surface water that are critical to the health of ecosystems. However, phytoplankton overgrowth due to eutrophication threatens ecological, economic, and public health. Therefore, assessing phytoplankton is fundamental for understanding the productivity, health, and trophic status of freshwater ecosystems. Light microscopy and chlorophyll a assessment are common approaches for studying phytoplankton. They are easy to use, cost-effective, and reliable but have significant limitations. Microscopy has a low throughput and is time-consuming and labor-intensive. Chlorophyll a assessment does not reveal phytoplankton community composition and structure. For comparison, quantitative polymerase chain reaction (qPCR) is widely applied in quantifying microorganisms, offering multiple advantages, including high throughput, sensitivity, accuracy, and robustness. However, a research gap remains regarding the feasibility of using qPCR to assess phytoplankton and indicate trophic status of freshwater bodies. We conducted a nationwide, multiyear study in the United States to compare the performance of qPCR, microscopy, and chlorophyll a assessment in assessing phytoplankton and trophic statuses of multiple freshwater rivers. From early summer to late fall in 2017, 2018, and 2019, we assessed phytoplankton, chlorophyll a , pheophytin a , and the overall Trophic Level Index ( TLI Overall ) at the sampling sites in 12 large freshwater rivers in three regions (western, midcontinent, and eastern) across the United States. The seasonal summed abundance of four major phytoplankton taxa [Bacillariophyta (diatoms), Cyanobacteria (blue-green algae), Chlorophyta (green algae), and Dinoflagellates (Dinophyta)] ranged from 6.88 log 10 (GCN·L –1 ) (the Connecticut River, 2017) to 9.29 log 10 (GCN·L –1 ) (the Kansas River, 2019) (GCN: gene or genome copy number). qPCR- and microscopy-based phytoplankton abundance of eight phytoplankton taxa had a significant positive allometric or log-linear correlation (adjusted R 2 = 0.836, p -value < 0.001, n = 815). In addition, qPCR-based phytoplankton abundance had positive allometric or log-linear correlations with chlorophyll a (adjusted R 2 = 0.5437, p -value < 0.001, n = 164), pheophytin a (adjusted R 2 = 0.3378, p -value < 0.001, n = 164), and TLI Overall (adjusted R 2 = 0.4789, p -value < 0.001, n = 164). Therefore, qPCR is a promising alternative to microscopy and chlorophyll a for studying phytoplankton and trophic status in freshwater rivers. Moreover, phytoplankton abundance had limited temporal variation within each sampling season and over the three sampling seasons in 2017, 2018, and 2019 but showed clear spatial variation. The midcontinent sites had significantly higher phytoplankton abundance, chlorophyll a concentrations, pheophytin a concentrations, and TLI Overall values than those in the eastern and western rivers, reflecting the higher trophic statuses of the midcontinent rivers. This work also provides the thresholds of qPCR-based phytoplankton abundance for delineating trophic statuses in freshwater rivers. Overall, this work demonstrates that qPCR is a promising tool for studying phytoplankton and characterizing the trophic status of freshwater rivers.

Book chapter↗

USGS2008

Rivers and streams: Ecosystem dynamics and integrating paradigms

Full understanding of running waters requires an ecosystem perspective, which encompasses the physical and chemical setting in interaction with dependent biological communities. Several conceptual models or paradigms of river and stream ecosystems that capture critical components of lotic ecosystems have been developed, including the ‘river continuum concept’, to describe fluxes of matter and energy within the stream or river channel together with exchanges between the channel and its terrestrial setting. A complete ecosystem perspective includes consideration of hierarchical spatial scales in a temporal context. Flow of energy in lotic ecosystems is driven by two alternative energy sources: sunlight regulating in-stream photosynthesis and plant litter derived from the stream-side riparian corridor or floodplain. Energy transfers within the ecosystem pass through micro- and macroproducers (algae and vascular hydrophytes) and micro- and macroconsumers (microorganisms, invertebrates, and vertebrates). Material fluxes encompass the cycling of key nutrients, such as nitrogen and phosphorus, and the transport, storage, and metabolism of dissolved (DOM) and particulate (POM) organic matter (OM). Growth of lotic periphyton (algae and associated microbes, microzoans, and detritus) and coarse (CPOM) and fine (FPOM) particulate organic matter constitute the food resources of nonpredaceous running-water invertebrates (e.g., shredders that consume CPOM and collectors that feed on FPOM and associated microbes of both).

