Diversity of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of a Hypernutrified Subtropical Estuary: Bahía del Tóbari, Mexico

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase α-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.     

Ecosystem services transcend boundaries: estuaries provide resource subsidies and influence functional diversity in coastal benthic communities

Background

Estuaries are highly productive ecosystems that can export organic matter to coastal seas (the ‘outwelling hypothesis’). However the role of this food resource subsidy on coastal ecosystem functioning has not been examined.

Methodology/Principal Findings

We investigated the influence of estuarine primary production as a resource subsidy and the influence of estuaries on biodiversity and ecosystem functioning in coastal mollusk-dominated sediment communities. Stable isotope values (δ¹³C, δ¹⁵N) demonstrated that estuarine primary production was exported to the adjacent coast and contributed to secondary production up to 4 km from the estuary mouth. Further, isotope signatures of suspension feeding bivalves on the adjacent coast (Dosinia subrosea) closely mirrored the isotope values of the dominant bivalves inside the estuaries (Austrovenus stutchburyi), indicating utilization of similar organic matter sources. However, the food subsidies varied between estuaries; with estuarine suspended particulate organic matter (SPOM) dominant at Tairua estuary, while seagrass and fringing vegetation detritus was proportionately more important at Whangapoua estuary, with lesser contributions of estuarine SPOM. Distance from the estuary mouth and the size and density of large bivalves (Dosinia spp.) had a significant influence on the composition of biological traits in the coastal macrobenthic communities, signaling the potential influence of these spatial subsidies on ecosystem functioning.

Conclusions/Significance

Our study demonstrated that the locations where ecosystem services like productivity are generated are not necessarily where the services are utilized. Further, we identified indirect positive effects of the nutrient subsidies on biodiversity (the estuarine subsidies influenced the bivalves, which in turn affected the diversity and functional trait composition of the coastal sediment macrofaunal communities). These findings highlight the importance of integrative ecosystem-based management that maintains the connectivity of estuarine and coastal ecosystems.     

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

Objectives

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.

Spatio-Temporal Patterns of the Microbial Communities

Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.

Macrofauna, Microbes and the Benthic N-Cycle

Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.     

Niche Differentiation of Ammonia-Oxidising Archaea (AOA) and Bacteria (AOB) in Response to Paper and Pulp Mill Effluent

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification–denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.     

The role of waves in the colonisation of terrestrial sediments deposited in the marine environment

Elevated rates of sediment run-off, as a result of changes in land-use and climate, are a significant threat to marine coastal communities, with a potential to cause broad-scale, long-term alteration of habitats. Individual sedimentation events can smother estuarine flats with terrigenous sediments, creating a significant disturbance to local benthic communities. Variations in the degree to which a habitat is altered, the rate at which mixing occurs, and species-specific dispersal and responses to the altered habitat, suggest that colonisation of terrestrial sediment depositions will vary with location, both between and within estuaries. This study was designed to explore the effect that variations in wave-induced hydrodynamics would have on long-term colonisation of terrestrial sediment depositions on intertidal flats. Sites for the experimental deposition of terrestrial sediment were located along a gradient in wave exposure, with only limited variation in immersion times (30 min) and ambient sediment particle sizes (predominantly fine sand). Over 20 months, periodic measurements were made of factors predicted to affect colonisation: the sediment characteristics of the deposited sediment; local-scale wave climate; bioturbation of the deposited sediment; and local populations of benthic invertebrates. Neither opportunistic use of the new resource, progressive recovery or facilitation by colonising macrofauna was observed. Little vertical mixing of the deposited and existing sediment by either waves or bioturbators occurred; instead bedload transport was the dominant process. Local differences in hydrodynamic conditions and macrobenthic communities resulted in site-specific colonisation of the experimental plots. The strength and duration of the macrofaunal response to deposited sediment observed in this study suggest that chronic small-scale (m's) patchy deposition of terrestrial sediment in the intertidal marine environment has a strong potential to alter both habitats and communities.     

Large Spatial Scale Variability in Bathyal Macrobenthos Abundance,Biomass, α- and β-Diversity along the Mediterranean Continental Margin

The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project (“Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna”), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas.     

