The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary.

Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000s and their rise has coincided with substantial decreases in several important fish species. Direct and indirect effects Microcystis blooms may have on the Delta food web were investigated. The Microcystis population was tracked for 2 years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including 6 different microcystin-producing strains. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin and piricyclamide. A sizable reduction was observed in microbial community diversity during a large Microcystis bloom (H' = 0.61) relative to periods preceding (H' = 2.32) or following (H' = 3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period. The elevated abundance of a cyanomyophage with high similarity to previously sequenced isolates known to infect Microcystis sp. was implicated in the bloom's collapse. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis.

HO2 formation from the photoexcitation of benzene/O2 mixtures at 248 nm: an energy dependence study.

The energy dependence of HO(2) radical formation from the irradiation of benzene (C(6)H(6)) in the presence of oxygen (O(2)) at 248 nm is studied. We investigate the origin of the HO(2) radicals, that is, whether they originate from the reaction of O(2) with products obtained by one- or two-photon excitation of C(6)H(6). The concentration-time profiles of HO(2) radicals are monitored by continuous-wave cavity ring-down spectroscopy (cw-CRDS) coupled to a laser photolysis reactor. HO(2) radicals are detected in the first vibrational overtone of the OH stretch at 6638.20 cm(-1), using a distributed feedback (DFB) diode laser. Two well-distinguished HO(2) radical-formation phases are observed: a fast initial formation of HO(2) radicals followed by a slower secondary formation. While the concentration of the initially formed HO(2) species increases linearly with the excitation energy, the concentration of the secondary slow HO(2) radicals appears to vary in accordance with a two-photon process.

Microbial Mats of the McMurdo Dry Valleys, Antarctica: Oases of Biological Activity in a Very Cold Desert.

Cyanobacterial mats in the Antarctic Dry Valleys are photosynthetic microbial ecosystems living at the extreme of conditions on Earth with respect to temperature, light, water and nutrient availability. They are metabolically active for about 8 weeks during the austral summer when temperatures briefly rise above freezing and glacial and lake melt waters are available. There is much to learn about the biogeochemical impact of mats in these environments and the microbial communities associated with them. Our data demonstrate that these mats attain surprisingly high rates of carbon (CO2) and dinitrogen (N2) fixation when liquid water is available, in some cases comparable to rates in warmer temperate or tropical environments. C and N2 fixation in Dry Valley mats in turn substantially elevate dissolved organic C and inorganic N pools and thereby promote enhanced microbial secondary production. Moreover, the microbial community fingerprint of these mats is unique compared with the more ubiquitous dry soils that do not contain mats. Components of the heterotrophic microbiota may also contribute substantially to N inputs through N2 fixation.

Spatial variability of phytoplankton in a shallow tidal freshwater system reveals complex controls on abundance and community structure.

Estuaries worldwide are undergoing changes to patterns of aquatic productivity because of human activities that alter flow, impact sediment delivery and thus the light field, and contribute nutrients and contaminants like pesticides and metals. These changes can influence phytoplankton communities, which in turn can alter estuarine food webs. We used multiple approaches-including high-resolution water quality mapping, synoptic sampling, productivity and nitrogen uptake rates, Lagrangian parcel tracking, enclosure experiments and bottle incubations-over a short time period to take a "spatial snapshot" of conditions in the northern region of the San Francisco Estuary (California, USA) to examine how environmental drivers like light availability, nutrients, water residence time, and contaminants affect phytoplankton abundance and community attributes like size distribution, taxonomic structure, and nutrient uptake rates. Zones characterized by longer residence time (15-60 days) had higher chlorophyll-a concentrations (9 ±â€¯4 µg L-1) and were comprised primarily of small phytoplankton cells (<5 µm, 74 ±â€¯8%), lower ammonium concentrations (1 ±â€¯0.8 µM), higher nitrate uptake rates, and higher rates of potential carbon productivity. Conversely, zones characterized by shorter residence time (1-14 days) had higher ammonium concentration (13 ±â€¯5 µM) and lower chlorophyll-a concentration (5 ±â€¯1 µg L-1) with diatoms making up a larger percent contribution. Longer residence time, however, did not result in the accumulation of large (>5 µm) cells considered important to pelagic food webs. Rather, longer residence time zones had a phytoplankton community comprised primarily of small cells, particularly picocyanobacteria that made up 38 ±â€¯17% of the chlorophyll-a - nearly double the concentration seen in shorter residence time zones (22 ±â€¯7% picocyanobacterial of chlorophyll-a). Our results suggest that water residence time in estuaries may have an effect as large or larger than that experimentally demonstrated for light, contaminants, or nutrients.

The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica.

The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.

Microbial community composition of transiently wetted Antarctic Dry Valley soils.

During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 µg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary.

Primary production in the Northern San Francisco Estuary (SFE) has been declining despite heavy loading of anthropogenic nutrients. The inorganic nitrogen (N) loading comes primarily from municipal wastewater treatment plant (WTP) discharge as ammonium (NH(4)). This study investigated the consequences for river and estuarine phytoplankton of the daily discharge of 15 metric tons NH(4)-N into the Sacramento River that feeds the SFE. Consistent patterns of nutrients and phytoplankton responses were observed during two 150-km transects made in spring 2009. Phytoplankton N productivity shifted from NO(3) use upstream of the WTP to productivity based entirely upon NH(4) downstream. Phytoplankton NH(4) uptake declined downstream of the WTP as NH(4) concentrations increased, suggesting NH(4) inhibition. The reduced total N uptake downstream of the WTP was accompanied by a 60% decline in primary production. These findings indicate that increased anthropogenic NH(4) may decrease estuarine primary production and increase export of NH(4) to the coastal ocean.

Microcontroller based resonance tracking unit for time resolved continuous wave cavity-ringdown spectroscopy measurements.

We present in this work a new tracking servoloop electronics for continuous wave cavity-ringdown absorption spectroscopy (cw-CRDS) and its application to time resolved cw-CRDS measurements by coupling the system with a pulsed laser photolysis set-up. The tracking unit significantly increases the repetition rate of the CRDS events and thus improves effective time resolution (and/or the signal-to-noise ratio) in kinetics studies with cw-CRDS in given data acquisition time. The tracking servoloop uses novel strategy to track the cavity resonances that result in a fast relocking (few ms) after the loss of tracking due to an external disturbance. The microcontroller based design is highly flexible and thus advanced tracking strategies are easy to implement by the firmware modification without the need to modify the hardware. We believe that the performance of many existing cw-CRDS experiments, not only time-resolved, can be improved with such tracking unit without any additional modification to the experiment.