Book chapter↗

USGS2009

Modeling Carbon Dioxide, pH and Un-Ionized Ammonia Relationships in Serial Reuse Systems

In serial reuse systems, excretion of metabolic carbon dioxide has a significant impact on ambient pH, carbon dioxide, and un-ionized ammonia concentrations. This impact depends strongly on alkalinity, water flow rate, feeding rate, and loss of carbon dioxide to the atmosphere. A reduction in pH from metabolic carbon dioxide can significantly reduce the un-ionized ammonia concentration and increase the carbon dioxide concentrations compared to those parameters computed from influent pH. The ability to accurately predict pH in serial reuse systems is critical to their design and effective operation. A trial and error solution to the alkalinity–pH system was used to estimate important water quality parameters in serial reuse systems. Transfer of oxygen and carbon dioxide across the air–water interface, at overflow weirs, and impacts of substrate-attached algae and suspended bacteria were modeled. Gas transfer at the weirs was much greater than transfer across the air–water boundary. This simulation model can rapidly estimate influent and effluent concentrations of dissolved oxygen, carbon dioxide, and un-ionized ammonia as a function of water temperature, elevation, water flow, and weir type. The accuracy of the estimates strongly depends on assumed pollutional loading rates and gas transfer at the weirs. The current simulation model is based on mean daily loading rates; the impacts of daily variation loading rates are discussed. Copies of the source code and executable program are available free of charge.

Aquacultural Engineering↗

USGS2022

Evidence of a dietary shift by the Florida manatee (Trichechus manatus latirostris) in the Indian River Lagoon inferred from stomach content analyses

Investigating the long-term fluctuations of the feeding ecology of megaherbivores such as sirenians is important, as any changes could be indicative of shifts in resource availability. The Indian River Lagoon (IRL), eastern Florida, USA, is a critical habitat for the Florida manatee ( Trichechus manatus latirostris ). However, the IRL has experienced a substantial decline in seagrass due to the persistence of several harmful algal blooms. Using microhistological analysis, we examined the diet of manatees over a discontinuous sampling period spanning over 38 years using stomach contents collected from carcasses recovered in the IRL. Samples collected between 2013–2015 (post-seagrass die-off, n = 90) were compared to archived stomach samples collected between 1977–1989 (pre-seagrass die-off, n = 103). Samples analyzed from 1977–1989 contained primarily seagrasses (61.7%), followed by algae (28.4%) and vascular plants (1.7%). In contrast, stomach samples from the post-seagrass die-off primarily contained algae (49.5%), followed by seagrasses (34%) and vascular plants (2.7%). Between 1977–1989 and 2013–2015, manatees in the IRL experienced a 44.9% decline in seagrass consumption, and a 74.3% increase in algal consumption. This dietary shift was not influenced by body length, a proxy of age, or sex. Our results indicate that the dietary shift experienced by manatees is due to the decline of available seagrass forage in the IRL, and highlight the dietary plasticity of manatees in the face of changes in resource availability. However, the individual health and population-level consequences of this dietary shift are unknown. An increase in mortality due to undetermined causes in this region since 2012 can be associated with deteriorating body conditions of manatees in the IRL, possibly resulting from a lack of seagrass diet. Future research should further investigate behavioral changes affecting manatees in relation to seagrass decline in the IRL, including the energetic costs of this dietary change.

Florida↗

USGS2007

Carbon isotopic compositions of organic matter across continental Cretaceous-Tertiary (K-T) boundary sections: Implications for paleoenvironment after the K-T impact event

