Effects of algal diversity on the production of biomass in homogeneous and heterogeneous nutrient environments: a microcosm experiment

Background

One of the most common questions addressed by ecologists over the past decade has been-how does species richness impact the production of community biomass? Recent summaries of experiments have shown that species richness tends to enhance the production of biomass across a wide range of trophic groups and ecosystems; however, the biomass of diverse polycultures only rarely exceeds that of the single most productive species in a community (a phenomenon called ‘transgressive overyielding’). Some have hypothesized that the lack of transgressive overyielding is because experiments have generally been performed in overly-simplified, homogeneous environments where species have little opportunity to express the niche differences that lead to ‘complementary’ use of resources that can enhance biomass production. We tested this hypothesis in a laboratory experiment where we manipulated the richness of freshwater algae in homogeneous and heterogeneous nutrient environments.

Methodology/Principal Findings

Experimental units were comprised of patches containing either homogeneous nutrient ratios (16∶1 nitrogen to phosphorus (N∶P) in all patches) or heterogeneous nutrient ratios (ranging from 4∶1 to 64∶1 N∶P across patches). After allowing 6–10 generations of algal growth, we found that algal species richness had similar impacts on biomass production in both homo- and heterogeneous environments. Although four of the five algal species showed a strong response to nutrient heterogeneity, a single species dominated algal communities in both types of environments. As a result, a ‘selection effect’–where diversity maximizes the chance that a competitively superior species will be included in, and dominate the biomass of a community–was the primary mechanism by which richness influenced biomass in both homo- and heterogeneous environments.

Conclusions/Significance

Our study suggests that spatial heterogeneity, by itself, is not sufficient to generate strong effects of biodiversity on productivity. Rather, heterogeneity must be coupled with variation in the relative fitness of species across patches in order for spatial niche differentiation to generate complementary resource use.     

Extremophile Microalgae: the potential for biotechnological application

Microalgae are photosynthetic microorganisms that use sunlight as an energy source, and convert water, carbon dioxide, and inorganic salts into algal biomass. The isolation and selection of microalgae, which allow one to obtain large amounts of biomass and valuable compounds, is a prerequisite for their successful industrial production. This work provides an overview of extremophile algae, where their ability to grow under harsh conditions and the corresponding accumulation of metabolites are addressed. Emphasis is placed on the high-value products of some prominent algae. Moreover, the most recent applications of these microorganisms and their potential exploitation in the context of astrobiology are taken into account.     

