Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans

Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.     

The Mechanisms of Coexistence and Competitive Exclusion in Complex Plankton Ecosystem Models

The biodiversity of plankton ecosystems may no longer be a paradox, but the mechanisms that determine coexistence of explicit competitors in ecosystems remain a mystery. This is particularly so in ecosystem models, where competitive exclusion remains the dominant process. Climate and fisheries models require plankton ecosystem sub-models that maintain competing plankton functional types extant, but coexistence can be reproduced in only a few ‘just so’ theoretical models. This limits our ability to predict the impacts of climate change and fisheries on ocean biota. We consider ecosystems of Kolmogorov form that conserve mass (CK systems). These systems describe a general class of ecosystem models that includes many theoretical and applied models. We develop heuristics that illuminate the key mechanisms that allow the coexistence of explicit competitors in these systems. These heuristics facilitate the identification of a large class of models with the structural property that all species coexist for all time. Our approach unifies many theoretical and applied models in a common biogeochemical framework, providing a powerful tool with the potential to generate new insights into the properties of complex ecosystems.     

Early Cambrian origin of modern food webs: evidence from predator arrow worms

Although palaeontological evidence from exceptional biota demonstrates the existence of diverse marine communities in the Early Cambrian (approx. 540-520 Myr ago), little is known concerning the functioning of the marine ecosystem, especially its trophic structure and the full range of ecological niches colonized by the fauna. The presence of a diverse zooplankton in Early Cambrian oceans is still an open issue. Here we provide compelling evidence that chaetognaths, an important element of modern zooplankton, were present in the Early Cambrian Chengjiang biota with morphologies almost identical to Recent forms. New information obtained from the lowermost Cambrian of China added to previous studies provide convincing evidence that protoconodont-bearing animals also belonged to chaetognaths. Chaetognaths were probably widespread and diverse in the earliest Cambrian. The obvious raptorial function of their circumoral apparatuses (grasping spines) places them among the earliest active predator metazoans. Morphology, body ratios and distribution suggest that the ancestral chaetognaths were planktonic with possible ecological preferences for hyperbenthic niches close to the sea bottom. Our results point to the early introduction of prey-predator relationships into the pelagic realm, and to the increase of trophic complexity (three-level structure) during the Precambrian-Cambrian transition, thus laying the foundations of present-day marine food chains.     

全球气候变化下的海洋浮游植物多样性

理解全球气候变化对地球生态系统的影响是全世界广泛关注的问题, 而相比于陆地生态系统, 海洋生态系统对全球气候变化更为敏感。全球气候变化对海洋的影响主要表现在海洋暖化、海洋酸化、大洋环流系统的改变、海平面上升、紫外线辐射增强等方面。浮游植物是海洋生态系统最重要的初级生产者, 同时对海洋碳循环起到举足轻重的作用, 其对全球气候变化的响应主要体现在物种分布、初级生产力、群落演替、生物气候学等方面。具体表现在以下方面: 暖水种的分布范围在扩大, 冷水种分布范围在缩小; 浮游植物全球初级生产力降低; 浮游植物群落会向细胞体积更小的物种占优势的方向转变; 浮游植物水华发生的时间提前、强度增强; 一些有害物种水华的发生频率也会增加; 海洋表层海水的酸化会影响浮游植物特别是钙化类群的生长和群落多样性; 紫外辐射增强对浮游植物的生长起到抑制作用; 厄尔尼诺、拉尼娜、降水量的增加通常抑制浮游植物生长。浮游植物生长和分布的变化会体现在多样性的各个层面上。对于浮游植物在全球变化各种驱动因子下的生理生态学和长周期变动观测等是今后研究的重要方向, 也将为理解全球变化下的浮游植物-多样性-生态系统响应与反馈机制提供基本信息。     