To assess the environmental perturbation induced by the impact event that marks the Cretaceous-Tertiary (K-T) boundary, concentrations and isotopic compositions of bulk organic carbon were determined in sedimentary rocks that span the terrestrial K-T boundary at Dogie Creek, Montana, and Brownie Butte, Wyoming in the Western Interior of the United States. The boundary clays at both sites are not bounded by coals. Although coals consist mainly of organic matter derived from plant tissue, siliceous sedimentary rocks, such as shale and clay, may contain organic matter derived from microbiota as well as plants. Coals record ??13C values of plant-derived organic matter, reflecting the ??13C value of atmospheric CO2, whereas siliceous sedimentary rocks record the ??13C values of organic matter derived from plants and microbiota. The microbiota ??13C value reflects not only the ??13C value of atmospheric CO2, but also biological productivity. Therefore, the siliceous rocks from these sites yields information that differs from that obtained previously from coal beds. Across the freshwater K-T boundary at Brownie Butte, the ??13C values decrease by 2.6??? (from - 26.15??? below the boundary clay to - 28.78??? above the boundary clay), similar to the trend in carbonate at marine K-T sites. This means that the organic ??13C values reflect the variation of ??13C of atmospheric CO2, which is in equilibrium with carbon isotopes at the ocean surface. Although a decrease in ??13C values is observed across the K-T boundary at Dogie Creek (from - 25.32??? below the boundary clay to - 26.11??? above the boundary clay), the degree of ??13C-decrease at Dogie Creek is smaller than that at Brownie Butte and that for marine carbonate. About 2??? decrease in ??13C of atmospheric CO2 was expected from the ??13C variation of marine carbonate at the K-T boundary. This ??13C-decrease of atmospheric CO2 should affect the ??13C values of organic matter derived from plant tissue. As such a decrease in ??13C value was not observed at Dogie Creek, a process that compensates the ??13C-decrease of atmospheric CO2 should be involved. For example, the enhanced contribution of 13C-enriched organic matter derived from algae in a high-productivity environment could be responsible. The ??13C values of algal organic matter become higher than, and thus distinguishable from, those of plant organic matter in situations with high productivity, where dissolved HCO3- becomes an important carbon source, as well as dissolved CO2. As the ??13C-decrease of atmospheric CO2 reflected a reduction of marine productivity, the compensation of the ??13C decrease by the enhanced activity of the terrestrial microbiota means that the microbiota at freshwater environment recovered more rapidly than those in the marine environment. A distinct positive ??13C excursion of 2??? in the K-T boundary clays is superimposed on the overall decreasing trend at Dogie Creek; this coincides with an increase in the content of organic carbon. We conclude that the K-T boundary clays include 13C-enriched organic matter derived from highly productive algae. Such a high biological productivity was induced by phenomena resulting from the K-T impact, such as nitrogen fertilization and/or eutrophication induced by enhanced sulfide formation. The high productivity recorded in the K-T boundary clays means that the freshwater environments (in contrast to marine environments) recovered rapidly enough to almost immediately (within 10??yr) respond to the impact-related environmental perturbations. ?? 2006 Elsevier B.V. All rights reserved.

Earth and Planetary Science Letters↗

USGS2011

Paleoenvironmental implications of taxonomic variation among δ 15 N values of chloropigments

Natural variations in the ratios of nitrogen isotopes in biomass reflect variations in nutrient sources utilized for growth. In order to use δ 15 N values of chloropigments of photosynthetic organisms to determine the corresponding δ 15 N values of biomass – and by extension, surface waters – the isotopic offset between chlorophyll and biomass must be constrained. Here we examine this offset in various geologically-relevant taxa, grown using nutrient sources that may approximate ocean conditions at different times in Earth’s history. Phytoplankton in this study include cyanobacteria (diazotrophic and non-diazotrophic), eukaryotic algae (red and green), and anoxygenic photosynthetic bacteria (Proteobacteria), as well as environmental samples from sulfidic lake water. Cultures were grown using N 2 , NO 3 − , and NH 4 + as nitrogen sources, and were examined under different light regimes and growth conditions. We find surprisingly high variability in the isotopic difference (δ 15 N biomass − δ 15 N chloropigment ) for prokaryotes, with average values for species ranging from −12.2&permil; to +11.7&permil;. We define this difference as ε por , a term that encompasses diagenetic porphyrins and chlorins, as well as chlorophyll. Negative values of ε por reflect chloropigments that are 15 N-enriched relative to biomass. Notably, this enrichment appears to occur only in cyanobacteria. The average value of ε por for freshwater cyanobacterial species is −9.8 ± 1.8&permil;, while for marine cyanobacteria it is −0.9 ± 1.3&permil;. These isotopic effects group environmentally but not phylogenetically, e.g., ε por values for freshwater Chroococcales resemble those of freshwater Nostocales but differ from those of marine Chroococcales. Our measured values of ε por for eukaryotic algae (range = 4.7–8.7&permil;) are similar to previous reports for pure cultures. For all taxa studied, values of ε por do not depend on the type of nitrogen substrate used for growth. The observed environmental control of ε por suggests that values of ε por could be useful for determining the fractional burial of eukaryotic vs. cyanobacterial organic matter in the sedimentary record.