Macrofaunal Functional Diversity Provides Resilience to Nutrient Enrichment in Coastal Sediments

The degradation of ecosystems is often associated with losses of large organisms and the concomitant losses of the ecological functions they mediate. Conversely, the resilience of ecosystems to stress is strongly influenced by faunal communities and their impacts on processes. Denitrification in coastal sediments is a process that may provide ecosystem resilience to eutrophication by removing excess bioavailable nitrogen. Here, we conducted a large-scale field experiment to test the effect of macrofaunal community composition on denitrification in response to two levels of nutrient enrichment at 28 sites across a biologically heterogeneous sandflat. After 7 weeks of enrichment, we measured denitrification enzyme activity (DEA) along with benthic macrofaunal community composition and environmental variables. We normalised treatment site specific DEA values by those in ambient sediments (DEA_CN) to reveal the underlying response across the heterogeneous landscape. Nutrient enrichment caused reductions in DEA_CN as well as functional changes in the community; these were both more pronounced under the highest level of nutrient loading (on average DEA_CN was reduced by 34%). The degree of suppression of DEA_CN following moderate nitrogen loading was mitigated by a key bioturbating species, but following high nitrogen loading (which reduced the key species density) the abundance and diversity of other nutrient processing species were the most important factors alleviating negative effects. This study provides a prime example of the context-dependent role of biodiversity in maintaining ecosystem functioning, underlining that different elements of biodiversity can become important as stress levels increase. Our results emphasise that management and conservation strategies require a real-world understanding of the community attributes that facilitate nutrient processing and maintain resilience in coastal ecosystems.     

Counting on β-Diversity to Safeguard the Resilience of Estuaries

Coastal ecosystems are often stressed by non-point source and cumulative effects that can lead to local-scale community homogenisation and a concomitant loss of large-scale ecological connectivity. Here we investigate the use of β-diversity as a measure of both community heterogeneity and ecological connectivity. To understand the consequences of different environmental scenarios on heterogeneity and connectivity, it is necessary to understand the scale at which different environmental factors affect β-diversity. We sampled macrofauna from intertidal sites in nine estuaries from New Zealand’s North Island that represented different degrees of stress derived from land-use. We used multiple regression models to identify relationships between β-diversity and local sediment variables, factors related to the estuarine and catchment hydrodynamics and morphology and land-based stressors. At local scales, we found higher β-diversity at sites with a relatively high total richness. At larger scales, β-diversity was positively related to γ-diversity, suggesting that a large regional species pool was linked with large-scale heterogeneity in these systems. Local environmental heterogeneity influenced β-diversity at both local and regional scales, although variables at the estuarine and catchment scales were both needed to explain large scale connectivity. The estuaries expected a priori to be the most stressed exhibited higher variance in community dissimilarity between sites and connectivity to the estuary species pool. This suggests that connectivity and heterogeneity metrics could be used to generate early warning signals of cumulative stress.     

Phosphorus chemistry and bacterial community composition interact in brackish sediments receiving agricultural discharges

Background

External nutrient discharges have caused eutrophication in many estuaries and coastal seas such as the Baltic Sea. The sedimented nutrients can affect bacterial communities which, in turn, are widely believed to contribute to release of nutrients such as phosphorus from the sediment.

Methods

We investigated relationships between bacterial communities and chemical forms of phosphorus as well as elements involved in its cycling in brackish sediments using up-to-date multivariate statistical methods. Bacterial community composition was determined by terminal restriction fragment length polymorphism and cloning of the 16S rRNA gene.

Results and Conclusions

The bacterial community composition differed along gradients of nutrients, especially of different phosphorus forms, from the estuary receiving agricultural phosphorus loading to the open sea. This suggests that the chemical composition of sediment phosphorus, which has been affected by riverine phosphorus loading, influenced on bacterial communities. Chemical and spatial parameters explained 25% and 11% of the variation in bacterial communities. Deltaproteobacteria, presumptively sulphate and sulphur/iron reducing, were strongly associated to chemical parameters, also when spatial autocorrelation was taken into account. Sulphate reducers correlated positively with labile organic phosphorus and total nitrogen in the open sea sediments. Sulphur/iron reducers and sulphate reducers linked to iron reduction correlated positively with aluminium- and iron-bound phosphorus, and total iron in the estuary. The sulphate and sulphur/iron reducing bacteria can thus have an important role both in the mineralization and mobilization of nutrients from sediment.

