Groundwater contribution to the nutrient budget of Tomales Bay, California

Tomales Bay, a graben structure along the San Andreas Fault, was selected for modeling ecosystem nutrient dynamics because of its linear, one-dimensional morphology and relatively pristine state. Groundwater is a potentially important term in the nutrient budget. The geologic complexities created by the San Anreas Fault, however, complicate the hydrogeology and require the area to be subdivided into three regions: granite to the west, Franciscan Formation to the east, and alluvial fill in the trough. Nutrient concentrations in the groundwater were determined through extensive well sampling; groundwater discharge was estimated using both Darcy's Law calculations and a soil moisture budget. Results indicate that groundwater discharge is of the same order of magnitude as summer streamflow into the Bay, while being significantly less than other freshwater inputs in winter. Dissolved nutrient (phosphate, nitrate + nitrite, ammonium, silica and DIC) concentrations in groundwater were consistently higher (by as much as an order of magnitude) than in surface water discharges. During the summer months, groundwater flow contributes about as much nutrient load to the bay as does streamflow. During the winter, the groundwater contribution to nutrient loading is about 20% of the streamflow contribution. Our findings indicate that groundwater is a significant component of terrestrial nutrient and freshwater loading to Tomales Bay, particularly so during the summer months. However, neither groundwater nor streamflow nutrient fluxes are large in comparison to the mixing flux at the bay mouth or the flux of N₂ gas across the air-water interface.     

Tidal marsh restoration stimulates the growth of winter shorebird populations in a temperate estuary

The regional responses of winter shorebird populations in the nearly 3,000 ha estuary of Tomales Bay, California, to the restoration of 223 ha of historic tidal wetlands were evaluated for 27 years: 19 years prior to tidal reintroduction and 8 years after tidal reintroduction. We used interrupted time series analyses to measure the spatial extent of the restoration effect and to model the magnitude and length of time associated with the gradual, restoration‐induced growth of winter shorebird populations in the bay. Expanded, regional benefits of the restoration were revealed by consistent patterns of winter shorebird population growth. Eight years after tidal reintroduction, overall shorebird abundances in southern Tomales Bay nearly tripled in response to the restoration. Substantial winter population growth by most species in southern Tomales Bay was evident within 3 years after tidal reintroduction, and maximum responses to the restoration were estimated to be predominantly achieved within 8 years. In contrast to strong effects of tidal marsh restoration on winter shorebird populations in southern Tomales Bay, no significant overall responses were exhibited by shorebirds in the northern portion of the bay, although marginal evidence of expanded effects on a few species in northern Tomales Bay were suggested. The results illustrate the importance of accounting for restoration effects beyond the spatial and temporal boundaries of the restored habitat, to consider both the potentially expanded benefits and the spatial limits of those benefits to regional wildlife populations.     

Sulfate reduction and sediment metabolism in Tomales Bay,California

Sulfate reduction rates (SRR) in subtidal sediments of Tomales Bay, California, were variable by sediment type, season and depth. Higher rates were measured in near-surface muds during summer (up to 45 nmol cm^-3 h^-1), with lower rates in sandy sediments, in winter and deeper in the sediment. Calculations of annual, average SRR throughout the upper 20 cm of muddy subtidal sediments (about 30 mmol S m^-2 d^-1) were much larger than previously reported net estimates of SRR derived from both benthic alkalinity flux measurements and bay wide, budget stoichiometry (3.5 and 2.6 mmol m^-2 d^-1, respectively), indicating that most reduced sulfur in these upper, well-mixed sediments is re-oxidized. A portion of the net alkalinity flux across the sediment surface may be derived from sulfate reduction in deeper sediments, estimated from sulfate depletion profiles at 1.5 mmol m^-2 d^-1. A small net flux of CO₂ measured in benthic chambers despite a large SRR suggests that sediment sinks for CO₂ must also exist (e.g., benthic microalgae).     

