Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay.

Saline-saturated DMSO-EDTA as a storage medium for microbial DNA analysis from coral mucus swab samples

The mucus surface layer of corals plays a number of integral roles in their overall health and fitness. This mucopolysaccharide coating serves as vehicle to capture food, a protective barrier against physical invasions and trauma, and serves as a medium to host a community of microorganisms distinct from the surrounding seawater. In healthy corals the associated microbial communities are known to provide antibiotics that contribute to the coral’s innate immunity and function metabolic activities such as biogeochemical cycling. Culture-dependent (Ducklow and Mitchell, 1979; Ritchie, 2006) and culture-independent methods (Rohwer, et al., 2001; Rohwer et al., 2002; Sekar et al., 2006; Hansson et al., 2009; Kellogg et al., 2009) have shown that coral mucus-associated microbial communities can change with changes in the environment and health condition of the coral. These changes may suggest that changes in the microbial associates not only reflect health status but also may assist corals in acclimating to changing environmental conditions. With the increasing availability of molecular biology tools, culture-independent methods are being used more frequently for evaluating the health of the animal host. Although culture-independent methods are able to provide more in-depth insights into the constituents of the coral surface mucus layer’s microbial community, their reliability and reproducibility rely on the initial sample collection maintaining sample integrity. In general, a sample of mucus is collected from a coral colony, either by sterile syringe or swab method (Woodley, et al., 2008), and immediately placed in a cryovial. In the case of a syringe sample, the mucus is decanted into the cryovial and the sealed tube is immediately flash-frozen in a liquid nitrogen vapor shipper (a.k.a., dry shipper). Swabs with mucus are placed in a cryovial, and the end of the swab is broken off before sealing and placing the vial in the dry shipper. The samples are then sent to a laboratory for analysis. After the initial collection and preservation of the sample, the duration of the sample voyage to a recipient laboratory is often another critical part of the sampling process, as unanticipated delays may exceed the length of time a dry shipper can remain cold, or mishandling of the shipper can cause it to exhaust prematurely. In remote areas, service by international shipping companies may be non-existent, which requires the use of an alternative preservation medium. Other methods for preserving environmental samples for microbial DNA analysis include drying on various matrices (DNA cards, swabs), or placing samples in liquid preservatives (e.g., chloroform/phenol/isoamyl alcohol, TRIzol reagent, ethanol). These methodologies eliminate the need for cold storage, however, they add expense and permitting requirements for hazardous liquid components, and the retrieval of intact microbial DNA often can be inconsistent (Dawson, et al., 1998; Rissanen et al., 2010). A method to preserve coral mucus samples without cold storage or use of hazardous solvents, while maintaining microbial DNA integrity, would be an invaluable tool for coral biologists, especially those in remote areas. Saline-saturated dimethylsulfoxide-ethylenediaminetetraacetic acid (20% DMSO-0.25M EDTA, pH 8.0), or SSDE, is a solution that has been reported to be a means of storing tissue of marine invertebrates at ambient temperatures without significant loss of nucleic acid integrity (Dawson et al., 1998, Concepcion et al., 2007). While this methodology would be a facile and inexpensive way to transport coral tissue samples, it is unclear whether the coral microbiota DNA would be adversely affected by this storage medium either by degradation of the DNA, or a bias in the DNA recovered during the extraction process created by variations in extraction efficiencies among the various community members. Tests to determine the efficacy of SSDE as an ambient temperature storage medium for coral mucus samples are presented here.

Threatened corals provide underexplored microbial habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.

