Biology Commons^™

Limestone Flora Of The Simonton Corner Quarry Preserve, Rockport, Maine, Usa, Margaret Stern, Ian D. Medeiros, Luka Negoita, N. Rajakaruna

Biological Sciences

Limestone is a distinctive substrate that has significant effects on soils and plants. The present study characterizes the diversity of vascular plants, bryophytes, and lichens at the Simonton Corner Quarry Preserve, an abandoned limestone quarry in Rockport, Maine, USA, which was in operation in the late 1800s. We document vascular plant diversity and associated edaphic features (i.e., soil pH and elemental chemistry) using 30 535 meter plots spread throughout the site. For vascular plants, 114 species in 96 genera and 50 families were observed; few of these species are known to prefer calcareous environments, and 38% are nonnative. Conversely, the …

Resource Partitioning Along Multiple Niche Axes Drives Functional Diversity In Parrotfishes On Caribbean Coral Reefs, Thomas C. Adam, Megan Kelley, Benjamin I. Ruttenberg, Deron E. Burkepile

Biological Sciences

The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes …

Complete Mitochondrial Genome Of The Speckled Dace Rhinichthys Osculus, A Widely Distributed Cyprinid Minnow Of Western North America, Samantha J. Bock, Morgan M. Malley, Sean Lema

Biological Sciences

The speckled dace Rhinichthys osculus (order Cypriniformes), also known as the carpita pinta, is a small cyprinid minnow native to western North America. Here, we report the sequencing of the full mitochondrial genome (mitogenome) of R. osculus from a male fish collected from the Amargosa River Canyon in eastern California, USA. The assembled mitogenome is 16 658 base pair (bp) nucleotides, and encodes 13 protein-coding genes, and includes both a 12S and a 16S rRNA, 22 tRNAs, and a 985 bp D-loop control region. Mitogenome synteny reflects that of other Ostariophysian fishes with the majority of genes and RNAs encoded …

Temperatures Experienced By Fresh-Cut Leafy Greens During Retail Storage And Display, W. Brown, E. Ryser, L. Gorman, Scott J. Steinmaus, Keith Vorst

Biological Sciences

There has been limited published work in the United States on temperature profiling of fresh-cut, bagged leafy greens during their transport, retail storage, and retail display. This study utilized temperature monitors placed in backrooms and display cases at nine supermarkets located in southern California: the Central Coast (Santa Barbara to Los Osos), Greater Los Angeles (Burbank area), and Greater Palm Desert. Sensors were installed midway along each 8-foot display case section containing fresh-cut leafy greens. Monitors were placed at the front and back of shelves and in the lower bin. In storage rooms, sensors were placed 4 feet from the …

Introduction Next Contents Vol 63(4) Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia), Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The ICSE conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia): A Summary And Synthesis, Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The Conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic (serpentine) ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

Role Of Bacterial-Fungal Interactions On Heavy Metal Phytotoxicity In Serpentine Soil, Mihiri Seneviratne, Gamini Seneviratne, H. M. S. P. Madawala, M.C.M. Iqbal, Nishanta Rajakaruna, Tharanga Bandara, Meththika Vithanage

Biological Sciences

This study was conducted to understand the role of bacterial–fungal interactions on heavy metal uptake by Zea mays plants. A pot experiment was conducted for 90 days with Z. mays in serpentine soil inoculated with a Gram-negative bacterium, fungus (Aspergilllus sp.) and both microbes to determine the effects of inoculation on nickel, manganese, chromium and cobalt concentrations in plant tissue and soil. Soil nutrients and soil enzyme activities were measured to determine the effect of inoculations on soil quality. Inoculation of microorganisms increased shoot and root biomass, and the maximum biomass was in the bacterial–fungal inoculation. This could be …

Transfer Of Heavy Metals Through Terrestrial Food Webs: A Review, Jillian E. Gall, Robert Boyd, Nishanta Rajakaruna