High evolutionary potential of marine zooplankton

Open ocean zooplankton often have been viewed as slowly evolving species that have limited capacity to respond adaptively to changing ocean conditions. Hence, attention has focused on the ecological responses of zooplankton to current global change, including range shifts and changing phenology. Here, we argue that zooplankton also are well poised for evolutionary responses to global change. We present theoretical arguments that suggest plankton species may respond rapidly to selection on mildly beneficial mutations due to exceptionally large population size, and consider the circumstantial evidence that supports our inference that selection may be particularly important for these species. We also review all primary population genetic studies of open ocean zooplankton and show that genetic isolation can be achieved at the scale of gyre systems in open ocean habitats (100s to 1000s of km). Furthermore, population genetic structure often varies across planktonic taxa, and appears to be linked to the particular ecological requirements of the organism. In combination, these characteristics should facilitate adaptive evolution to distinct oceanographic habitats in the plankton. We conclude that marine zooplankton may be capable of rapid evolutionary as well as ecological responses to changing ocean conditions, and discuss the implications of this view. We further suggest two priority areas for future research to test our hypothesis of high evolutionary potential in open ocean zooplankton, which will require (1) assessing how pervasive selection is in driving population divergence and (2) rigorously quantifying the spatial and temporal scales of population differentiation in the open ocean.     

Accommodating dynamic oceanographic processes and pelagic biodiversity in marine conservation planning

Pelagic ecosystems support a significant and vital component of the ocean's productivity and biodiversity. They are also heavily exploited and, as a result, are the focus of numerous spatial planning initiatives. Over the past decade, there has been increasing enthusiasm for protected areas as a tool for pelagic conservation, however, few have been implemented. Here we demonstrate an approach to plan protected areas that address the physical and biological dynamics typical of the pelagic realm. Specifically, we provide an example of an approach to planning protected areas that integrates pelagic and benthic conservation in the southern Benguela and Agulhas Bank ecosystems off South Africa. Our aim was to represent species of importance to fisheries and species of conservation concern within protected areas. In addition to representation, we ensured that protected areas were designed to consider pelagic dynamics, characterized from time-series data on key oceanographic processes, together with data on the abundance of small pelagic fishes. We found that, to have the highest likelihood of reaching conservation targets, protected area selection should be based on time-specific data rather than data averaged across time. More generally, we argue that innovative methods are needed to conserve ephemeral and dynamic pelagic biodiversity.     

Lack of Congruence in Species Diversity Indices and Community Structures of Planktonic Groups Based on Local Environmental Factors

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups–zooplankton, rotifers, ciliates, and phytoplankton–under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.     

Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems

Background

Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems.

Methodology/Principal Findings

The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean''s surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities.

Conclusions/Significance

This first synthesis of global bacterial distribution across different ecosystems of the World''s oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.     

Effects of macroalgal species identity and richness on primary production in benthic marine communities

Plant biodiversity can enhance primary production in terrestrial ecosystems, but biodiversity effects are largely unstudied in the ocean. We conducted a series of field and mesocosm experiments to measure the relative effects of macroalgal identity and richness on primary productivity (net photosynthetic rate) and biomass accumulation in hard substratum subtidal communities in North Carolina, USA. Algal identity consistently and strongly affected production; species richness effects, although often significent, were subtle. Partitioning of the net biodiversity effect indicated that complementarity effects were always positive and species were usually more productive in mixtures than in monoculture. Surprisingly, slow growing species performed relatively better in the most diverse treatments than the most productive species, thus selection effects were consistently negative. Our results suggest that several basic mechanisms underlying terrestrial plant biodiversity effects also operate in algal-based marine ecosystems, and thus may be general.     