Influence of microbial interactions on the susceptibility of Karenia spp. to algicidal bacteria

A bacterial strain (D38BY) belonging to the family Flavobacteriaceae and antagonistic towards an algicidal bacterium (strain S03; Flavobacteriaceae) was isolated from a culture of the red tide dinoflagellate Karenia brevis that had previously been characterized as resistant to attack by strain S03. This antagonistic bacterium increased the survival time of otherwise susceptible, bacteriafree K. brevis cultures in a concentration-dependent manner during exposure to the algicidal bacterium. Experimental evidence indicated that direct contact was required in order for strain D38BY to inhibit the killing activity of algicidal strain S03. While further work is needed to determine its precise mode of action, the antagonistic properties of strain D38BY provide further evidence that the resistance or susceptibility of certain algal taxa to algicidal attack can be more a function of interactions within the ambient microbial community than an intrinsic property of the alga.

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs

Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.

Report of the 2005 Workshop on Ocean Ecodynamics Comparison in the Subarctic Pacific

I. Scientific Issues Posed by OECOS II. Participant Contributions to the OECOS Workshop A. ASPECTS OF PHYTOPLANKTON ECOLOGY IN THE SUBARCTIC PACIFIC Microbial community compositions by Karen E. Selph Subarctic Pacific lower trophic interactions: Production-based grazing rates and grazing-corrected production rates by Nicholas Welschmeyer Phytoplankton bloom dynamics and their physiological status in the western subarctic Pacific by Ken Furuya Temporal and spatial variability of phytoplankton biomass and productivity in the northwestern Pacific by Sei-ichi Saitoh, Suguru Okamoto, Hiroki Takemura and Kosei Sasaoka The use of molecular indicators of phytoplankton iron limitation by Deana Erdner B. IRON CONCENTRATION AND CHEMICAL SPECIATION Iron measurements during OECOS by Zanna Chase and Jay Cullen 25 The measurement of iron, nutrients and other chemical components in the northwestern North Pacific Ocean by Kenshi Kuma The measurement of iron, nutrients and other chemical components in the northwestern North Pacific Ocean by Kenshi Kuma C. PHYSICAL OCEANOGRAPHY, FINE-SCALE DISTRIBUTION PATTERNS AND AUTONOMOUS DRIFTERS The use of drifters in Lagrangian experiments: Positives, negatives and what can really be measured by Peter Strutton The interaction between plankton distribution patterns and vertical and horizontal physical processes in the eastern subarctic North Pacific by Timothy J. Cowles D. MICROZOOPLANKTON Microzooplankton processes in oceanic waters of the eastern subarctic Pacific: Project OECOS by Suzanne Strom Functional role of microzooplankton in the pelagic marine ecosystem during phytoplankton blooms in the western subarctic Pacific by Takashi Ota and Akiyoshi Shinada E. MESOZOOPLANKTON Vertical zonation of mesozooplankton, and its variability in response to food availability, density stratification, and turbulence by David L. Mackas and Moira Galbraith Marine ecosystem characteristics and seasonal abundance of dominant calanoid copepods in the Oyashio region by Atsushi Yamaguchi, Tsutomu Ikeda and Naonobu Shiga OECOS: Proposed mesozooplankton research in the Oyashio region, western subarctic Pacific by Tsutomu Ikeda Some background on Neocalanus feeding by Michael Dagg Size and growth of interzonally migrating copepods by Charles B. Miller Growth of large interzonal migrating copepods by Toru Kobari F. MODELING Ecosystem and population dynamics modeling by Harold P. Batchelder III. Reports from Workshop Breakout Groups A. PHYSICAL AND CHEMICAL ASPECTS WITH EMPHASIS ON IRON AND IRON SPECIATION B. PHYTOPLANKTON/MICROZOOPLANKTON STUDIES C. MESOZOOPLANKTON STUDIES IV. Issues arising during the workshop A. PHYTOPLANKTON STOCK VARIATIONS IN HNLC SYSTEMS AND TROPHIC CASCADES IN THE NANO AND MICRO REGIMES B. DIFFERENCES BETWEEN EAST AND WEST IN SITE SELECTION FOR OECOS TIME SERIES C. TIMING OF OECOS EXPEDITIONS D. CHARACTERIZATION OF PHYSICAL OCEANOGRAPHY V. Concluding Remarks VI. References (109 page document)

