We have applied “whole-genome shotgun sequencing” to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity. Microorganisms are responsible for most of the biogeochemical cycles that shape the environment of Earth and its oceans. Yet, these organisms are the least well understood on Earth, as the ability to study and understand the metabolic potential of microorganisms has been hampered by the inability to generate pure cultures. Recent studies have begun to explore environ

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Environmental Genome Shotgun Sequencing of the Sargasso Sea

Although algal blooms, including those considered toxic or harmful, can be natural phenomena, the nature of the global problem of harmful algal blooms (HABs) has expanded both in extent and its public perception over the last several decades. Of concern, especially for resource managers, is the potential relationship between HABs and the accelerated eutrophication of coastal waters from human activities. We address current insights into the relationships between HABs and eutrophication, focusing on sources of nutrients, known effects of nutrient loading and reduction, new understanding of pathways of nutrient acquisition among HAB species, and relationships between nutrients and toxic algae. Through specific, regional, and global examples of these various relationships, we offer both an assessment of the state of understanding, and the uncertainties that require future research efforts. The sources of nutrients poten- tially stimulating algal blooms include sewage, atmospheric deposition, groundwater flow, as well as agricultural and aquaculture runoff and discharge. On a global basis, strong correlations have been demonstrated between total phos- phorus inputs and phytoplankton production in freshwaters, and between total nitrogen input and phytoplankton pro- duction in estuarine and marine waters. There are also numerous examples in geographic regions ranging from the largest and second largest U.S. mainland estuaries (Chesapeake Bay and the Albemarle-Pamlico Estuarine System), to the Inland Sea of Japan, the Black Sea, and Chinese coastal waters, where increases in nutrient loading have been linked with the development of large biomass blooms, leading to anoxia and even toxic or harmful impacts on fisheries re- sources, ecosystems, and human health or recreation. Many of these regions have witnessed reductions in phytoplankton biomass (as chlorophyll a) or HAB incidence when nutrient controls were put in place. Shifts in species composition have often been attributed to changes in nutrient supply ratios, primarily N:P or N:Si. Recently this concept has been extended to include organic forms of nutrients, and an elevation in the ratio of dissolved organic carbon to dissolved organic nitrogen (DOC:DON) has been observed during several recent blooms. The physiological strategies by which different groups of species acquire their nutrients have become better understood, and alternate modes of nutrition such as heterotrophy and mixotrophy are now recognized as common among HAB species. Despite our increased un- derstanding of the pathways by which nutrients are delivered to ecosystems and the pathways by which they are assimilated differentially by different groups of species, the relationships between nutrient delivery and the development of blooms and their potential toxicity or harmfulness remain poorly understood. Many factors such as algal species presence/ abundance, degree of flushing or water exchange, weather conditions, and presence and abundance of grazers contribute to the success of a given species at a given point in time. Similar nutrient loads do not have the same impact in different environments or in the same environment at different points in time. Eutrophication is one of several mechanisms by which harmful algae appear to be increasing in extent and duration in many locations. Although important, it is not the only explanation for blooms or toxic outbreaks. Nutrient enrichment has been strongly linked to stimulation of some harmful species, but for others it has not been an apparent contributing factor. The overall effect of nutrient over- enrichment on harmful algal species is clearly species specific.

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Harmful Algal Blooms and Eutrophication: Nutrient Sources, Composition, and Consequences

Our increasing knowledge of the geochemical processes of present-day sedimentation conditions provides a basis for evaluating the role of oxic and anoxic sedimentary environments. In particular, there are organic geochemical parameters, such as lipid composition, sulphur and organic pigments, which link Recent sediments with their geologically older counterparts, and these may therefore be used to assign the depositional palaeoenvironments of ancient sediments and petroleums.

Organic geochemical indicators of palaeoenvironmental conditions of sedimentation

The aim of the present study is to review and tentatively to interpret the optical behavior of oceanic case I waters, those waters for which phytoplankton and their derivative play a predominant role in determining their optical properties. Chlorophyll-like pigment concentration is used as the index to quantify the algal material (living and detrital), and statistical relationships between this index and the depth of the euphotic layer, the spectral values of the attenuation coefficient for downwelling irradiance, or the scattering coefficient are investigated. On the basis of these statistical relationships a pigment-dependent optical model is developed. It allows the propagation of the visible radiant energy within the ocean or the backscattered radiation from the upper layer to be predicted as a function of the local phytoplanktonic content. Other geophysical or geochemical applications are derived which concern the heating rate due to penetrating visible radiations or the rate of energy storage due to photosynthesis. The nonlinear trends observed in the algal biomass-attenuation relationships are analyzed by (1) considering the rather regular change of the living-to-detrital organic carbon ratio which seems to occur in oceanic waters ranging from oligotrophic to eutrophic, and (2) accounting for the respective contributions of absorption (by pigmented cells) and of scattering (by all kind of particulates) in the attenuation process of radiant energy.

https://hal.archives-ouvertes.fr/hal-03277765/document

Optical modeling of the upper ocean in relation to its biogenous matter content (case I waters)