The impact of marine nutrient abundance on early eukaryotic ecosystems

The rise of eukaryotes to ecological prominence represents one of the most dramatic shifts in the history of Earth's biosphere. However, there is an enigmatic temporal lag between the emergence of eukaryotic organisms in the fossil record and their much later ecological expansion. In parallel, there is evidence for a secular increase in the availability of the key macronutrient phosphorus (P) in Earth's oceans. Here, we use an Earth system model equipped with a size‐structured marine ecosystem to explore relationships between plankton size, trophic complexity, and the availability of marine nutrients. We find a strong dependence of planktonic ecosystem structure on ocean nutrient abundance, with a larger ocean nutrient inventory leading to greater overall biomass, broader size spectra, and increasing abundance of large Zooplankton. If existing estimates of Proterozoic marine nutrient levels are correct, our results suggest that increases in the ecological impact of eukaryotic algae and trophic complexity in eukaryotic ecosystems were directly linked to restructuring of the global P cycle associated with the protracted rise of surface oxygen levels. Our results thus suggest an indirect but potentially important mechanism by which ocean oxygenation may have acted to shape marine ecological function during late Proterozoic time.     

Antarctic terrestrial biodiversity in a changing world

Recent analyses of Antarctic terrestrial biodiversity data, in combination with molecular biological studies, have created a new paradigm that long-term persistence and regional isolation are general features of most of the major groups of Antarctic terrestrial biota, overturning the previously widely assumed view of a generally recent colonisation history. This paradigm, as well as incorporating a new and much longer timescale in which to consider the evolution and adaptation of Antarctic terrestrial biota, opens important new cross-disciplinary linkages with geologists and glaciologists seeking to unravel the history of the continent itself. This unique biota now faces the twin challenges of responding to the complex processes of climate change facing some parts of the continent, and the direct impacts associated with human occupation and activity. In many instances, this biota is likely to benefit, initially at least, from the current environmental changes, and there is an expectation of increased production, biomass, population size, community complexity, and colonisation. However, the impacts of climate change may themselves be outweighed by other, direct, impacts of human activities, and in particular, the introduction of non-indigenous organisms from which until recently the terrestrial ecosystems of the continent have been protected. The Antarctic research community and those responsible for governance under the Antarctic treaty system are faced with the pressing challenges of (1) ensuring there is sufficient baseline monitoring and survey activity to enable identification of these changes, however caused and (2) ensuring that effective operational management and biosecurity procedures are in place to minimise the threat from anthropogenic activities.     

Component elements of the carbon cycle in the middle and lower Yenisei River

An integrated study of the middle and lower Yenisei River was performed in the summer of 2012. It involved monitoring the key elements and ecological processes associated with the carbon cycle of the river ecosystem (the study area is more than 1800 km long). Measurements of the production and destruction processes have shown the failure of the “neutral pipe” hypothesis claiming that any river is a simple drain of carbon from terrestrial ecosystems to the ocean. The Yenisei River is not a purely heterotrophic ecosystem. It also has autotrophic areas, where the primary production of planktonic photosynthesis is higher than respiration (above the Angara River and near the Bolshaya and Malaya Heta rivers). According to the data, the respiration rate of the plankton community in the river depends mostly on the water temperature and the content of inorganic phosphorous that can restrict the amount of organic matter consumed by bacterioplankton.     

Diversity of urea‐degrading microorganisms in open‐ocean and estuarine planktonic communities

Urea is an important and dynamic natural component of marine nitrogen cycling and also a major contributor to anthropogenic eutrophication of coastal ecosystems, yet little is known about the identities or diversity of ureolytic marine microorganisms. Primers targeting the gene encoding urease were used to PCR‐amplify, clone and sequence 709 urease gene fragments from 31 plankton samples collected at both estuarine and open‐ocean locations. Two hundred and eighty‐six amplicons belonged to 22 distinct sequence types that were closely enough related to named organisms to be identified, and included urease sequences both from typical marine planktonic organisms and from bacteria usually associated with terrestrial habitats. The remaining 423 amplicons were not closely enough related to named organisms to be identified, and belonged to 96 distinct sequence types of which 43 types were found in two or more different samples. The distributions of unidentified urease sequence types suggested that some represented truly marine microorganisms while others reflected terrestrial inputs to low‐salinity estuarine areas. The urease primers revealed this great diversity of ureolytic organisms because they were able to amplify many previously unknown, environmentally relevant urease genes, and they will support new approaches for exploring the role of urea in marine ecosystems.     