The microbiological quality of water: the nature of the problem

Improvements in methods for the detection and enumeration of microbes in water, particularly the application of techniques of molecular biology, have highlighted shortcomings in the ”standard methods” for assessing water quality. Higher expectations from the consumer and increased publicity associated with pollution incidents can lead to an uncoupling of the cycle which links methodological development with standard-setting and legislation. The new methodology has also highlighted problems within the water cycle, related to the introduction, growth and metabolism of microbes. A greater understanding of the true diversity of the microbial community and the ability to transmit genetic information within aquatic systems ensures that the subject of this symposium and volume provides an ideal forum to discuss the problems encountered by both researcher and practitioner.

Magnitude and Extent of Contaminated Sediment and Toxicity in Chesapeake Bay

INTRODUCTION: This report summarizes the results of NOAA's sediment toxicity, chemistry, and benthic community studies in the Chesapeake Bay estuary. As part of the National Status and Trends (NS&T) Program, NOAA has conducted studies to determine the spatial extent and severity of chemical contamination and associated adverse biological effects in coastal bays and estuaries of the United States since 1991. Sediment contamination in U.S. coastal areas is a major environmental issue because of its potential toxic effects on biological resources and often, indirectly, on human health. Thus, characterizing and delineating areas of sediment contamination and toxicity and demonstrating their effect(s) on benthic living resources are viewed as important goals of coastal resource management. Benthic community studies have a history of use in regional estuarine monitoring programs and have been shown to be an effective indicator for describing the extent and magnitude of pollution impacts in estuarine ecosystems, as well as for assessing the effectiveness of management actions. Chesapeake Bay is the largest estuarine system in the United States. Including tidal tributaries, the Bay has approximately 18,694 km of shoreline (more than the entire US West Coast). The watershed is over 165,000 km2 (64,000 miles2), and includes portions of six states (Delaware, Maryland, New York, Pennsylvania, Virginia, and West Virginia) and the District of Columbia. The population of the watershed exceeds 15 million people. There are 150 rivers and streams in the Chesapeake drainage basin. Within the watershed, five major rivers - the Susquehanna, Potomac, Rappahannock, York and James - provide almost 90% of the freshwater to the Bay. The Bay receives an equal volume of water from the Atlantic Ocean. In the upper Bay and tributaries, sediments are fine-grained silts and clays. Sediments in the middle Bay are mostly made of silts and clays derived from shoreline erosion. In the lower Bay, by contrast, the sediments are sandy. These particles come from shore erosion and inputs from the Atlantic Ocean. The introduction of European-style agriculture and large scale clearing of the watershed produced massive shifts in sediment dynamics of the Bay watershed. As early as the mid 1700s, some navigable rivers were filled in by sediment and sedimentation caused several colonial seaports to become landlocked. Toxic contaminants enter the Bay via atmospheric deposition, dissolved and particulate runoff from the watershed or direct discharge. While contaminants enter the Bay from several sources, sediments accumulate many toxic contaminants and thus reveal the status of input for these constituents. In the watershed, loading estimates indicate that the major sources of contaminants are point sources, stormwater runoff, atmospheric deposition, and spills. Point sources and urban runoff in the Bay proper contribute large quantities of contaminants. Pesticide inputs to the Bay have not been quantified. Baltimore Harbor and the Elizabeth River remain among the most contaminated areas in the Unites States. In the mainstem, deep sediment core analyses indicate that sediment accumulation rates are 2-10 times higher in the northern Bay than in the middle and lower Bay, and that sedimentation rates are 2-10 times higher than before European settlement throughout the Bay (NOAA 1998). The core samples show a decline in selected PAH compounds over the past several decades, but absolute concentrations are still 1 to 2 orders of magnitude above 'pristine' conditions. Core data also indicate that concentrations of PAHs, PCBs and, organochlorine pesticides do not demonstrate consistent trends over 25 years, but remain 10 times lower than sediments in the tributaries. In contrast, tri-butyl-tin (TBT) concentrations in the deep cores have declined significantly since it=s use was severely restricted. (PDF contains 241 pages)