Geochimica et Cosmochimica Acta↗

USGS2017

Relationship between water and aragonite barium concentrations in aquaria reared juvenile corals

Coral barium to calcium (Ba/Ca) ratios have been used to reconstruct records of upwelling, river and groundwater discharge, and sediment and dust input to the coastal ocean. However, this proxy has not yet been explicitly tested to determine if Ba inclusion in the coral skeleton is directly proportional to seawater Ba concentration and to further determine how additional factors such as temperature and calcification rate control coral Ba/Ca ratios. We measured the inclusion of Ba within aquaria reared juvenile corals ( Favia fragum ) at three temperatures (∼27.7, 24.6 and 22.5 °C) and three seawater Ba concentrations (73, 230 and 450 nmol kg −1 ). Coral polyps were settled on tiles conditioned with encrusting coralline algae, which complicated chemical analysis of the coral skeletal material grown during the aquaria experiments. We utilized Sr/Ca ratios of encrusting coralline algae (as low as 3.4 mmol mol −1 ) to correct coral Ba/Ca for this contamination, which was determined to be 26 ± 11% using a two end member mixing model. Notably, there was a large range in Ba/Ca across all treatments, however, we found that Ba inclusion was linear across the full concentration range. The temperature sensitivity of the distribution coefficient is within the range of previously reported values. Finally, calcification rate, which displayed large variability, was not correlated to the distribution coefficient. The observed temperature dependence predicts a change in coral Ba/Ca ratios of 1.1 μmol mol −1 from 20 to 28 °C for typical coastal ocean Ba concentrations of 50 nmol kg −1 . Given the linear uptake of Ba by corals observed in this study, coral proxy records that demonstrate peaks of 10–25 μmol mol −1 would require coastal seawater Ba of between 60 and 145 nmol kg −1 . Further validation of the coral Ba/Ca proxy requires evaluation of changes in seawater chemistry associated with the environmental perturbation recorded by the coral as well as verification of these results for Porites species, which are widely used in paleo reconstructions.

Geochimica et Cosmochimica Acta↗

USGS2011

Polymethylene-interrupted fatty acids: Biomarkers for native and exotic mussels in the Laurentian Great Lakes

Freshwater organisms synthesize a wide variety of fatty acids (FAs); however, the ability to synthesize and/or subsequently modify a particular FA is not universal, making it possible to use certain FAs as biomarkers. Herein we document the occurrence of unusual FAs (polymethylene-interrupted fatty acids; PMI-FAs) in select freshwater organisms in the Laurentian Great Lakes. We did not detect PMI-FAs in: (a) natural seston from Lake Erie and Hamilton Harbor (Lake Ontario), (b) various species of laboratory-cultured algae including a green alga ( Scenedesmus obliquus ), two cyanobacteria ( Aphanizomenon flos-aquae and Synechococystis sp.), two diatoms ( Asterionella formosa , Diatoma elongatum ) and a chrysophyte ( Dinobryon cylindricum ) or, (c) zooplankton ( Daphnia spp., calanoid or cyclopoid copepods) from Lake Ontario, suggesting that PMI-FAs are not substantively incorporated into consumers at the phytoplankton–zooplankton interface. However, these unusual FAs comprised 4-6% of total fatty acids (on a dry tissue weight basis) of native fat mucket ( Lampsilis siliquoidea ) and plain pocketbook ( L. cardium ) mussels and in invasive zebra ( Dreissena polymorpha ) and quagga ( D. bugensis ) mussels. We were able to clearly partition Great Lakes' mussels into three separate groups (zebra, quagga, and native mussels) based solely on their PMI-FA profiles. We also provide evidence for the trophic transfer of PMI-FAs from mussels to various fishes in Lakes Ontario and Michigan, further underlining the potential usefulness of PMI-FAs for tracking the dietary contribution of mollusks in food web and contaminant-fate studies.