Significance

Novelty in our study is that relationships between bacterial community composition and different phosphorus forms, instead of total phosphorus, were investigated. Total phosphorus does not necessarily bring out interactions between bacteria and phosphorus chemistry since proportions of easily usable mobile (reactive) phosphorus and immobile phosphorus forms in different sediments can vary. Our study suggested possible feedbacks between different forms of phosphorus and bacterial community composition.     

Free-living nematodes and macrobenthos in a high-latitude glacial fjord

Kongsfjord is an open glacial fjord on the west coast of Svalbard, where the influence of the West Spitzbergen current ameliorates the effects of high latitude (79°N). The fjord is heavily influenced by glacial discharges of meltwater, ice and till, and related environmental gradients in sediments from the glaciers to the open sea include sediment deposition, organic content and disturbance. Other factors, such as the formation and break up of sea ice, also affect benthic communities. In this study spatial patterns in nematode and macrofaunal communities, in samples collected using box-corers and van Veen grabs during a cruise in September 1997, are described, compared and contrasted. Non-parametric multivariate analyses demonstrate that there were clear differences in community structure between stations in both macrofaunal and nematode assemblages. At stations where macrofauna were sampled using both box-cores and grabs there were also significant differences between samples collected by different methods, although there is evidence that these were influenced in part by slight differences in sampling location. Some evidence of disturbance to macrofaunal assemblages in the centre of the fjord is apparent. Macrofaunal community composition varied most closely with a combination of depth and sediment C : N ratio, whereas that of nematodes varied most closely with C : N alone. Proportions of feeding groups of nematodes showed little variation along the fjord. There is no evidence of a specialised nematode assemblage inhabiting the part of the fjord subject to the heaviest deposition of sediment. The taxonomic distinctness of nematodes decreased with increasing distance from the source of disturbance. This is in contrast to studies showing that the taxonomic distinctness of nematodes tends to decrease with increasing anthropogenic stress.     

High levels of sediment contamination have little influence on estuarine beach fish communities

While contaminants are predicted to have measurable impacts on fish assemblages, studies have rarely assessed this potential in the context of natural variability in physico-chemical conditions within and between estuaries. We investigated links between the distribution of sediment contamination (metals and PAHs), physico-chemical variables (pH, salinity, temperature, turbidity) and beach fish assemblages in estuarine environments. Fish communities were sampled using a beach seine within the inner and outer zones of six estuaries that were either heavily modified or relatively unmodified by urbanization and industrial activity. All sampling was replicated over two years with two periods sampled each year. Shannon diversity, biomass and abundance were all significantly higher in the inner zone of estuaries while fish were larger on average in the outer zone. Strong differences in community composition were also detected between the inner and outer zones. Few differences were detected between fish assemblages in heavily modified versus relatively unmodified estuaries despite high concentrations of sediment contaminants in the inner zones of modified estuaries that exceeded recognized sediment quality guidelines. Trends in species distributions, community composition, abundance, Shannon diversity, and average fish weight were strongly correlated to physico-chemical variables and showed a weaker relationship to sediment metal contamination. Sediment PAH concentrations were not significantly related to the fish assemblage. These findings suggest that variation in some physico-chemical factors (salinity, temperature, pH) or variables that co-vary with these factors (e.g., wave activity or grain size) have a much greater influence on this fish assemblage than anthropogenic stressors such as contamination.     

The effect of artificial defaunation on bacterial assemblages of intertidal sediments

The use of the artificial defaunation of sediments is widespread among studies examining the disturbance and recovery of benthic macrofaunal communities. Standard methods of defaunation include driving the sediment to anoxia, freezing and sieving. In this study we performed a field experiment to test the assumption that the bacterial assemblages are unaffected by these methods of defaunation. Same-sized patches of sediment were defaunated by covering sediment with plastic sheeting (weighted by concrete blocks), freezing or sieving (1-mm mesh). Macrofaunal counts of sediment cores, taken to determine the effectiveness of each defaunation method, indicated that although none of the treatments removed 100% of macrofauna, all resulted in reduced macrofaunal presence, with the sieved treatment being the most effective. Bacterial samples were taken over the course of a month to determine both the initial and long-term effects of defaunation on bacterial community structure. Numerical effects were determined via epifluorescence microscopy, whereas differences in community composition were followed using PCR and denaturing gradient gel electrophoresis (DGGE). The anoxic treatments resulted in significant numerical changes in both active and total cell counts over time, while the frozen and sieved treatments caused less apparent changes. All of the treatments initially changed the composition of the community; however, anoxic and sieved treatments resulted in subtle changes while the frozen treatment produced more notable and variable changes within the community. The composition of the bacterial community in all of the treatment plots trended towards recovery, or convergence towards that of ambient sediments, by the t = 25-day sampling period.     