Nutrient couplings between on-site sewage disposal systems,groundwaters, and nearshore surface waters of the Florida Keys

We performed a one-year study to determine the effects of on-site sewage disposal systems (OSDS, septic tanks) on the nutrient relations of limestone groundwaters and nearshore surface waters of the Florida Keys. Monitor wells were installed on canal residences with OSDS and a control site in the Key Deer National Wildlife Refuge on Big Pine Key. Groundwater and surface water samples were collected monthly during 1987 and analyzed for concentrations of dissolved inorganic nitrogen (DIN = NO_f3/sup- + NO_f2/sup- + NH_4/su+), soluble reactive phosphate (SRP), temperature and salinity. Significant nutrient enrichment (up to 5000-fold) occurred in groundwaters contiguous to OSDS; DIN was enriched an average of 400-fold and SRP some 70-fold compared to control groundwaters. Ammonium was the dominant nitrogenous species and its concentration ranged from a low of 0.77 μM in control wells to 2.75 mM in OSDS-enriched groundwaters. Concentrations of nitrate plus nitrite were also highly enriched and ranged from 0.05 μM in control wells to 2.89 mM in enriched groundwaters. Relative to DIN, concentrations of SRP were low and ranged from 30 nM in control wells to 107 μM in enriched groundwaters. N : P ratios of enriched groundwaters were consistently > 100 and increased with increasing distance from the OSDS, suggesting significant, but incomplete, adsorption of SRP by subsurface flow through carbonate substrata. Nutrient concentrations of groundwaters also varied seasonally and were approximately two-fold higher during the winter (DIN = 1035 μM; SRP = 10.3 μM) compared to summer (DIN = 470 μM; SRP = 4.0 μM). In contrast, surface water nutrient concentrations were two-fold higher during the summer (DIN = 5.0 μM; SRP = 0.50 μM) compared to winter (DIN = 2.5 μM; SRP = 0.15 μM). Direct measurement of subsurface groundwater flow rate indicated that tides and increased groundwater recharge enhanced flow some two-fold and six-fold, respectively. Accordingly, the observed seasonal coupling of OSDS-derived nutrients from groundwaters to surface waters is maximum during summer because of seasonally maximum tides and increased hydraulic head during the summer wet season. The yearly average benthic flux of anthropogenic DIN into contiguous canal surface waters is 55 mmol m^-2 day^-1, a value some five-fold greater than the highest rate of benthic N-fixation measured in carbonate-rich tropical marine waters.     

The Influence of Environmental Variables on the Distribution and Abundance of Three Elasmobranchs in Tomales Bay, California

We tested the hypothesis that temperature, salinity, and dissolved oxygen affect elasmobranch distribution and abundance in Tomales Bay, California, with monthly longline samples over a 20 month period. We used a Poisson regression under generalized least squares and found that temperature and salinity were the most important factors determining the distribution and abundance of the three most common elasmobranch species, bat ray, Myliobatis californica, leopard shark, Triakis semifasciata, and brown smoothhound shark, Mustelis henlei. Females of all three species were more abundant than males throughout the Bay, and were most abundant in the warmer, more saline inner bay. All three species apparently left Tomales Bay in late fall as water temperatures in the bay decreased to <10–12° C, and returned in early spring after temperatures increased to > 10° C. Three of 257 bat rays tagged in Tomales Bay were recaptured, all within 1km of their tagging location despite having been free for up to 583d.     

Biological tags for stock separation in Pacific herring Clupea harengus pallasi in California.

A survey of the parasites of Pacific herring (Clupea harengus pallasi) off northern California identified 1 species of Acanthocephala, 1 species of Cestoda, 2 species of Copepoda, 1 species and 1 family of Digenea, 3 species of Nematoda, and 3 species of Protozoa. From this survey, Lacistorhynchus dollfusi (Cestoda), Parahemiurus merus (Digenea), and Anisakis simplex, Contracaecum sp., Hysterothylacium sp. (Nematoda) were selected as potential tags. Herring were collected in Tomales, San Francisco, and Monterey bays for the following 9 yr and examined for these select parasites. The results suggest that these parasites can be used to distinguish the spawning stocks of San Francisco and Tomales bays. The distribution of the definitive hosts of the respective parasites suggests that the Tomales Bay fish are offshore during the nonbreeding season and the San Francisco Bay fish onshore. The similarity in parasitism between San Francisco Bay and the nonspawning population in Monterey Bay suggests that these 2 populations represent a single stock.     

