David M. Karl

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

The worlds oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

VERTEX: carbon cycling in the northeast Pacific

Abstract Particulate organic carbon fluxes were measured with free-floating particle traps at nine locations during VERTEX and related studies. Examination of these data indicated that there was relatively little spatial variability in open ocean fluxes. To obtain mean rates representative of the oligotrophic environment, flux data from six stations were combined and fitted to a normalized power function, F = F 100 ( z /100) b ; e.g. the open ocean composite C flux in mol m −2 y −1 = 1.53 ( z /100 −0.858 with depth z in meters. It is shown that the vertical derivative of particulate fluxes may indicate solute regeneration rates, and accordingly regeneration rates for C, H and N were estimated. Oxygen utilization rates were also estimated under the assumption that 1.5, 1.0 and 0.25 moles of O 2 were used for each mole of N, C and H regenerated. Regeneration ratios of these elements were depth-dependent: i.e. N:C:H:−O 2 = 1.0 N: 6.2 ( z /100) 0.130 C: 10.0( z /100) 0.146 H: [1.5 + 6.2 ( z /100) 0.130 + 2.5 ( z /100) 0.146 ]− O 2 . Comparisons of our rates with those in the literature indicate that trap-derived new productivities in the open Pacific (≈1.5 mol C m −2 y −1 ) are substantially less than those estimated from oxygen utilization rates in the Sargasso Sea (≈4 mol C m −2 y −1 ). A hypothesis is presented which attempts to explain this discrepancy on the basis of the lateral transport and decomposition of slow or non-sinking POC in the Sargasso Sea. Data gathered during the VERTEX studies are also used for various global estimates. Open ocean primary productivities are estimated at 130 g C m −2 y −1 which results in a global open ocean productivity of 42 Gt y −1 . Organic C removal from the surface of the ocean via particulate sinking (new production) is on the order of 6 Gt y −1 . Fifty percent of this C is regenerated in the upper 300 m of the water column. The ratio of new production (measured with traps) to total primary production (measured via 14 C) is 0.14. It is concluded that the 14 C technique yields reasonable estimates of primary productivity provided that care is taken to prevent heavy metal contamination.

The role of nitrogen fixation in biogeochemical cycling in the subtropical North Pacific Ocean

Seven years of time-series observations of biogeochemical processes in the subtropical North Pacific Ocean gyre have revealed dramatic changes in the microbial community structure and in the mechanisms of nutrient cycling in response to large-scale ocean–atmosphere interactions. Several independent lines of evidence show that the fixation of atmospheric nitrogen by cyanobacteria can fuel up to half of the new production. These and other observations demand a reassessment of present views of nutrient and carbon cycling in one of the Earth′s largest biomes.

Dinitrogen fixation in the world's oceans

The surface water of themarine environment has traditionally beenviewed as a nitrogen (N) limited habitat, andthis has guided the development of conceptualbiogeochemical models focusing largely on thereservoir of nitrate as the critical source ofN to sustain primary productivity. However,selected groups of Bacteria, includingcyanobacteria, and Archaea canutilize dinitrogen (N2) as an alternativeN source. In the marine environment, thesemicroorganisms can have profound effects on netcommunity production processes and can impactthe coupling of C-N-P cycles as well as the netoceanic sequestration of atmospheric carbondioxide. As one component of an integrated ‘Nitrogen Transport and Transformations’ project, we have begun to re-assess ourunderstanding of (1) the biotic sources andrates of N2 fixation in the worldsoceans, (2) the major controls on rates ofoceanic N2 fixation, (3) the significanceof this N2 fixation for the global carboncycle and (4) the role of human activities inthe alteration of oceanic N2 fixation. Preliminary results indicate that rates ofN2 fixation, especially in subtropical andtropical open ocean habitats, have a major rolein the global marine N budget. Iron (Fe)bioavailability appears to be an importantcontrol and is, therefore, critical inextrapolation to global rates of N2fixation. Anthropogenic perturbations mayalter N2 fixation in coastal environmentsthrough habitat destruction and eutrophication,and open ocean N2 fixation may be enhancedby warming and increased stratification of theupper water column. Global anthropogenic andclimatic changes may also affect N2fixation rates, for example by altering dustinputs (i.e. Fe) or by expansion ofsubtropical boundaries. Some recent estimatesof global ocean N2 fixation are in therange of 100–200 Tg N (1–2 × 1014 g N)yr−1, but have large uncertainties. Theseestimates are nearly an order of magnitudegreater than historical, pre-1980 estimates,but approach modern estimates of oceanicdenitrification.

Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity

Phosphorus is an obligate requirement for the growth of all organisms; major biochemical reservoirs of phosphorus in marine plankton include nucleic acids and phospholipids. However, eukaryotic phytoplankton and cyanobacteria (that is, ‘phytoplankton’ collectively) have the ability to decrease their cellular phosphorus content when phosphorus in their environment is scarce. The biochemical mechanisms that allow phytoplankton to limit their phosphorus demand and still maintain growth are largely unknown. Here we show that phytoplankton, in regions of oligotrophic ocean where phosphate is scarce, reduce their cellular phosphorus requirements by substituting non-phosphorus membrane lipids for phospholipids. In the Sargasso Sea, where phosphate concentrations were less than 10 nmol l-1, we found that only 1.3 ± 0.6% of phosphate uptake was used for phospholipid synthesis; in contrast, in the South Pacific subtropical gyre, where phosphate was greater than 100 nmol l-1, plankton used 17 ± 6% (ref. 6). Examination of the planktonic membrane lipids at these two locations showed that classes of sulphur- and nitrogen-containing membrane lipids, which are devoid of phosphorus, were more abundant in the Sargasso Sea than in the South Pacific. Furthermore, these non-phosphorus, ‘substitute lipids’ were dominant in phosphorus-limited cultures of all of the phytoplankton species we examined. In contrast, the marine heterotrophic bacteria we examined contained no substitute lipids and only phospholipids. Thus heterotrophic bacteria, which compete with phytoplankton for nutrients in oligotrophic regions like the Sargasso Sea, appear to have a biochemical phosphorus requirement that phytoplankton avoid by using substitute lipids. Our results suggest that phospholipid substitutions are fundamental biochemical mechanisms that allow phytoplankton to maintain growth in the face of phosphorus limitation.

The Hawaii Ocean Time-series (HOT) program: Background, rationale and field implementation

Abstract Long-term ocean observations are needed to gain a comprehensive understanding of natural habitat variability as well as global environmental change that might arise from human activities. In 1988, a multidisciplinary deep-water oceanographic station was established at a site north of Oahu, Hawaii, with the intent of establishing a long-term ( > 20 years) data base on oceanic variability. The primary objective of the Hawaii Ocean Time-series (HOT) program is to obtain high-quality time-series measurements of selected oceanographic properties, including: water mass structure, dynamic height, currents, dissolved and particulate chemical constituents, biological processes and particulate matter fluxes. These data will be used, in part, to help achieve the goals of the World Ocean Circulation Experiment (WOCE) and the Joint Global Ocean Flux Study (JGOFS) research programs. More importantly, these data sets will be used to improve our description and understanding of ocean circulation and ocean climatology, to elucidate further the processes that govern the fluxes of carbon into and from the oceans, and to generate novel hypotheses. These are necessary prerequisites for developing a predictive capability for global environmental change.

A Sea of Change: Biogeochemical Variability in the North Pacific Subtropical Gyre

ABSTRACT The North Pacific Subtropical Gyre (NPSG) is the largest ecosystem on our planet. However, this expansive habitat is also remote, poorly sampled, and therefore not well understood. For example, the most abundant oxygenic phototroph in the NPSG, Prochlorococcus, was described only a decade ago. Other novel Bacteria, Archaea and Eukarya, recently identified by nucleic acid sequence analysis, have not been isolated. In October 1988, an ocean time-series research program was established to study ecosystem processes in the gyre, including rates and pathways of carbon and energy flow, spatial and temporal scales of variability, and coupling of ocean physics to biogeochemical processes. After a decade of ecosystem surveillance, this sentinel observatory has produced an unprecedented data set and some new views of an old ocean. Foremost is evidence for dramatic changes in microbial community structure and in mechanisms of nutrient cycling in response to large-scale ocean–atmosphere interactions. These and other observations demand reassessment of current views of physical-biogeochemical processes in this and other open-ocean ecosystems.