Biological Sciences

Heavy metals are released into the environment by both anthropogenic and natural sources. Highly reactive and often toxic at low concentrations, they may enter soils and groundwater, bioaccumulate in food webs, and adversely affect biota. Heavy metals also may remain in the environment for years, posing long-term risks to life well after point sources of heavy metal pollution have been removed. In this review, we compile studies of the community-level effects of heavy metal pollution, including heavy metal transfer from soils to plants, microbes, invertebrates, and to both small and large mammals (including humans). Many factors contribute to heavy metal …

A Preliminary Survey Of The Diversity Of Soil Algae And Cyanoprokaryotes On Mafic And Ultramafic Substrates In South Africa, Arthurita Venter, Anatoliy Levanets, Stefan Siebert, Nishanta Rajakaruna

Biological Sciences

Despite a large body of work on the serpentine-substrate effect on vascular plants, little work has been undertaken to describe algal communities found on serpentine soils derived from peridotite and other ultramafic rocks. We report a preliminary study describing the occurrence of algae and cyanoprokaryotes on mafic and ultramafic substrates from South Africa. Results suggest that slope and aspect play a key role in species diversity and community composition and, although low pH, nutrients and metal content do not reduce species richness, these edaphic features also influence species composition. Further, typical soil genera such as Leptolyngbya, Microcoleus, Phormidium …

Growth And Nickel Uptake By Serpentine And Non-Serpentine Populations Of Fimbristylis Ovata (Cyperaceae) From Sri Lanka, P. K. D. Chathuranga, S. K. A. T. Dharmasena, Nishanta Rajakaruna, M.C.M. Iqbal

Biological Sciences

Compared with serpentine floras of Southeast Asia, the serpentine vegetation of Sri Lanka is impoverished in regard to serpentine endemics and nickel hyperaccumulators. All species so far documented from the serpentine outcrops of Sri Lanka also have non-serpentine populations; it is unclear whether the serpentine populations are physiologically distinct and deserve ecotypic recognition. We conducted a preliminary study to examine whether serpentine and non-serpentine populations of Fimbristylis ovata represent locally adapted ecotypes by investigating their growth and potential for nickel uptake and tolerance under greenhouse conditions. Although both populations of F. ovata showed a similar growth pattern in serpentine soil …

Calcium : Magnesium Ratio Affects Environmental Stress Sensitivity In The Serpentine-Endemic Alyssum Inflatum (Brassicaceae), Rasoul Ghasemi, Zohreh Zare Chavoshi, Robert S. Boyd, Nishanta Rajakaruna

Biological Sciences

Plants endemic to serpentine soils are adapted to harsh environmental conditions typical of those soils, particularly, low (<1) calcium (Ca) : magnesium (Mg) ratios. We compared survival of two perennial Alyssum species native to Iran under experimental manipulations of Ca : Mg ratio, including when Ca : Mg ratio was varied under conditions of high ammonium concentration and heat stress. Alyssum inflatum is a serpentine endemic capable of nickel (Ni) hyperaccumulation, whereas A. lanceolatum is found on non-serpentine soils and is not known to hyperaccumulate Ni. We grew plants of both species under four Ca : Mg ratios (0.4, 2, 20, 40) and tested survival when plants were exposed to elevated ammonium …

Vegetation Dynamics And Mesophication In Response To Conifer Encroachment Within An Ultramafic System, J. Burgess, K. Szlavecz, N. Rajakaruna, S. Lev, C. Swan

Biological Sciences

The biological, ecological, and evolutionary significance of serpentine habitats has long been recognised. We used an integrated physiochemical dataset combining plot spatial data with temporal data from tree cores to evaluate changes in soils and vegetation. Data suggest that this unique habitat is undergoing a transition, endangering local biodiversity and endemic plant species. The objective of this work was to analyse the vegetation dynamics of a xeric serpentine savanna located in the Mid-Atlantic, USA. We employed vegetation surveys of 32 10 × 15 m quadrats to obtain woody species composition, density, basal area, and developed a spatial physiochemical dataset of …

A Preliminary Report On Escherichia Coli Strain Diversity In Cows, Alison T. Stivers