Time scales and mechanisms of estuarine variability,a synthesis from studies of San Francisco Bay

This review of the preceding papers suggests that temporal variability in San Francisco Bay can be characterized by four time scales (hours, days-weeks, months, years) and associated with at least four mechanisms (variations in freshwater inflow, tides, wind, and exchange with coastal waters). The best understood component of temporal variability is the annual cycle, which is most obviously influenced by seasonal variations in freshwater inflow. The winter season of high river discharge is characterized by: large-scale redistribution of the salinity field (e.g. the upper estuary becomes a riverine system); enhanced density stratification and gravitational circulation with shortened residence times in the bay; decreased tissue concentrations of some contaminants (e.g. copper) in resident bivalves; increased estuarine inputs of river-borne materials such as dissolved inorganic nutrients (N, P, Si), suspended sediments, and humic materials; radical redistributions of pelagic organisms such as copepods and fish; low phutoplankton biomass and primary productivity in the upper estuary; and elimination of freshwater-intolerant species of macroalgae and benthic infauna from the upper estuary. Other mechanisms modulate this river-driven annual cycle: (1) wind speed is highly seasonal (strongest in summer) and causes seasonal variations in atmosphere-water column exchange of dissolved gases, resuspension, and the texture of surficial sediments; (2) seasonal variations in the coastal ocean (e.g. the spring-summer upwelling season) influence species composition of plankton and nutrient concentrations that are advected into the bay; and (3) the annual temperature cycle influences a few selected features (e.g. production and hatching of copepod resting eggs). Much of the interannual variability in San Francisco Bay is also correlated with freshwater inflow: wet years with persistently high river discharge are characterized by persistent winter-type conditions.Mechanisms of short-term variability are not as well understood, although some responses to storm events (pulses in residual currents from wind forcing, erosion of surficial sediments by wind waves, redistribution of fish populations) and the neap-spring tidal cycle (enhanced salinity stratification, gravitational circulation, and phytoplankton biomass during neap tides) have been quantified. In addition to these somewhat predictable features of variability are (1) largely unexplained episodic events (e.g. anomalous blooms of drift macroalgae), and (2) long-term trends directly attributable to human activities (e.g. introduction of exotic species that become permanent members of the biota).     

Distribution and abundance of fishes in the San Francisco Bay estuary between 1980 and 1982

In 1980 a long-term study of the fishery resources of the San Francisco Bay estuary was initiated in an effort to delineate the importance of freshwater inflow to fish and invertebrate abundance and distribution in the bay. An analysis of the trawl data collected between January 1980 and December 1982 illustrates the influence of the timing and magnitude of freshwater inflows on fish fistribution and abundance in this estuary from the perspective of monthly, seasonal and annual time scales. Normally found in the delta, Suisun Bay and San Pablo Bay during periods of increased salinity, pelagic species moved downstream after the two peak flows studied, while demersal species usually found in Central San Francisco Bay moved upstream. Such upstream movements may be due in part to transport by strong density-driven currents.Timing and magnitude of monthly catches of some species varied on a seasonal cycle coincident with variations of freshwater inflow. Most species, especially the marine species, showed no consistent cycle of monthly catches. In the wet years of 1980 and 1982 the distributions of freshwater, estuarine and anadromous species were extended downstream into San Pablo, Central and South San Francisco Bays and some marine species, including the flatfish, were more abundant in the upstream areas. In the dry year of 1981 when bay salinities were higher, few marine species extended their distributions upstream into San Pablo and Suisun Bays. Jacksmelt was the only fish of the 15 most abundant species with its peak abundance in 1981. Most marine species were more abundant in the San Francisco Bay estuary in the wet years.     

Swimming against the flow—Environmental DNA can detect bull sharks (Carcharhinus leucas) across a dynamic deltaic interface

Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly disparate systems. As upper trophic level predators, bull sharks (Carcharhinus leucas) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama, suggest that bull sharks extensively use the northern portions of the bay, an estuarine–freshwater interface known as the Mobile‐Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 × 1 L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile‐Tensaw Delta, and ten sites throughout the Mobile‐Tombigbee and Tensaw‐Alabama Rivers. Water samples were vacuum‐filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species‐specific primers and an internal probe to amplify a 237‐base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less‐urbanized, riverine habitats up to 120 km upriver during Alabama''s dry summer season.     

Diel Movements of Bat Rays, Myliobatis californica, in Tomales Bay, California: Evidence for Behavioral Thermoregulation?

We used ultrasonic telemetry to examine movement patterns of 11 bat rays, Myliobatis californica, in Tomales Bay, California. Tomales Bay is long (20km) and narrow (1.4km), and is hydrographically separated into outer and inner bay regions. The outer bay (the outermost 8km) is characterized by oceanic conditions while the shallow inner bay (the innermost 12km) features wide seasonal temperature shifts. Five rays were tracked monthly from October 1990 to November 1991 and six rays (four of which carried temperature-sensing transmitters) were tracked daily from 30 June to 16 July 1992. Mean bat ray movement rate was 8.84mmin^–1 (range 4.49 to 13.40mmin^–1) and was not significantly affected by size (p=0.592), tidal stage (p=0.610), or time of day (p=0.327). Movement direction was unrelated to tidal stage (p=0.472) but showed a highly significant diel pattern (p<0.001). From 2:50–14:50h, rays moved toward the warmer and shallower inner bay, while from 14:50–2:50h they moved toward the cooler and deeper outer bay. These telemetry data, along with known bat ray foraging patterns and respiratory temperature-sensitivity, argue for behavioral thermoregulation as the primary influence on this movement pattern.     