Correlation of space-time ranges in ecological hierarchies of various nature

Relations between characteristic scales of time and space are analyzed for the hierarchical systems of a various nature. The available data fit well to the power relation: [T] = a[L]b, where [T] and [L] are characteristic ranges of time and space, b--scaling exponent, a--conversion coefficient. The spatio-temporal scales of ocean physical and biological (pelagic) processes are closely overlapped. Contrastingly, the scale for terrestrial and benthic ecosystems and their environments differ noticeably. For terrestrial and benthic ecological systems, and also for atmospheric phenomena, the b values significantly less than 1, that indicates a significant coherence of structure-generating processes integrating lower-level hierarchical units to a higher-level entity. For geomorphological structures, both terrestrial and oceanic, the scaling parameters has appeared close to 1 (a "direct transfer" type of generating processes). For plankton systems, which are related with water masses, the b values vary from 1 (processes of direct transfer) up to 2 (random dispersal or diffusion processes). The author attributes this difference to the principle distinctions in dynamic properties of the physical environments for terrestrial (and probably, benthic) and plankton organisms. Finally, for the units (structures or processes) of one and the same organization level, scaling exponents are significantly higher and close to 2 (diffusive dynamics) or more (rigid spatial limitation). Thus, the development of many ecological structures looks dynamically like diffusion or gradual growth, but their putting in the higher-level order (integrity) is a qualitative leap forward and demands appropriate cooperative organizational processes.     

Marine Biodiversity in Japanese Waters

To understand marine biodiversity in Japanese waters, we have compiled information on the marine biota in Japanese waters, including the number of described species (species richness), the history of marine biology research in Japan, the state of knowledge, the number of endemic species, the number of identified but undescribed species, the number of known introduced species, and the number of taxonomic experts and identification guides, with consideration of the general ocean environmental background, such as the physical and geological settings. A total of 33,629 species have been reported to occur in Japanese waters. The state of knowledge was extremely variable, with taxa containing many inconspicuous, smaller species tending to be less well known. The total number of identified but undescribed species was at least 121,913. The total number of described species combined with the number of identified but undescribed species reached 155,542. This is the best estimate of the total number of species in Japanese waters and indicates that more than 70% of Japan''s marine biodiversity remains un-described. The number of species reported as introduced into Japanese waters was 39. This is the first attempt to estimate species richness for all marine species in Japanese waters. Although its marine biota can be considered relatively well known, at least within the Asian-Pacific region, considering the vast number of different marine environments such as coral reefs, ocean trenches, ice-bound waters, methane seeps, and hydrothermal vents, much work remains to be done. We expect global change to have a tremendous impact on marine biodiversity and ecosystems. Japan is in a particularly suitable geographic situation and has a lot of facilities for conducting marine science research. Japan has an important responsibility to contribute to our understanding of life in the oceans.     

The co-evolution of phytoplankton and trace element cycles in the oceans

The composition of the oceans and of its biota have influenced each other through Earth's history. Of all the biologically essential elements, nitrogen is the only one whose seawater concentration is clearly controlled biologically; this is presumably the main reason why the stoichiometry of nitrogen (defined as its mol ratio to phosphorus), but not that of the trace nutrients manganese, iron, cobalt, nickel, copper, zinc and cadmium, is the same in seawater and in the plankton. Like the major nutrients, the trace nutrients are depleted in surface seawater as a result of quasi-complete utilization by the biota. This is made possible in part by the ability of marine phytoplankton to replace one trace metal by another in various biochemical functions. This replacement also results in an equalization of the availability of most essential trace metals in surface seawater. The difference in the stoichiometric composition of the plankton and of deep seawater, which is the dominant source of new nutrients to the surface, indicates that some nutrients are likely recycled with different efficiencies in the photic zone. The difference in the composition of the ocean and its biota provides insight into the coupling of biochemistry and biogeochemistry in seawater.     