Michigan, Ontario, Prince Edward Island, Wisconsin↗

USGS2014

Gross and microscopic pathology of lesions in Pocillopora spp. from the subtropical eastern Pacific

Coral reefs are threatened by a variety of factors including diseases that have caused significant damage in some regions such as in the Caribbean. At present, no data are available on coral diseases in the Mexican Pacific where Pocillopora spp. is a dominant component of coral communities. Here, we describe gross and microscopic morphology of lesions found in pocilloporids at four sites in the Mexican Pacific. Corals were identified and their lesions photographed and quantified in the field. Tissue samples were collected from healthy and affected colonies for histopathology. We recorded seven species of pocilloporids at the study sites with Isla Isabel being the location with the highest coral diversity ( H ′ = 1.27). Lesions were present in 42% of the colonies and included discoloration (32%), predation-induced tissue loss (30%), unexplained tissue loss (3%) and overgrowth by sponges or algae (35%). The most affected species, P . damicornis (50%), was also one of the most common in the region. No species was more prone to a particular lesion, but there was a significant association between location and the presence of lesions. Northern Islas Marietas (61%) and Isla Isabel (41%) had the highest prevalence of lesions, followed by Manzanillo (37%) and Bahías de Huatulco (23%). Histological changes included atrophy of the surface body wall with depletion of zooxanthellae (91%) in corals with discoloration (bleaching). Ablation of tissue from mesoglea (18%) was also observed. Colonies with unexplained tissue loss showed atrophy and thinning of the epidermis (89%), characterized by cuboidal instead of pseudocolumnar cells normally found in healthy pseudocolumnar ciliated epithelium. Bacterial aggregates between the mesoglea and gastrodermis (11%) were very conspicuous in healthy and diseased corals. Lesions produced by fish bites and gastropods were associated with tissue atrophy (40%) and, in some cases, algal overgrowth near the lesion (20%). No infectious agents associated with cell pathology were detected microscopically. Bleaching and overgrowth by algae and sponges, as well as unexplained tissue loss, are common in Pocillopora . These lesions and anatomical changes warrant further study since their incidence is potentially indicative of reef degradation.

Mexican Pacific↗

USGS2005

Strange bedfellows - A deep-water hermatypic coral reef superimposed on a drowned barrier island; Southern Pulley Ridge, SW Florida platform margin

The southeastern component of a subtle ridge feature extending over 200 km along the western ramped margin of the south Florida platform, known as Pulley Ridge, is composed largely of a non-reefal, coastal marine deposit. Modern biostromal reef growth caps southern Pulley Ridge (SPR), making it the deepest hermatypic reef known in American waters. Subsurface ridge strata are layered, lithified, and display a barrier island geomorphology. The deep-water reef community is dominated by platy scleractinian corals, leafy green algae, and coralline algae. Up to 60% live coral cover is observed in 60-75 m of water, although only 1-2% of surface light is available to the reef community. Vertical reef accumulation is thin and did not accompany initial ridge submergence during the most recent sea-level rise. The delayed onset of reef growth likely resulted from several factors influencing Gulf waters during early stages of the last deglaciation (???14 kyr B.P.) including; cold, low-salinity waters derived from discrete meltwater pulses, high-frequency sea-level fluctuations, and the absence of modern oceanic circulation patterns. Currently, reef growth is supported by the Loop Current, the prevailing western boundary current that impinges upon the southwest Florida platform, providing warm, clear, low-nutrient waters to SPR. The rare discovery of a preserved non-reefal lowstand shoreline capped by rich hermatypic deep-reef growth on a tectonically stable continental shelf is significant for both accurate identification of late Quaternary sea-level position and in better constraining controls on the depth limits of hermatypic reefs and their capacity for adaptation to extremely low light levels. ?? 2004 Elsevier B.V. All rights reserved.