Nutrient cycling and plant dynamics in estuaries: A brief review

Eutrophication of European estuaries due to massive nutrient loading from urban areas and diffuse runoff from extensively cultivated land areas is analysed. Consequences for the ecology of estuaries, namely changes in plant species composition, which also affects heterotrophic organisms, are approached based on examples showing that the result is often a fundamental structural change of the ecosystem, from a grazing and/or nutrient controlled stable systems to unstable detritus/mineralisation systems, where the turnover of oxygen and nutrients is much more dynamic and oscillations between aerobic and anaerobic states frequently occur. Several relevant aspects are examined, namely the influence of rooted macrophytes on nutrient dynamics, by comparing bare bottom sediments with eelgrass covered sediments, primary production and the development of organic detritus, and hydrodynamics and its relations to the spatial distribution of macrophytes in estuarine systems.     

The relative importance of sediment and water column supplies of nutrients to the growth and tissue nutrient content of the green macroalga Enteromorpha intestinalis along an estuarine resource gradient

Large blooms of opportunistic green macroalgae such as Enteromorpha intestinalis are of ecological concern in estuaries worldwide. Macroalgae derive their nutrients from the water column but estuarine sediments may also be an important nutrient source. We hypothesized that the importance of these nutrient sources to E. intestinalis varies along a nutrient-resource gradient within an estuary. We tested this in experimental units constructed with water and sediments collected from 3 sites in Upper Newport Bay estuary, California, US, that varied greatly in water column nutrient concentrations. For each site there were three treatments: sediments + water; sediments + water + Enteromorpha intestinalis (algae); inert sand + water + algae. Water in units was exchanged weekly simulating low turnover characteristic of poorly flushed estuaries. The importance of the water column versus sediments as a source of nutrients to E. intestinalis varied with the magnitude of the different sources. When initial water column levels of dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) were low, estuarine sediments increased E. intestinalis growth and tissue nutrient content. In experimental units from sites where initial water column DIN was high, there was no effect of estuarine sediments on E. intestinalis growth or tissue N content. Salinity, however, was low in these units and may have inhibited growth. E. intestinalis growth and tissue P content were highest in units from the site with highest initial sediment nutrient content. Water column DIN was depleted each week of the experiment. Thus, the water column was a primary source of nutrients to the algae when water column nutrient supply was high, and the sediments supplemented nutrient supply to the algae when water column nutrient sources were low. Depletion of water column DIN in sediment + water units indicated that the sediments may have acted as a nutrient sink in the absence of macroalgae. Our data provide direct experimental evidence that macroalgae utilize and ecologically benefit from nutrients stored in estuarine sediments.     

Geomorphology of Australian estuaries: Review and prospect

Over the past 30 years there has been a wealth of research examining the geomorphology of Australian estuaries. This paper reviews the major regional controls on estuarine geomorphic development and discusses the focus of research efforts to understand estuarine evolution, configuration and processes controlling geomorphic development and change. The presence and position of estuaries along the Australian coastline is controlled by large-scale climate-led changes in sea-level, the antecedent structure of the coast and tectonic activity. The configuration of Australia’s estuaries is controlled by a number of environmental factors identified by 34 including climate, oceanographic regime, sediment availability, structure and mineralogy, and tectonics. Interaction of these factors produce a range of estuarine configurations around the Australian continent from wave-dominated, microtidal, bar-built estuaries in the south to low energy macrotidal estuaries in the north which have produced extensive low-lying coastal plains. The principle focus of geomorphologists during the past 30 years has been understanding the medium to long-term development of estuaries in response to fluctuating sea-level over the past 125 000 years. Classifications and models of estuarine development and associated biological community response to estuary development have been identified based on lateral and vertical sedimentary sequences. Results have provided essential information on the physical resources and characteristics of estuarine systems including the distribution of sediment facies that host a variety of different ecological communities. There has been a paucity of research examining contemporary processes controlling geomorphic change in Australia’s estuaries. A morphodynamic approach to the study of estuaries is advocated that evaluates morphology-process responses as estuaries evolve. This approach requires increased research efforts to identify regional differences in estuarine geomorphic development, hydrodynamic processes and sedimentation. It is also advocated that studies examine how the morphodynamic behaviour of estuaries over thousands of years has influenced estuary ecology. Such studies will provide a more complete understanding of the factors influencing the morphology and ecology of contemporary estuaries.     