Biological Sciences

Pyroprinting is a strain typing method that relies on the simultaneous pyrosequencing of the multi-copy rRNA intergenic transcribed spacer regions of E. coli (Black, et al., 2014). These pyroprints can be used to identify the source of E. coli in the environment. Currently, Cal Poly’s Center for Applications in Biotechnology (CAB) is augmenting the existing E. coli pyroprint library. By pyroprinting the intestinal E. coli of cows, we can quantify the strain diversity present, evaluate persistence, and determine the minimum sample size required for a complete overview of the cow intestinal E. coli population. These pyroprints can then be added …

Ecotypic Differentiation Of Mid-Atlantic Quercus Species In Response To Ultramafic Soils, Jerry Burgess, Katalin Szlavecz, Nishanta Rajakaruna, Christopher Swan

Biological Sciences

Spatial heterogeneity of soil conditions combined with intraspecific variation confer site-specific edaphic tolerance, resulting in local adaptation and speciation. To understand the geoecological processes controlling community assembly of woodland tree species on serpentine and mafic soils, we investigated resource gradients and provenance (geographic area of propagule collection) as variables affecting typical representative upland oak (Quercus) species distribution. Accordingly, we conducted a year-long reciprocal transplant experiment in the greenhouse with serpentine and mafic soils, using seedlings of five oak species (Quercus marilandica, Q. stellata, Q. montana, Q. michauxii and Q. alba). All seedlings, regardless …

Herbivory And The Resilience Of Caribbean Coral Reefs: Knowledge Gaps And Implications For Management, Thomas C. Adam, Deron E. Burkepile, Benjamin I. Ruttenberg, Michelle J. Paddack

Biological Sciences

Herbivory is a key process on coral reefs that can facilitate reef-building corals by excluding algae that otherwise negatively impact coral settlement, growth, and survivorship. Over the last several decades, coral cover on Caribbean reefs has declined precipitously. On many reefs, large structurally complex corals have been replaced by algae and other non-reef-building organisms, resulting in the collapse of physical structure and the loss of critical ecosystem services. The drivers of coral decline on Caribbean reefs are complex and vary among locations. On many reefs, populations of key herbivores have been greatly reduced by disease and overfishing, and this has …

Protemic Identification Of Germline Proteins In Caenorhabditis Elegans, B Elizabeth Turner, Sophia M. Basecke, Grace E. Bazan, Eric S. Dodge, Cassy M. Haire, Dylan J. Heussman, Chelsey L. Johnson, Chelsea K. Mukai, Adrianna M. Naccarati, Sunny-June Norton, Jennifer R. Sato, Chihara O. Talavera, Michael V. Wade, Kenneth J. Hillers

Biological Sciences

Sexual reproduction involves fusion of 2 haploid gametes to form diploid offspring with genetic contributions from both parents. Gamete formation represents a unique developmental program involving the action of numerous germline-specific proteins. In an attempt to identify novel proteins involved in reproduction and embryonic development, we have carried out a proteomic characterization of the process in Caenorhabditis elegans. To identify candidate proteins, we used 2D gel electrophoresis (2DGE) to compare protein abundance in nucleus-enriched extracts from wild-type C. elegans, and in extracts from mutant worms with greatly reduced gonads (glp-4(bn2) worms reared at 25°C); 84 proteins whose …

Immobilization And Phytotoxicity Reduction Of Heavy Metals In Serpentine Soil Using Biochar, I. Herath, P. Kumarathilaka, A. Navarantne, N. Rajakaruna, M. Vithanage

Biological Sciences

Purpose

Serpentine soils derived from ultramafic rocks release elevated concentrations of toxic heavy metals into the environment. Hence, crop plants cultivated in or adjacent to serpentine soil may experience reduced growth due to phytotoxicity as well as accumulate toxic heavy metals in edible tissues. We investigated the potential of biochar (BC), a waste byproduct of bioenergy industry in Sri Lanka, as a soil amendment to immobilize Ni, Cr, and Mn in serpentine soil and minimize their phytotoxicity.