Florida↗

USGS2006

Impact of eutrophication on shallow marine benthic foraminifers over the last 150 years in Osaka Bay, Japan

High-resolution foraminiferal analysis was conducted on a short sediment core from the inner part of Osaka Bay, Japan. Changes in foraminiferal assemblages were associated with eutrophication, bottom water hypoxia, and changes in red tide-causing algae. Before the 1920s, the calcareous species Ammonia beccarii , and the agglutinated species Eggerella advena and Trochammina hadai were rare, but calcareous foraminifers in general were abundant. Between the 1920s and 1940s, calcareous foraminifers decreased abruptly in abundance, while A . beccarii , E . advena and T . hadai increased in abundance. This faunal change corresponded in time to an increase in nutrients flowing in through the Yodo River, and bottom water hypoxia related to eutrophication. In the 1960s and 1970s, A. beccarii , E . advena and T . hadai further increased in abundance to become dominant, and many calcareous foraminifers nearly disappeared, corresponding to increasing bottom water hypoxia related to the rapid increase in discharged nutrients during the high economic growth period from 1953 to 1971. After the 1990s, A. beccarii decreased rapidly in abundance and E . advena and Uvigerinella glabra increased in abundance. The main components of red tide-causing algae changed from dinoflagellates to diatoms in the 1980s through 1990s, thus there was a change in the food supply to the benthos, which may have caused the increase in abundance of E. advena and U. glabra .

Marine Micropaleontology↗

USGS2017

A Holocene pollen record of persistent droughts from Pyramid Lake, Nevada, USA

Pollen and algae microfossils preserved in sediments from Pyramid Lake, Nevada, provide evidence for periods of persistent drought during the Holocene age. We analyzed one hundred nineteen 1-cm-thick samples for pollen and algae from a set of cores that span the past 7630 years. The early middle Holocene, 7600 to 6300 cal yr B.P., was found to be the driest period, although it included one short but intense wet phase. We suggest that Lake Tahoe was below its rim for most of this period, greatly reducing the volume and depth of Pyramid Lake. Middle Holocene aridity eased between 5000 and 3500 cal yr B.P. and climate became variable with distinct wet and dry phases. Lake Tahoe probably spilled intermittently during this time. No core was recovered that represented the period between 3500 and 2600 cal yr B.P. The past 2500 years appear to have had recurrent persistent droughts. The timing and magnitude of droughts identified in the pollen record compares favorably with previously published ??18O data from Pyramid Lake. The timing of these droughts also agrees with the ages of submerged rooted stumps in the Eastern Sierra Nevada and woodrat midden data from central Nevada. Prolonged drought episodes appear to correspond with the timing of ice drift minima (solar maxima) identified from North Atlantic marine sediments, suggesting that changes in solar irradiance may be a possible mechanism influencing century-scale drought in the western Great Basin. ?? 2004 University of Washington. All rights reserved.

Quaternary Research↗

USGS1983

Nearshore phytoplankton of Hammond Bay, Lake Huron

To predict the effects of increased nutrient loading on nearshore phytoplankton populations in northern Lake Huron, we collected phytoplankton from a small, nearshore water intake at Hammond Bay four times per week from August 1973 to July 1975. Phytoplankton density, taxonomic composition, and biomass in the nearshore waters followed predictable, seasonal fluctuations during each of two 12-month periods. The density of total phytoplankton was high (450600 cells/mL) in June and low (60 to 210 cells/mL) from January to April each year. The mean annual composition of the phytoplankton assemblage by number for the study period was 33% cryptomonads, 24% diatoms, 16% chrysophytes, 16% blue-green algae, and 10% green algae. Phytoplankton biomass was low through each year (range, 0.09 to 0.66 g/m 3 ), resembling values previously reported from Lake Superior. Pennate diatoms contributed 60 to 80% of the total biomass from December to April and in July. Phytoflagellates consisting of chrysophytes and cryptomonads accounted for 35% of the biomass throughout the 2-year study.

Journal of Great Lakes Research↗

USGS2017

Diet of the Antillean manatee (Trichechus manatus manatus) in Belize, Central America

Belize contains important habitat for Antillean manatees (Trichechus manatus manatus) and provides refuge for the highest known population density of this subspecies. As these animals face impending threats, knowledge of their dietary habits can be used to interpret resource utilization. The contents of 13 mouth, 6 digestive tract (stomach, duodenum and colon), and 124 fecal samples were microscopically examined using a modified point technique detection protocol to identify key plant species consumed by manatees at two important aggregation sites in Belize: Southern Lagoon and the Drowned Cayes. Overall, 15 different items were identified in samples from manatees in Belize. Five species of seagrasses (Halodule wrightii, Thalassia testudinum, Ruppia maritima, Syringodium filiforme, and Halophila sp.) made up the highest percentage of items. The red mangrove (Rhizophora mangle), was also identified as an important food item. Algae (Ulva sp., Chara sp., Lyngbya sp.) and invertebrates (sponges and diatoms) were also consumed. Variation in the percentage of seagrasses, other vascular plants, and algae consumption was analyzed as a 4-factor analysis of variance (ANOVA) with main effects and interactions for locality, sex, size classification, and season. While sex and season did not influence diet composition, differences for locality and size classification were observed. These results suggest that analysis of diet composition of Antillean manatees may help to determine critical habitat and use of associated food resources which, in turn can be used to aid conservation efforts in Belize.