Sediment Quality in Puget Sound Year 3 - Southern Puget Sound

As a component of a three-year cooperative effort of the Washington State Department of Ecology and the National Oceanic and Atmospheric Administration, surficial sediment samples from 100 locations in southern Puget Sound were collected in 1999 to determine their relative quality based on measures of toxicity, chemical contamination, and benthic infaunal assemblage structure. The survey encompassed an area of approximately 858 km2, ranging from East and Colvos Passages south to Oakland Bay, and including Hood Canal. Toxic responses were most severe in some of the industrialized waterways of Tacoma’s Commencement Bay. Other industrialized harbors in which sediments induced toxic responses on smaller scales included the Port of Olympia, Oakland Bay at Shelton, Gig Harbor, Port Ludlow, and Port Gamble. Based on the methods selected for this survey, the spatial extent of toxicity for the southern Puget Sound survey area was 0% of the total survey area for amphipod survival, 5.7% for urchin fertilization, 0.2% for microbial bioluminescence, and 5- 38% with the cytochrome P450 HRGS assay. Measurements of trace metals, PAHs, PCBs, chlorinated pesticides, other organic chemicals, and other characteristics of the sediments, indicated that 20 of the 100 samples collected had one or more chemical concentrations that exceeded applicable, effects-based sediment guidelines and/or Washington State standards. Chemical contamination was highest in eight samples collected in or near the industrialized waterways of Commencement Bay. Samples from the Thea Foss and Middle Waterways were primarily contaminated with a mixture of PAHs and trace metals, whereas those from Hylebos Waterway were contaminated with chlorinated organic hydrocarbons. The remaining 12 samples with elevated chemical concentrations primarily had high levels of other chemicals, including bis(2-ethylhexyl) phthalate, benzoic acid, benzyl alcohol, and phenol. The characteristics of benthic infaunal assemblages in south Puget Sound differed considerably among locations and habitat types throughout the study area. In general, many of the small embayments and inlets throughout the study area had infaunal assemblages with relatively low total abundance, taxa richness, evenness, and dominance values, although total abundance values were very high in some cases, typically due to high abundance of one organism such as the polychaete Aphelochaeta sp. N1. The majority of the samples collected from passages, outer embayments, and larger bodies of water tended to have infaunal assemblages with higher total abundance, taxa richness, evenness, and dominance values. Two samples collected in the Port of Olympia near a superfund cleanup site had no living organisms in them. A weight-of-evidence approach used to simultaneously examine all three “sediment quality triad” parameters, identified 11 stations (representing 4.4 km2, 0.5% of the total study area) with sediment toxicity, chemical contamination, and altered benthos (i.e., degraded sediment quality), 36 stations (493.5 km2, 57.5% total study area) with no toxicity or chemical contamination (i.e., high sediment quality), 35 stations (274.1 km2, 32.0% total study area) with one impaired sediment triad parameter (i.e., intermediate/high sediment quality), and 18 stations (85.7km2, 10.0% total study area) with two impaired sediment parameters (i.e., intermediate/degraded quality sediments). Generally, upon comparison, the number of stations with degraded sediments based upon the sediment quality triad of data was slightly greater in the central Puget Sound than in the northern and southern Puget Sound study areas, with the percent of the total study area degraded in each region decreasing from central to north to south (2.8, 1.3 and 0.5%, respectively). Overall, the sediments collected in Puget Sound during the combined 1997-1999 surveys were among the least contaminated relative to other marine bays and estuaries studied by NOAA using equivalent methods. (PDF contains 351 pages)