Investigating uncertainties in zooplankton composition shifts under climate change scenarios in the Mediterranean Sea

Ensemble niche modelling has become a common framework to predict changes in assemblages composition under climate change scenarios. The amount of uncertainty generated by the different components of this framework has rarely been assessed. In the marine realm forecasts have usually focused on taxa representing the top of the marine food‐web, thus overlooking their basal component: the plankton. Calibrating environmental niche models at the global scale, we modelled the habitat suitability of 106 copepod species and estimated the dissimilarity between present and future zooplanktonic assemblages in the surface Mediterranean Sea. We identified the patterns (species replacement versus nestedness) driving the predicted dissimilarity, and quantified the relative contributions of different uncertainty sources: environmental niche models, greenhouse gas emission scenarios, circulation model configurations and species prevalence. Our results confirm that the choice of the niche modelling method is the greatest source of uncertainty in habitat suitability projections. Presence‐only and presence–absence methods provided different visions of the niches, which subsequently lead to different future scenarios of biodiversity changes. Nestedness with decline in species richness is the pattern driving dissimilarity between present and future copepod assemblages. Our projections contrast with those reported for higher trophic levels, suggesting that different components of the pelagic food‐web may respond discordantly to future climatic changes.     

Can we detect oceanic biodiversity hotspots from space?

Understanding the variability of marine biodiversity is a central issue in microbiology. Current observational programs are based on in situ studies, but their implementation at the global scale is particularly challenging, owing to the ocean extent, its temporal variability and the heterogeneity of the data sources on which compilations are built. Here, we explore the possibility of identifying phytoplanktonic biodiversity hotspots from satellite. We define a Shannon entropy index based on patchiness in ocean color bio-optical anomalies. This index provides a high resolution (1 degree) global coverage. It shows a relation to temperature and mid-latitude maxima in accordance with those previously evidenced in microbiological biodiversity model and observational studies. Regional maxima are in remarkable agreement with several known biodiversity hotspots for plankton organisms and even for higher levels of the marine trophic chain, as well as with some in situ planktonic biodiversity estimates (from Atlantic Meridional Transect cruise). These results encourage to explore marine biodiversity with a coordinated effort of the molecular, ecological and remote sensing communities.     

Effects of expected global climate change on marine faunas

Anthropogenically induced global climate change is likely to have a major impact on marine ecosystems, affecting both biodiversity and productivity. These changes will, in turn, have a large impact on humankind's interactions with the sea. By examining the effects of past climate changes on the ocean, as well as by determining how shifts in physical parameters of the ocean may affect physiology, biochemistry and community interactions, scientists are beginning to explore the possible effects of global climate change on marine biota.     

Are indicator groups and cross-taxon congruence useful for predicting biodiversity in aquatic ecosystems?

Resources for biodiversity surveys and conservation planning are limited, and conservation biologists and environmental managers are thus striving to find suitable surrogates for mapping and predicting biodiversity. Among popular surrogates are indicator groups that could be used for predicting variation in the biodiversity of other taxonomic groups. Despite some success at large scales, surveys of multiple taxonomic groups across ecosystems have suggested that no single group can be used effectively to predict variation in the biodiversity of other taxonomic groups. This paper concentrates on indicator groups and cross-taxon congruence in species richness and assemblage composition patterns in inland aquatic ecosystems. As has been found in studies of terrestrial ecosystems, there is low utility for indicator groups in predicting the biodiversity of other taxa in aquatic ecosystems. Even when statistically highly significant correlations between taxonomic groups have been detected, these correlations have been too weak to provide reliable predictions of biodiversity among various taxonomic groups or biodiversity in general. Indicator groups and, more generally, cross-taxon congruence thus do not appear to be particularly relevant for conservation in the freshwater realm.