A nonlinear inverse method is applied to nutrient data upon approximately 20 neutral surfaces in each of the South Atlantic, Indian, and Pacific basins, between 400 and 4000 m depth By accounting for the gradients in nutrients due to the mixing of [open quotes]preformed[close quotes] concentrations of the major water masses, the nutrient changes due to biological activity are examined, and the time-mean, basin-wide Redfield ratios calculated It is found that the P/N/C[sub org]/[sup O][sub 2] ratios of nutrient regeneration between 400 and 4000 m (corrected for the effect of denitrification) are approximately constant with depth and basin, at a value of 1/16[+-]1/117[+-]14/170[+-]10 These ratios agree with those of fresh organic matter, suggesting that the flux of organic material to the deep ocean may be dominated by fast-sinking matter produced by sporadic, high-productivity events Sedimentary denitrification reduces the N/P utilization ratio to 12 [+-] 2 between 1000 and 3000 m In the Indian and Pacific basins the C[sub org]/C[sub inorg] regeneration ratio decreases from approximately 7 [+-] 13 at 400 m to 3 [+-] 1 at 1000 m and to 1 [+-] 05 at 4000 m, suggesting a significant amount of calcium carbonate dissolution above the calcite lysoclines in themore » Indian and Pacific oceans 74 refs, 8 figs, 3 tabs« less

Redfield ratios of remineralization determined by nutrient data analysis

Biological oceanographic processes / , Biological oceanographic processes / , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

Biological oceanographic processes

The use of stable isotope of carbon, 13C, for the determination of the photosynthetic rate of a marine phytoplankton population was examined. Particular concern was paid to the effects of non-phytoplanktonic organic carbon and the enrichment of inorganic carbon on the estimation of the photosynthetic rate. Photosynthetic rates determined by the 13C method showed a remarkable agreement with those determined by the 14C method. Insitu determinations of photosynthetic rate were made in three different water types: open ocean, coastal and neritic waters, which included oligo- and mesotrophic waters, by using the 13C method established.

Measurement of photosynthetic production of a marine phytoplankton population using a stable 13C isotope

In a subtropical Hawaiian ecosystem, phytoplanton size structure analyses (November–December, 1980) showed that ultraplankton (>3μm), nanoplankton (>20μm) and netplankton (>20μm) accounted for ca. 80, 98, and 2% of total chlorophyll standing stock, respectively, on the basis of chlorophyll. Similar trends were evident, for other biomass indices (e.g. cell numbers, total cell volume, ATP, particulate organic carbon, particulate organic nitrogen). The ultraplankton fraction consisted primarily of small flagellates (1 to 3 μm diam) and coccoid cells (≊1 μm diam); the 3 to 20 μm fraction was represented by dinoflagellates, coccolithophores, diatoms, and chrysophytes; and the netplankton fraction consisted principally of dinoflagellates and centric diatoms. Community photosynthesis had a size distribution similar to that of biomass. Sinking rates for the 3 μm, 3 to 20 μm, and >20 μm fractions averaged 0.0, 0.09, and 0.29m d−1, respectively. The absence of measurable sinking rates for the ultraplankton, together with the relative abundance of biomass in this fraction, result in very small phytoplankton losses due to sinking in such subtropical surface waters.

Size structure of phytoplankton biomass and photosynthesis in subtropical Hawaiian waters

The role of photosynthetic sulfur bacteria as primary producers in stagnant lakes having hydrogen sulfide is described. Photosynthetic bacteria normally appear at the boundary layer of the oxidative and reductive zones, where H2S is present and the light intensity is lower than 10% of the surface value. The water of this layer was milky green or pink due to dense populations of Thiorhodaceae or Chlorobacteriaceae. The amount of photosynthetic bacterial biomass measured on a chlorophyll basis ranged from 100 to 828 mg/m3 for Chl-650, 60.7 to 79.5 mg/m3 for Chl-660, and 19.8 to 186 mg/m3 for BChl in the growing period from July to October.

In the lakes studied, organic matter was produced by phytoplankton in the epilimnion and mainly by photosynthetic sulfur bacteria in the reducing zone. The organic matter synthesized by these bacteria ranged from 9 to 25% of the total annual production in lakes rich in H2S and from about 3 to 5% in lakes poor in it.

https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1968.13.4.0644

Vertical distribution and organic matter production of photosynthetic sulfur bacteria in japanese lakes

A distinctive chlorophyll maximum was detected around 60-m depth in the western North Pacific Ocean and the South China Sea, and almost 55% of the total chlorophyll in the entire water column was found within 50 m around the subsurface chlorophyll maximum (SCM) layer. More than 70% of the chlorophyll was contained in picoplankton which passed through a 3-μm Nuclepore but retained on 0.22-μm Millipore filters at the SCM as well as the surface layers. By transmission electron microscopic observations, the picoplankton were identified as aChlorella-like coccoid green alga having a section size of 1.2 to 1.5 μm and cyanobacteria of 0.5 to 2 μm. No obvious difference in these two dominant groups was observed in the SCM and the surface samples except in numerous and heavily stacked thylakoids in the former samples.

Masayuki Takahashi

Papers

Biological oceanographic processes

Measurement of photosynthetic production of a marine phytoplankton population using a stable 13C isotope

Size structure of phytoplankton biomass and photosynthesis in subtropical Hawaiian waters

Vertical distribution and organic matter production of photosynthetic sulfur bacteria in japanese lakes

Abundance of picophytoplankton in the subsurface chlorophyll maximum layer in subtropical and tropical waters