Genetic and historical evidence disagree on likely sources of the Atlantic amethyst gem clam Gemma gemma (Totten, 1834) in California

Aim Historical information about source populations of invasive species is often limited; therefore, genetic analyses are used. We compared inference about source populations from historical and genetic data for the oyster‐associated clam, Gemma gemma that invaded California from the USA Atlantic coast. Location Mid‐Atlantic (North Carolina, Maryland), Northeastern (New Jersey, New York, Massachusetts) and the California coasts (Elkhorn Slough, San Francisco Bay, Bolinas Lagoon, Tomales Bay, Bodega Harbor). Methods The documented history of transplantation of Eastern oysters to California was reviewed. Cytochrome c oxidase subunit I (COI) sequences from recent and archived clams were examined in a haplotype network. We used AMOVA to detect geographic genetic structure and a permutation test for significant reductions in diversity. Results Chesapeake Bay oysters were transplanted to New York prior to shipment to San Francisco Bay and from there to peripheral bays. Gemma in the Northeastern and Mid‐Atlantic regions were genetically differentiated. In California, populations in Bodega Harbor and Tomales Bay were genetically similar to those in the Mid‐Atlantic area while clams in San Francisco Bay, Elkhorn Slough and Bolinas Lagoon resembled populations in the Northeastern region. In California, genetic variation was not highest in San Francisco Bay despite greater magnitude of oyster plantings. Haplotypes varied over time in native and introduced populations. Main Conclusions Historical records and inferences from genetics agree that both Northeastern and Mid‐Atlantic regions were sources for Gemma in California. Only complex genetic hypotheses reconcile the strong segregation of haplotypes in California to the historical evidence of mixing in their proximate source (New York). These hypotheses include sorting of mixtures of haplotypes or selection in non‐native areas. Haplotype turnover in San Francisco and Massachusetts samples over time suggests that the sorting hypothesis is plausible. We suggest, however, that Gemma was introduced independently and recently to Tomales Bay and Bodega Harbor.     

Time scales of circulation and mixing processes of San Francisco Bay waters

Conceptual models for tidal period and low-frequency variations in sea level, currents, and mixing processes in the northern and southern reaches of San Francisco Bay describe the contrasting characteristics and dissimilar processes and rates in these embayments: The northern reach is a partially mixed estuary whereas the southern reach (South Bay) is a tidally oscillating lagoon with density-driven exchanges with the northern reach.The mixed semidiurnal tides are mixtures of progressive and standing waves. The relatively simple oscillations in South Bay are nearly standing waves, with energy propagating down the channels and dispersing into the broad shoal areas. The tides of the northern reach have the general properties of a progressive wave but are altered at the constriction of the embayments and gradually change in an upstream direction to a mixture of progressive and standing waves. The spring and neap variations of the tides are pronounced and cause fortnightly varying tidal currents that affect mixing and salinity stratification in the water column.Wind stress on the water surface, freshwater inflow, and tidal currents interacting with the complex bay configuration are the major local forcing mechanisms creating low-frequency variations in sea level and currents. These local forcing mechanisms drive the residual flows which, with tidal diffusion, control the water-replacement rates in the estuary. In the northern reach, the longitudinal density gradient drives an estuarine circulation in the channels, and the spatial variation in tidal amplitude creates a tidally-driven residual circulation. In contrast, South Bay exhibits a balance between wind-driven circulation and tidally-driven residual circulation for most of the year. During winter, however, there can be sufficient density variations to drive multilayer (2 to 3) flows in the channel of South Bay.Mixing models (that include both diffusive and dispersive processes) are based on time scales associated with salt variations at the boundaries and those associated with the local forcing mechanisms, while the spatial scales of variations are dependent upon the configuration of the embayments. In the northern reach, where the estuarine circulation is strong, the salt flux is carried by the mean advection of the mean salt field. Where large salinity gradients are present, the tidal correlation part of the salt flux is of the same order as the advective part. Our knowledge of mixing and exchange rates in South Bay is poor. As this embayment is nearly isohaline, the salt flux is dominated entirely by the mean advection of the mean salt field. During and after peaks in river discharge, water mixing becomes more dynamic, with a strong density-driven current creating a net exchange of both water mass and salt. These exchanges are stronger during neap tides.Residence times of the water masses vary seasonally and differ between reaches. In the northern reach, residence times are on the order of days for high winter river discharge and of months for summer periods. The residence times for South Bay are fairly long (on the order of several months) during summer, and typically shorter (less than a month) during winter when density-driven exchanges occur.     