Materials and methods

The BC used in this study was a waste byproduct obtained from a Dendro bioenergy industry in Sri Lanka. This …

Diversity And Soil-Tissue Elemental Relations Of Vascular Plants Of Callahan Mine, Brooksville, Maine, U.S.A., Margaret R. Mansfield, Nathaniel S. Pope, Glen H. Mittelhauser, Nishanta Rajakaruna

Biological Sciences

Metal-contaminated soils provide numerous stressors to plant life, resulting in unique plant communities worldwide. The current study focuses on the vascular plants of Callahan Mine in Brooksville, ME, USA, a Superfund site contaminated with Cu, Zn, Pb, and other pollutants. One hundred and fifty-five taxa belonging to 50 families were identified, with the Asteraceae (21%), Poaceae (11%), and Rosaceae (9%) as the most species-rich families. Ninety-six species encountered at the Mine were native to North America (62%), including 11 taxa (7%) with rarity status in at least one New England state. Fifty-one species were non-native (33%), including nine taxa (6%) …

Metal Release From Serpentine Soils In Sri Lanka, Meththika Vithanage, Anushka Upamali Rajapaksha, Christopher Oze, Nishanta Rajakaruna, C. B. Dissanayake

Biological Sciences

Ultramafic rocks and their related soils (i.e., serpentine soils) are non-anthropogenic sources of metal contamination. Elevated concentrations of metals released from these soils into the surrounding areas and groundwater have ecological-, agricultural-, and human health-related consequences. Here we report the geochemistry of four different serpentine soil localities in Sri Lanka by coupling interpretations garnered from physicochemical properties and chemical extractions. Both Ni and Mn demonstrate appreciable release in water from the Ussangoda soils compared to the other three localities, with Ni and Mn metal release increasing with increasing ionic strengths at all sites. Sequential extraction experiments, utilized to identify “elemental …

Using Crossword Puzzles To Enhance Students' Learning Of Technical Biological Terms, William D. Stansfield

Biological Sciences

No abstract provided.

The Role Of Elevation And Soil Chemistry In The Distribution And Ion Accumulation Of Floral Morphs Of Streptanthus Polygaloides Gray (Brassicaceae), A Californian Nickel Hyperaccumulator, Nathaniel S. Pope, Michael Fong, Robert S. Boyd, Nishanta Rajakaruna

Biological Sciences

Background: The flora of serpentine/ultramafic soils provides an excellent model system for the study of natural selection in plant populations. Streptanthus polygaloides is a nickel hyperaccumulator that is endemic to serpentine soils in the Sierra Nevada of California, and has four floral morphs (yellow, purple, yellow-to-purple and undulate).

Aims: We investigate three hypotheses: (1) the purple morph occurs in colder, wetter climates than the yellow morph; (2) tissue–soil ionic relationships differ among morphs; and (3) morphs occur on soils with differing elemental concentrations.

Methods: We queried herbarium records to investigate patterns of occurrence among the yellow and purple floral morphs, …

Little Evidence For Local Adaptation To Soils Or Microclimate In The Post-Fire Recruitment Of Three Californian Shrubs, Annette Bieger, Nishanta Rajakaruna, Susan Harrison

Biological Sciences

Background: Seedling recruitment following fire is an infrequent yet critical demographic transition for woody plants in Mediterranean ecosystems.

Aims: Here we examine whether post-fire seedling recruitment of three widespread Californian chaparral shrubs is affected by local adaptation within an edaphically and topographically complex landscape.

Methods: We reciprocally transplanted 6-month-old seedlings of Adenostema fasciculatum, Ceanothus cuneatus and Eriodictyon californicum to serpentine and sandstone soils, and cool northerly and warm southerly slopes.

Results: At the age of 2 years, none of the species manifested higher survival or growth on ‘home’ compared with ‘away’ soils or slopes, indicating an absence of local …

Census And Mapping Of Chorro Creek Bog Thistle In Reservoir Canyon, San Luis Obispo, Ca, Tyler Michael Lutz

Biological Sciences

Chorro Creek bog thistle (Cirsium fontinale var. obispoense) is a federally endangered variety of Fountain thistle endemic to western San Luis Obispo County. The U.S. Fish and Wildlife Service knows of nineteen populations, many with multiple colonies. A population was discovered in the Reservoir Canyon Natural Reserve in 2001, but has not been monitored or described since the time of its discovery. In fall of 2013, a census of the population was performed, the four colonies were mapped, and a floristic survey was conducted. A field experiment was initiated to determine if reducing the riparian canopy coverage can …

