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

Publisher Summary The degree of match and mismatch in the time of larval production and production of their food has been put forward as an explanation of part of the variability in recruitment to a stock of fish. The magnitude of recruitment is not completely determined until the year-class finally joins the adult stock, and the processes involved probably begin early in the life-history of the fish when both their growth and mortality rates are high. The match/mismatch hypothesis is given in this chapter to cover the subsequent development through larval life up to metamorphosis, and possibly just beyond. The match/mismatch hypothesis has now been extended to the upwelling areas and oceanic divergences equatorward of 40° latitude on the basis that fish in these regions release batches of eggs more frequently when they are well fed and, more generally, that pelagic fish may modify their reproductive strategies such that they can feed and spawn at the same time. A delay in predation is of great importance, particularly when production peaks in early development. This model illustrates the difficulties that occur when growth and mortality are allowed to interact. On the other hand, there are three consequences of the match/mismatch hypothesis that are presented in this chapter. However, the limited conclusion drawn in this chapter is that, investigations of fish larvae should continue to be a part of the study of population dynamics of fishes.

Plankton Production and Year-class Strength in Fish Populations: an Update of the Match/Mismatch Hypothesis

Introduction.- Data management and software.- Advice for teachers.- Exploration.- Linear regression.- Generalised linear modelling.- Additive and generalised additive modelling.- Introduction to mixed modelling.- Univariate tree models.- Measures of association.- Ordination--first encounter.- Principal component analysis and redundancy analysis.- Correspondence analysis and canonical correspondence analysis.- Introduction to discriminant analysis.- Principal coordinate analysis and non-metric multidimensional scaling.- Time series analysis--Introduction.- Common trends and sudden changes.- Analysis and modelling lattice data.- Spatially continuous data analysis and modelling.- Univariate methods to analyse abundance of decapod larvae.- Analysing presence and absence data for flatfish distribution in the Tagus estuary, Portugual.- Crop pollination by honeybees in an Argentinean pampas system using additive mixed modelling.- Investigating the effects of rice farming on aquatic birds with mixed modelling.- Classification trees and radar detection of birds for North Sea wind farms.- Fish stock identification through neural network analysis of parasite fauna.- Monitoring for change: using generalised least squares, nonmetric multidimensional scaling, and the Mantel test on western Montana grasslands.- Univariate and multivariate analysis applied on a Dutch sandy beach community.- Multivariate analyses of South-American zoobenthic species--spoilt for choice.- Principal component analysis applied to harbour porpoise fatty acid data.- Multivariate analysis of morphometric turtle data--size and shape.- Redundancy analysis and additive modelling applied on savanna tree data.- Canonical correspondence analysis of lowland pasture vegetation in the humid tropics of Mexico.- Estimating common trends in Portuguese fisheries landings.- Common trends in demersal communities on the Newfoundland-Labrador Shelf.- Sea level change and salt marshes in the Wadden Sea: a time series analysis.- Time series analysis of Hawaiian waterbirds.- Spatial modelling of forest community features in the Volzhsko-Kamsky reserve.

Analysing Ecological Data

We estimate the global rate of biogenic silica production in the ocean to be between 200 and 280 × 1012 mol Si yr−1. The upper limit is derived from information on the primary productivity of the oceans, the relative contribution of diatoms to primary production and diatom Si/C ratios. The lower limit is derived independently using a multi-compartment model of nutrient transport and biogenic particle flux, and field data on the balance between silica production and dissolution in the upper ocean. Our upper limit is 30–50% lower than several previous estimates, due to new data indicating lower values for both the relative contribution of diatoms to primary productivity and their Si/C ratios. Globally, at least 50% of the silica produced by diatoms in the euphotic zone dissolves in the upper 100 m, resulting in an estimated export of 100–140 × 1012 mol Si yr−l to the deep ocean. Our estimates correspond to a global mean rate of biogenic silica production between 0.6 and 0.8 mol Si m−2 yr−1. Incubation experiments indicate that silica production rates exceed that mean by a factor of 3–12 in coastal areas and are 2–4 times less than the global average in the oligotrophic mid-ocean gyres. The mean silica production rate in waters overlying diatomaceous sediments (approximately 10–12% of the surface area of the oceans) is 0.7–1.2 mol Si m−2 yr−1. That rate is only slightly higher than the global average, indicating that the silica produced in those regions is only 10–25% of the global total. The estimated production of biogenic silica in surface waters of the mid-ocean gyres is approximately equal to that for all major areas of opal sediment accumulation combined. Regional comparison of silica production and accumulation rates suggests a strongly bimodal character in the efficiency of opal preservation in the sea. In waters overlying diatom-rich sediments 15–25% of the silica produced in the surface layer accumulates in the seabed, while virtually none of the silica produced in other areas is preserved. The global burial/production ratio of ˜ 3% is a composite of those two very different systems. The mechanisms leading to more efficient opal preservation in regions of silica accumulation are presently unknown, but they have no simple relationship to primary productivity. Regional differences in opal preservation appear to be controlled by factors such as low surface temperature, selective grazing and aggregate formation, which diminish the rate of silica dissolution in surface waters and/or accelerate its transport to the seafloor.

Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation

Variations in sea-surface temperatures over the past 500,000 years are inferred from the relative abundance behaviour of two organic compounds, C37 alkenones over the upper 8 metres of a sediment core from the eastern equatorial Atlantic. This molecular record, ascribed to contributions from prymnesiophyte algae, correlates well with the variations in the δ18 signal for the calcareous skeletons of certain planktonic foraminifera, thus providing the first demonstration of a new stratigraphical technique, which may be especially valuable where methods based on carbonate δ18 fail.

A. J. Southward

Papers

Plankton and Productivity in the Oceans