Stable carbon and nitrogen isotopes in multiple tissues of wild and captive harbor seals (Phoca vitulina) off the California coast

Stable carbon and nitrogen isotope ratios (δ¹³C and δ¹⁵N) of serum, red blood cells (RBC), muscle, and blubber were measured in captive and wild northeast Pacific harbor seals (Phoca vitulina richardii) at three coastal California sites (San Francisco Bay, Tomales Bay, and Channel Islands). Trophic discrimination factors (Δ_{Tissue‐Diet}) were calculated for captive seals and then applied in wild counterparts in each habitat to estimate trophic position and feeding behavior. Trophic discrimination factors for δ¹⁵N of serum (+3.8‰), lipid‐extracted muscle (+1.6‰), and lipid‐blubber (+6.5‰) are proposed to determine trophic position. An offset between RBC and serum of +0.3‰ for δ¹³C and ?0.6‰ for δ¹⁵N was observed, which is consistent with previous research. Specifically, weaner seals (<1 yr) had large offsets, suggesting strong trophic position shifts during this life stage. Isotopic values indicated an average trophic position of 3.6 at both San Francisco Bay and Tomales Bay and 4.2 at Channel Islands. Isotopic means were strongly dependent on age class and also suggested that mean diet composition varies considerably between all locations. Together, these data indicate that isotopic composition of blood fractions can be an effective approach to estimate trophic position and dietary behavior in wild pinnipeds.     

Interannual variability in dissolved inorganic nutrients in northern San Francisco Bay estuary

Nearly two decades of seasonal dissolved inorganic nutrient-salinity distributions in northern San Francisco Bay estuary (1960–1980) illustrate interannual variations in effects of river flow (a nutrient source) and phytoplankton productivity (a nutrient sink). During winter, nutrient sources dominate the nutrient-salinity distribution patterns (nutrients are at or exceed conservative mixing concentrations). During summer, however, the sources and sinks are in close competition. In summers of wet years, the effects of increased river flow often dominate the nutrient distributions (nutrients are at or less than conservative mixing concentrations), whereas in summers of dry years, phytoplankton productivity dominates (the very dry years 1976–1977 were an exception for reasons not yet clearly known). Such source/sink effects also vary with chemical species. During summer the control of phytoplankton on nutrient distributions is apparently strongest for ammonium, less so for nitrate and silica, and is the least for phosphate. Furthermore, the strength of the silica sink (diatom productivity) is at a maximum at intermediate river flows. This relation, which is in agreement with other studies based on phytoplankton abundance and enumeration, is significant to the extent that diatoms are an important food source for herbivores.The balance or lack of balance between nutrient sources and sinks varies from one estuary to another just as it can from one year to another within the same estuary. At one extreme, in some estuaries river flow dominates the estuarine dissolved inorganic nutrient distributions throughout most of the year. At the other extreme, phytoplankton productivity dominates. In northern San Francisco Bay, for example, the phytoplankton nutrient sink is not as strong as in less turbid estuaries. In this estuary, however, river effects, which produce or are associated with near-conservative nutrient distributions, are strong even at flows less than mean-annual flow. Thus, northern San Francisco Bay appears to be an estuary in between the two extremes and is shifted closer to one extreme or the other depending on interannual variations in river flow.     

Seasonal and interannual variation in distribution and population abundance of the shrimp Crangon franciscorum in San Francisco Bay

Shrimp are an important component of the San Francisco Bay biota, both as predators on benthic fauna, and as a food source for predatory fish. Of three common species in the bay, Crangon franciscorum is the most abundant. The bay is predominantly a nursery area for maturing shrimp of this species. During the main reproductive period in the early spring, ovigerous females and planktonic larvae are in most years centered outside the bay in the nearshore ocean, although both are also present in the bay. Juveniles move into both the southern reach and the northern reach shortly after settling, and landward-flowing bottom currents are possibly instrumental in this migration. The seasonal cycle of shrimp abundance in the bay, dominated by this spring immigration of newly settled juveniles, is characterized by a progressive migration of the growing shrimp up the estuary coincident with upstream penetration of higher salinity water during summer. Differences in abundance and distribution between the years 1980, 1981, and 1982 suggest that the level of river discharge and accompanying salinity regime are important controlling factors in the distribution, recruitment levels, and subsequent survival and growth of C. franciscorum in the San Francisco Bay.     

Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments.

The phylogenetic compositions of bacterioplankton assemblages from San Francisco Bay and Tomales Bay, Calif., differed substantially when analyzed by PCR-denaturing gradient gel electrophoresis; these differences are consistent with the results of previous studies demonstrating differences in their metabolic capabilities. PCR-denaturing gradient gel electrophoresis analysis of complex microbial assemblages was sensitive and reliable, and the results were reproducible as shown by experiments with constructed and naturally occurring assemblages.     

Population structure of the South American Estuarine crab, Chasmagnathus granulatus (Brachyura: Varunidae) near the southern limit of its geographical distribution: comparison with northern populations

Crabs are among the most conspicuous and ecologically important invertebrates of the large intertidal zones that characterize estuarine and protected coastal areas in temperate regions. The habitat, population structure and breeding cycle of Chasmagnathus granulatus (Brachyura: Varunidae), a semiterrestrial burrowing crab endemic to the warm temperate coasts of the Southwestern Atlantic, were studied in San Antonio Bay (Argentina), near the southern limit of its range. San Antonio Bay has no freshwater input, winter is relatively colder, and summer warmer, than northern habitats of this species. Crabs lived both in vegetated and unvegetated zones, but density and sex ratio varied among dates and zones. The maximum observed density was 136 crabs/m² , the maximum carapace width (CW) was 32 mm (males) and 29.8 mm (females), ovigerous females were found only in November and January, and the smallest ovigerous female measured 17 mm CW. The population structure, spatial distribution, and recruitment pattern of C. granulatusdid not differ between San Antonio Bay and northern habitats. The higher density, smaller maximum size and shorter reproductive cycle observed in San Antonio cannot be atributed to changes associated with a latitudinal cline and other factors, such as thermal amplitude and food availability, need to be studied.     

Changes in Sediment Bacterial Community in Response to Long-Term Nutrient Enrichment in a Subtropical Seagrass-Dominated Estuary

Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m² plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.     

Environmental setting of San Francisco Bay

San Francisco Bay, the largest bay on the California coast, is a broad, shallow, turbid estuary comprising two geographically and hydrologically distinct subestuaries: the northern reach lying between the connection to the Pacific Ocean at the Golden Gate and the confluence of the Sacramento-San Joaquin River system, and the southern reach (herein called South Bay) between the Golden Gate and the southern terminus of the bay. The northern reach is a partially mixed estuary dominated by seasonally varying river inflow, and the South Bay is a tidally oscillating lagoon-type estuary. Freshwater inflows, highest during winter, generate strong estuarine circulation and largely determine water residence times. They also bring large volumes of dissolved and particulate materials to the estuary. Tidal currents, generated by mixed semidiurnal and diurnal tides, mix the water column and, together with river inflow and basin geometry, determine circulation patterns. Winds, which are strongest during summer and during winter storms, exert stress on the bay's water surface, thereby creating large waves that resuspend sediment from the shallow bay bottom and, together with the tidal currents, contribute markedly to the transport of water masses throughout the shallow estuary.     

Distinct patterns of marine bacterial communities in the South and North Pacific Oceans

The study of oceanic microbial communities is crucial for our understanding of the role of microbes in terms of biomass, diversity and ecosystem function. In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively. Summer and winter sampling from each water mass revealed highly diverse bacterial communities, containing ~900 Operational Taxonomic Units (OTUs). The microbial distribution and highly heterogeneous composition observed at both sampling sites were different from those of most macroorganisms. The bacterial communities in the seawater at both sites were most abundant in Proteobacteria during the summer in Gosung and in Bacterioidetes during the winter. The proportion of Cyanobacteria was higher in summer than in winter in Chuuk and similar in Gosung. Additionally, the microbial community during summer in Gosung was significantly different from other communities observed based on the unweighted UniFrac distance. These data suggest that in both oceanic areas sampled, the bacterial communities had distinct distribution patterns with spatially- and temporally-heterogeneous distributions.