Journal of the Marine Biological Association of th↗

USGS2014

Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches

Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 ( eae O157 ), shiga-toxin producing E. coli ( stx2 ), Campylobacter jejuni ( mapA ), Shigella spp. ( ipaH ), and a Salmonella enterica -specific ( SE ) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA > stx2 > ipaH > SE > eae O157 . Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA , stx2 , and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log 10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2 , ipaH , and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

Environmental Science & Technology↗

USGS1997

Marine bacterial degradation of brominated methanes

Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.Brominated methanes are ozone-depleting compounds whose natural sources include marine algae such as kelp. Brominated methane degradation by bacteria was investigated to address whether bacterial processes might effect net emission of these compounds to the atmosphere. Bacteria in seawater collected from California kelp beds degraded CH2Br2 but not CHBr3. Specific inhibitors showed that methanotrophs and nitrifiers did not significantly contribute to CH2Br2 removal. A seawater enrichment culture oxidized 14CH2Br2 to 14CO2 as well as 14CH3Br to 14CO2. The rates of CH2Br2 degradation in laboratory experiments suggest that bacterial degradation of CH2Br2 in a kelp bed accounts for <1% of the CH2Br2 produced by the kelp. However, the half-life of CH2Br2 due to bacterial removal appears faster than hydrolysis and within an order of magnitude of volatilization to the atmosphere.

Environmental Science & Technology↗

USGS2000

Responses of physical, chemical, and biological indicators of water quality to a gradient of agricultural land use in the Yakima River Basin, Washington

The condition of 25 stream sites in the Yakima River Basin, Washington, were assessed by the U.S. Geological Survey's National Water-Quality Assessment Program. Multimetric condition indices were developed and used to rank sites on the basis of physical, chemical, and biological characteristics. These indices showed that sites in the Cascades and Eastern Cascades ecoregions were largely unimpaired. In contrast, all but two sites in the Columbia Basin ecoregion were impaired, some severely. Agriculture (nutrients and pesticides) was the primary factor associated with impairment and all impaired sites were characterized by multiple indicators of impairment. All indices of biological condition (fish, invertebrates, and algae) declined as agricultural intensity increased. The response exhibited by invertebrates and algae suggested a threshold response with conditions declining precipitously at relatively low levels of agricultural intensity and little response at moderate to high levels of agricultural intensity. This pattern of response suggests that the success of mitigation will vary depending upon where on the response curve the mitigation is undertaken. Because the form of the community condition response is critical to effective water-quality management, the National Water-Quality Assessment Program is conducting studies to examine the response of biota to gradients of land-use intensity and the relevance of these responses to water-quality management. These land-use gradient pilot studies will be conducted in several urban areas starting in 1999.

Environmental Monitoring and Assessment↗

USGS2024

River control points for algal productivity revealed by transport analysis

Measurement of planktonic chlorophyll- a —a proxy for algal biomass—in rivers may represent local production or algae transported from upstream, confounding understanding of algal bloom development in flowing waters. We modeled 3 years of chlorophyll- a transport through a 394-km portion of the Illinois River and found that although algal biomass is longitudinally widespread, most net production occurs at river control points in the upper reaches (up to 3.7 Mg chlorophyll- a y −1 km −1 ). Up to 69% of the algal biomass in the upper river was a result of within-reach production, with the remainder recruited from headwaters and tributaries. High chlorophyll- a measured farther downstream was largely because of transport from source-area control points, with substantial net losses of algal biomass occurring in the lower river. Modeling the often-overlooked river transport component is necessary to characterize where, when, and why planktonic algae grow and predict how far and fast they move downstream.

Illinois↗