Phylogeography Of The California Sheephead, Semicossyphus Pulcher: The Role Of Deep Reefs As Stepping Stones And Pathways To Antitropicality, Marloes Poortvliet, Gary C. Longo, Kimberly Selkoe, Paul H. Berber, Crow White, Jennifer E. Caselle, Alejandro Perez-Matus, Steven D. Gaines, Giacomo Bernardi

Biological Sciences

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well …

Luxs In Bacteria Isolated From 25- To 40-Million-Year-Old Amber, Tasha M. Santiago-Rodriguez, Ana R. Patrício, Jessica I. Rivera, Mariel Coradin, Alfredo Gonzalez, Gabriela Tirado, Raúl J. Cano, Gary A. Toranzos

Biological Sciences

Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., …

Rov-Based Tracking Of A Shallow Water Nocturnal Squid, Samuel Yim, Christopher M. Clark, Timothy Peters, Vladimir Prodanov, Pat Fidopiastis

Biological Sciences

This paper describes the use of a Remotely Operated Vehicle (ROV) equipped with a monocular vision system to find and track the squid Euprymna scolopes, so that motion behaviors of the squid could be characterized through the use of off-line image processing and state estimation. The ROV was deployed for several nights at several nearshore locations off Oahu, resulting in 10 hours of squid footage. Using blob-tracking image processing techniques and a Particle Filter state estimator, the squid can be detected and tracked. The position, velocity, and acceleration of the squid relative to the stationary ROV can be determined. Experiment …

Evaluation Of Species Distribution Models By Resampling Of Sites Surveyed A Century Ago By Joseph Grinnell, Adam B. Smith, Maria J. Santos, Michelle S. Koo, Karen M.C. Rowe, Kevin C. Rowe, James L. Patton, John D. Perrine, Steven R. Beissinger, Craig Moritz

Biological Sciences

Species distribution models (SDMs) are commonly applied to predict species’ responses to anticipated global change, but lack of data from future time periods precludes assessment of their reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high-confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900–1939) or modern (1970–2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the …

Assessing Coral Reef Fish Population And Community Changes In Response To Marine Reserves In The Dry Tortugas, Florida, Usa, Jerald S. Ault, Steven G. Smith, James A. Bohnsack, Jiangang Luo, Natalia Zurcher, David B. Mcclellan, Tracy A. Ziegler, David E. Hallac, Matt Patterson, Michael W. Feeley, Benjamin I. Ruttenberg, John Hunt, Dan Kimball, Billy Causey

Biological Sciences

The efficacy of no-take marine reserves (NTMRs) to enhance and sustain regional coral reef fisheries was assessed in Dry Tortugas, Florida, through 9 annual fishery-independent research surveys spanning 2 years before and 10 years after NTMR implementation. A probabilistic sampling design produced precise estimates of population metrics of more than 250 exploited and non-target reef fishes. During the survey period more than 8100 research dives utilizing SCUBA Nitrox were optimally allocated using stratified random sampling. The survey domain covered 326 km², comprised of eight reef habitats in four management areas that offered different levels of resource protection: the …

Microbial Communities In Pre-Columbian Coprolites, Tasha M. Santiago-Rodriguez, Yvonne M. Narganes-Storde, Luis Chanlatte, Edwin Crespo-Torres, Gary A. Toranzos, Rafael Jiménez-Flores, Alice Hamrick, Raul J. Cano

Biological Sciences

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial …

The Correlation Between Veldt Grass (Ehrharta Calycina) And Reproductive Condition Of The Lompoc Kangaroo Rat (Dipodomys Heermanni Arenae), Jacqueline Mae Bates

Biological Sciences

The invasive species, Veldt grass (Ehrharta calycina), has come to dominate coastal dune shrub vegetation along the Central Coast of California. Along with creating many land management obstacles, this grass has become dominant in the open habitat of Lompoc Kangaroo Rats (Dipodomys heermanni arenae). It is hypothesized that, due to a lack of suitable kangaroo rat habitat, during the breeding season months of March and April, there will be significantly fewer reproductively active females in areas of relatively high Veldt grass cover as opposed to relatively low Veldt grass cover. This study used data from a …