Seasonal and interannual variability in primary production and particle flux at Station ALOHA

A 5-year time-series study of primary production and euphotic-zone particle export in the subtropical North Pacific Ocean near Hawaii (Sta. ALOHA, 22°45′N, 158°W) with measurements collected at approximately monthly intervals has revealed significant variability in both ecosystem processes. Depth-integrated (0–200 m) primary production averaged 463 mg C m−2 day−1 (s = 156, n = 54) or 14.1 mol C m−2 year−1. This mean value is greater than estimates for the North Pacific Ocean gyre made prior to 1984, but conforms to data obtained since the advent of trace metal-clean techniques. Daily rates of primary productivity at Sta. ALOHA exhibited interannual variability including a nearly 3-year sustained increase during the period 1990–1992 that coincided with a prolonged El Nifio-Southern Oscillation (ENSO) event. Export production, defined as the particulate carbon (PC) flux measured at the 150 m reference depth, also varied considerably during the initial 5 years of the ongoing field experiment. The PC flux averaged 29 mg C m−2 day−1 (s = 11, n = 43) or 0.88 mol Cm−2 year−1. A 5-fold variation between the minimum and maximum fluxes, measured in any given year, was observed. During the first 3 years of this program (1989–1991), a pattern was resolved that included two major export events per annum one centered in late winter and the other in late summer. After 1991, export production exhibited a systematic decrease with time during the prolonged ENSO event. When expressed as a percentage of the contemporaneous primary production, PC export ranged from 2 to 16.9%, with a 5-year mean of 6.7% (s = 3.3, n = 40). Contrary to existing empirical models, contemporaneous primary production and PC flux were poorly correlated, and during the ENSO period they exhibited a significant inverse correlation. This unexpected decoupling of particle production and flux has numerous implications for oceanic biogeochemical cycles and for the response of the ocean to environmental perturbations.

Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus

The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9 ± 0.1 × 1027 and 7.0 ± 0.3 × 1026 cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% for Prochlorococcus and Synechococcus, respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production of Prochlorococcus and Synechococcus, these changes may have large impacts on ocean ecosystems and biogeochemical cycles.

Long-term changes in plankton community structure and productivity in the North Pacific Subtropical Gyre : The domain shift hypothesis

Oceanic productivity, fishery yields and the net marine sequestration of atmospheric greenhouse gases are all controlled by the structure and function of planktonic communities. Detailed paleoceanographic studies have documented abrupt changes in these processes over timescales ranging from centuries to millennia. Most of these major shifts in oceanic productivity and biodiversity are attributable to changes in Earths climate, manifested through large-scale ocean–atmosphere interactions. By comparison, contemporary biodiversity and plankton community dynamics are generally considered to be “static”, in part due to the lack of a suitable time frame of reference, and the absence of oceanic data to document ecosystem change over relatively short timescales (decades to centuries). Here we show that the average concentrations of chlorophyll a (chl a) and the estimated rates of primary production in the surface waters of the North Pacific Subtropical Gyre (NPSG) off Hawaii have more than doubled while the concentrations of dissolved silicate and phosphate have decreased during the past three decades. These changes are accompanied by an increase in the concentration of chl b, suggesting a shift in phytoplankton community structure. We hypothesize that these observed ecosystem trends and other related biogeochemical processes in the upper portion of the NPSG are manifestations of plankton community succession in response to climate variations. The hypothesized photosynthetic population “domain shift” toward an ecosystem dominated by prokaryotes has altered nutrient flux pathways and affected food web structure, new and export production processes, and fishery yields. Further stratification of the surface ocean resulting from global warming could lead to even more enhanced selection pressures and additional changes in biogeochemical dynamics.