Diatom-Derived Carbohydrates as Factors Affecting Bacterial Community Composition in Estuarine Sediments

Microphytobenthic biofilms in estuaries, dominated by epipelic diatoms, are sites of high primary productivity. These diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides and glycoproteins, providing a substantial pool of organic carbon available to heterotrophs within the sediment. In this study, sediment slurry microcosms were enriched with either colloidal carbohydrates or colloidal EPS (cEPS) or left unamended. Over 10 days, the fate of these carbohydrates and changes in β-glucosidase activity were monitored. Terminal restriction fragment length polymorphism (T-RFLP), DNA sequencing, and quantitative PCR (Q-PCR) analysis of 16S rRNA sequences were used to determine whether sediment bacterial communities exhibited compositional shifts in response to the different available carbon sources. Initial heterotrophic activity led to reductions in carbohydrate concentrations in all three microcosms from day 0 to day 2, with some increases in β-glucosidase activity. During this period, treatment-specific shifts in bacterial community composition were not observed. However, by days 4 and 10, the bacterial community in the cEPS-enriched sediment diverged from those in colloid-enriched and unamended sediments, with Q-PCR analysis showing elevated bacterial numbers in the cEPS-enriched sediment at day 4. Community shifts were attributed to changes in cEPS concentrations and increased β-glucosidase activity. T-RFLP and sequencing analyses suggested that this shift was not due to a total community response but rather to large increases in the relative abundance of members of the γ-proteobacteria, particularly Acinetobacter-related bacteria. These experiments suggest that taxon- and substrate-specific responses within the bacterial community are involved in the degradation of diatom-derived extracellular carbohydrates.     

Patterns of fungal diversity and composition along a salinity gradient

Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.     

Functional Role of Large Organisms in Intertidal Communities: Community Effects and Ecosystem Function

In marine soft sediments, large organisms are potentially important players in the nonlinear interactions that occur among animals, their food, and their chemical environment, all of which influence the contribution of benthos to ecosystem function. We investigated the consequences of removing large individuals of two functionally contrasting benthic communities on nutrient regeneration, microphyte standing stock, and macrobenthic community composition. The experiment was conducted at two adjacent sites that were physically similar but biologically different, one dominated by large deposit feeders and the other by large suspension feeders. Chemical fluxes were measured in experimental plots, and sediments were sampled to assess changes in macrofauna, sediment grain size, organic content, and microphyte standing stock. Our results demonstrate that the removal of large suspension feeders or deposit feeders influenced the flux of nitrogen and oxygen, surficial sediment characteristics, and community composition. In the deposit-feeder community, interactions between nutrient regeneration and grazing highlight important feedbacks between large macrofauna and biogeochemical processes and production by microphytes, indicating that the loss of large infauna driven by increased rates of anthropogenic disturbance may lead to functional extinction and cause shifts in community structure and ecosystem performance.     

Isolation of Non-O1 Vibrio cholerae Serovars from Oregon Coastal Environments

Water, sediment, and shellfish from three Oregon estuaries were cultured for pathogenic Vibrio species. Non-O1 serovars of V. cholerae were the most common pathogenic Vibrio species recovered. Non-O1 V. cholerae were isolated from all three estuaries sampled, covering an area of about 170 miles along the Oregon coast. Non-O1 V. cholerae were isolated from water and sediment, but not shellfish, at temperatures ranging from 11 to 19°C and salinities of 2.3 to 26‰. Sixteen isolates representing 12 different non-O1 serovars were identified, while four non-O1 V. cholerae isolates failed to react with any of the 54 antisera tested. These results indicate that non-O1 V. cholerae serovars can be found over a large geographic area and under a variety of environmental conditions. These organisms are apparently an autochthonous component of these estuarine microbial communities.