Survey of sediment quality in Sabine Lake, Texas and vicinity

The toxicity of sediments in Sabine Lake, Texas, and adjoining Intracoastal Waterway canals was determined as part of bioeffects assessment studies managed by NOAA’s National Status and Trends Program. The objectives of the survey were to determine: (1) the incidence and degree of toxicity of sediments throughout the study area; (2) the spatial patterns (or gradients) in chemical contamination and toxicity, if any, throughout the study area; (3) the spatial extent of chemical contamination and toxicity; and (4) the statistical relationships between measures of toxicity and concentrations of chemicals in the sediments. Surficial sediment samples were collected during August, 1995 from 66 randomly-chosen locations. Laboratory toxicity tests were performed as indicators of potential ecotoxicological effects in sediments. A battery of tests was performed to generate information from different phases (components) of the sediments. Tests were selected to represent a range in toxicological endpoints from acute to chronic sublethal responses. Toxicological tests were conducted to measure: reduced survival of adult amphipods exposed to solid-phase sediments; impaired fertilization success and abnormal morphological development in gametes and embryos, respectively, of sea urchins exposed to pore waters; reduced metabolic activity of a marine bioluminescent bacteria exposed to organic solvent extracts; and induction of a cytochrome P-450 reporter gene system in exposures to solvent extracts of the sediments. Chemical analyses were performed on portions of each sample to quantify the concentrations of trace metals, polynuclear aromatic hydrocarbons, and chlorinated organic compounds. Correlation analyses were conducted to determine the relationships between measures of toxicity and concentrations of potentially toxic substances in the samples. Based upon the compilation of results from chemical analyses and toxicity tests, the quality of sediments in Sabine Lake and vicinity did not appear to be severely degraded. Chemical concentrations rarely exceeded effects-based numerical guidelines, suggesting that toxicant-induced effects would not be expected in most areas. None of the samples was highly toxic in acute amphipod survival tests and a minority (23%) of samples were highly toxic in sublethal urchin fertilization tests. Although toxic responses occurred frequently (94% of samples) in urchin embryo development tests performed with 100% pore waters, toxicity diminished markedly in tests done with diluted pore waters. Microbial bioluminescent activity was not reduced to a great degree (no EC50 <0.06 mg/ml) and cytochrome P-450 activity was not highly induced (6 samples exceeded 37.1 ug/g benzo[a]pyrene equivalents) in tests done with organic solvent extracts. Urchin embryological development was highly correlated with concentrations of ammonia and many trace metals. Cytochrome P450 induction was highly correlated with concentrations of a number of classes of organic compounds (including the polynuclear aromatic hydrocarbons and chlorinated compounds). (PDF contains 51 pages)

Mussel Community Studies [Year One].

Mytilus californianus communities (mussel beds) were examined from six geographic localities in Southern California. These included two mainland sites, Coal Oil Point and San Diego; and four island sites, San Miguel, Santa Cruz, San Nicholas, and Santa Barbara Islands. Optimal sample sizes were determined for each locality. In general, a sample, size of 1500 cm2 (five cores) was optimal for the "typical" mussel bed. However, structurally unique mussel beds required individual consideration. Community biomass, diversity, species richness, and species evenness were calculated quarterly for the island localities and biannually for mainland locations. The molluscs, primarily the mussels, accounted for 90% of the total biomass while all other groups combined accounted for 10% or less of the total biomass. The mussel communities from all localities contributed to the master species list which conservatively contained 346 species. The most diverse localities were Coal Oil Point and Santa Cruz Island with an average number of 73 and 74 species/O.lS m respectively. No overall seasonal patterns existed in community composition. The community similarity analyses showed the mainland localities biotically dissimilar from the islands and both groups were characterized by distinct faunal assemblages. In addition, San Miguel Island biota were unique among the island sites. The most important mussel bed structural attributes provided habitats for the associated community and included sediment and coarse fraction features. Food-related resources provided by the mussel bed were secondarily important. Community diversity generally increased with the quantity of habitat and food resources. (PDF contains 138 pages)

Mussel Community Studies [Year Three].

The communities associated with Mytilus californianus (mussel) beds from 20 geographic sites in southern California were examined. The study areas included six mainland sites - Government Point, Goleta Point, Ventura, Corona del Mar, Carlsbad, and San Diego,and two sites on opposite sides of seven offshore islands - San Miguel Island, Santa Rosa Island, Santa Cruz Island, Anacapa Island, San Nicholas Island, Santa Cruz Island and San Clemente Island. : The mussel communities from all areas contributed to the master species list which now encompasses conservatively, 610 species of animals and 141 species of algae. The most diverse collection came from Cat Rock, Anacapa Island where the mussel beds supported 174 species of invertebrates. The lowest diversity was recorded for mussel beds from Ben Weston, Santa Catalina Island which contained 46 species. In general, the island mussel beds supported a greater diversity of both animals and plants. Mussel community samples were collected from upper and lower intertidal areas occupied by the mussel beds within a locality. Community differences in both composition and abundance were associated with these collections. Overall. community similarity analysis revealed five major patterns which corresponded to characteristic species assemblages occupying the mussel beds from the various geographic areas. The patterns included: (1) clusters of localities which display a north-south geographic pattern with respect to the similarity of their respective mussel communities, (2) a separation of selected island and mainland communities because of dissimilarities in their species composition, (3) differences between mussel communities. on opposite sides of the offshore islands, (4) clusters of species whose highest abundances characterize selected localities, (5) species groups ubiquitous to all mussel beds examined. The results of the community analysis further suggest that predictions can be made delineating the probable mussel community inhabitants of areas not sampled. The species distribution patterns observed appear to correspond in part to the influence of currents and water masses which bear planktonic larvae and impinge on selected localities. The most important mussel bed features associated with community differences were quantitative and qualitative differences in the potential microhabitats. Those features associate~ with greater species diversity include the pore base of coarse fraction shell and rock debris, skewness and kurtosis of the sediment grain-size distributions and mussel bed thickness. Those features associated with lower species diversity included the quantity of tar. and rock and shell debris trapped within the mussel bed. (PDF contains 51 pages)

Sediment quality triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment condensed. A NOAA/NOS/NCCOS/CCMA Special Report

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using standardized National Status and Trends Bioeffects Program methods. Three sites near the village of Port Graham were also sampled for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (e.g. depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. The following is the synopsis of findings • Sediments were mostly mixed silt and sand with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, chlorinated pesticides) were detected throughout the bay but at relatively low concentrations. With some exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. • Homer Harbor had elevated concentrations of metallic and organic contaminants. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Tributyltin was elevated in Homer Harbor relative to the other areas. • There was no evidence of residual PAHs attributable to oil spills, outside of local input in the confines of the harbor. • The benthic community is very diverse. Specific community assemblages were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. • Significant toxicity was virtually absent. • The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. • Selected metal concentrations were elevated at Port Graham relative to Kachemak Bay, probably due to local geology. Organic contaminants were elevated at a site south of the village.

Sediment Quality Triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota. Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent. Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site.

Nitrogen fixing bacteria, Azotobacter sp. in aquatic sediment

Non-symbiotic, free living, nitrogen fixing bacteria, Azotobacter sp. was estimated in sediments of estuarine, marine, backwater and mangrove environments of Portonovo. Number of colony forming units (CFU) of Azotobacter sp. was less (5 to 27 cells/g of dry sediment). CFU of total heterotrophic bacteria (THB), actinomycetes and fungi were between 4.1x10 super(6) and 4.5x10 super (7), 0.8x10 super(5) and 4.9x10 super(5), 1.1x10 super(5) and 3.8x10 super(5)/g respectively. Mangrove sediments contained more CFU of the above microbial groups.