Massing life

Research into biomass and food chains attracts increasing attention, given the biosphere''s capacity to sequester CO₂ from the atmosphereResearch into biomass—the mass of living organisms in a given area or ecosystem—has grown steadily during the past decade. This interest has been driven mainly by the need to assess, predict and mitigate the ongoing impact of human activities on ecosystems at different scales, particularly in light of anthropogenic climate change. Scientists, and to some extend policy-makers, are increasingly interested in how organisms and whole ecosystems react to environmental changes, and in whether the biosphere can sequester some of the carbon dioxide that is the main cause of climate disruption. In addition, biomass research has gathered momentum in its own right by shedding light on the long-range interactions in marine and terrestrial food chains that underpin the global carbon cycle.It therefore seems that viruses themselves make a solid contribution to global biomass…There have been plenty of surprises, such as the recent discovery of biomass hotspots in the so-called benthic zones at the bottom of oceans, where life had been thought to be relatively sparse. Deep ocean research has also shown that viruses are crucial for the benthic ecosystem and are responsible for the turnover of the organic matter on which bacteria—and ultimately all life at depths below 1,000 m—depends (de Leo et al, 2010).The study found that viruses killed more bacteria as depths increased and that they are responsible for 80% of deaths at the very bottom. The result of this viral carnage is the release of 0.37–0.63 gigatons (Gt; 10¹⁵ g) of carbon per year—a crucial source of nutrients for bacteria in particular and deep-sea ecosystems as a whole. The authors of the paper argue that this process actually sustains a large prokaryotic biomass and allows the whole ecosystem to cope with the otherwise severe depletion of organic resources at great depths.…it was thought that plants make the largest contribution, particularly given the huge biomass locked up in trees, but prokaryotes might account for an equal amountGiven this efficiency, bacteriophages must also be more abundant at great depths than thought previously—a fact now confirmed by several studies. Parada et al (2007), for instance, found that although there was a tenfold decline for picoplankton, including bacteria, at a depth of 4,000 m—roughly the average depth of the ocean floor—viral concentrations suffered only a twofold reduction. It therefore seems that viruses themselves make a solid contribution to global biomass, although some researchers dismiss this as irrelevant as viruses are not independent living organisms. “Because viruses are not cellular, it is my opinion that they are part of the organisms they infect,” said William Whitman, head of the department of microbiology at the University of Georgia (Athens, GA, USA).Yet, William Wiebe, also from the University of Georgia, suggested that viruses must make a big contribution, especially in the oceans, because they exist at such a high density throughout a huge volume of water. In fact, a recent study estimated that phage viruses beneath the sea ice in the Arctic Ocean were around 26 times more numerous than the bacteria they infected, and weighed about 0.02–0.05 g per m³, compared with the 0.27–0.85 g of their hosts (Steward et al, 2007).Discounting viruses, however, the two main components of biomass in terms of bulk are plants and prokaryotes (Fig 1). Until a decade ago it was thought that plants make the largest contribution, particularly given the huge biomass locked up in trees, but prokaryotes might account for an equal amount. Whitman and Wiebe were two of the three authors of the first paper that made a serious attempt to weigh the world''s prokaryotes (Whitman et al, 1998). They assumed that the preponderance of the world''s prokaryotes resided in three habitats—seawater, soil, and the sediment below the surface of both land and sea—and sampled areas considered to be representative of each. By extrapolation they considered the total weight of cellular carbon in prokaryotes was 350–550 Gt, and that this represented 60–100% of the total carbon bound in plants at any one time.Open in a separate windowFigure 1The different sources of biomass.Carbon, of course, is not the only component, and biomass can be measured in different ways, sometimes within individual ecosystems; for example, fish farms could be taken as the complete total mass of all organisms in the water, but more commonly as the total dry weight after discounting water. Biomass can also be presented as a portfolio of different measurements, as some are most relevant in particular circumstances. Nitrogen content, for example, is a particularly important component of biomass in soil because its presence is essential for many plants, which lack the capability of sequestering it from the atmosphere and therefore rely on soil bacteria to fix it for them. Indeed, the contribution of prokaryotes dominates because they have a higher concentration of protein—and therefore nitrogen—than plants. The same holds true for phosphorus, which is an important constituent of nucleic acids. These are highly concentrated in bacteria, or indeed in any given cell, but plants have large intracellular spaces low in phosphorus and therefore contribute less to this measure. Whitman et al estimated that the earth''s prokaryotes accounted for 85–130 Gt of nitrogen and 9–14 Gt of phosphorus; in each case, about 10 times as much as plants.…social insects account for just 2% of all insect species, but more than half the total insect biomassIt would seem intuitive that primary producers account for the most biomass as each ‘trophic'' level relies on the one below for its carbon and other organic molecules. But this assumption ignores the role of reproduction, the rate of which has an impact on the relative mass of different trophic levels; indeed, in some aquatic and marine systems, primary producers do not account for most biomass. The calculation also takes into account the relative sizes of the primary producers and the animals that consume them. On land, herbivores tend to be smaller or comparable in size to the plants they feed on; moreover, plants metabolize and reproduce relatively slowly. In the oceans and some freshwater ecosystems, primary producers are tiny phytoplankton with high rates of metabolism and reproduction. If their total biomass were larger than the primary consumers, such as krill, shrimps and forage fish, their population would explode. The dynamics of the ecosystem have therefore led to an expansion of consumers and a decline in the number of producers to reach equilibrium. This leads to the seemingly counter-intuitive inverted pyramid, where the mass of consumers is greater than that of producers.Intuition has also been proven wrong in the case of insects, which collectively are the most successful animals both in terms of biomass and diversity. In the insect class, beetles constitute the biggest and arguably most successful order, with more than 350,000 known species—including the largest and smallest insects—colonizing almost all habitats. But in terms of biomass, they are dwarfed by ‘social'' insects—notably termites, bees, wasps and ants. Social insects have evolved the ability to live in colonies with much greater population densities than beetles, often comprising many clones of genetically identical individuals. As Edward O. Wilson, a US entomologist and conservationist, pointed out, social insects account for just 2% of all insect species, but more than half the total insect biomass (Wilson, 1990).In terms of generating biomass, sociality and community was the most successful evolutionary strategy until humans came up with an even more effective method…The evolution of sociality does not lead automatically to an increase in biomass, even if it does enhance the prospect of survival for a species through cooperation and pooling of resources. For biomass to increase, social insects need to husband resources more efficiently. Among social insects this has been accomplished through the creation of communities, which cooperate to gather food effectively from a wide area, whether this is nectar from plants or detritus from both plants and animals.…cattle continue to outweigh us in biomass, with 1.3 billion individuals scaling about 130 million tonnes…In terms of generating biomass, sociality and community was the most successful evolutionary strategy until humans came up with an even more effective method around 10,000 years ago: agriculture. At that time the human population started to increase from its previously stable level of around 1 million to between 170 million and 400 million 2,000 years ago. The next significant growth spurt came with the industrial revolution in Europe where the population doubled in both the eighteenth and nineteenth centuries. Finally, modern medicine has enabled today''s population of almost 7 billion, equating to a biomass of 100 million tonnes—far greater than other mammals, with the exception of domesticated animals, the numbers of which have increased in step with humans. Indeed, cattle continue to outweigh us in biomass, with 1.3 billion individuals scaling about 130 million tonnes and contributing to atmospheric greenhouse gas concentration by producing methane.Biomass calculations are also shedding light on another man-made impact on the environment, namely the acidification of the oceans in response to rising levels of carbon dioxide in the atmosphere. It recently became clear that fish have an important role alongside marine plankton in sequestering carbon by absorbing calcium and then re-emitting it in their faeces as various forms of carbonate. However, their contribution was not clear as the total biomass of fish was previously unknown. Now, however, two independent studies have calculated fish biomass and have produced results in the same range by using entirely different methods to overcome the difficulty of directly measuring fish populations.The first study, led by Simon Jennings from the Centre for Environment, Fisheries and Aquaculture Science in Lowestoft, UK, estimated total fish biomass at 0.9 billion tonnes (Jennings et al, 2008). The authors combined remote sensing temperature data with existing data on the underlying primary production of biomass, mostly through photosynthesis by phytoplankton. The second study, led by Rod Wilson from Exeter University in the UK, came to an estimate of two billion tonnes, based on the evaluation of fish catches, thus focusing on outputs rather than inputs of the system (Wilson et al, 2009). “Given the errors and uncertainty inherent in both methods it is impossible to say which is likely to be more accurate, but the encouraging thing is that such different approaches can yield similar results,”Jennings commented.The second study computed biomass as a first step towards assessing the role of fish in the global carbon cycle through their production of calcium carbonate. Before this, marine plankton had been thought to account for nearly all oceanic carbonate production, but according to Wilson, fish produce 3–15% as much and possibly up to 45%, depending on various assumptions.The study also indicated that, as the ocean becomes more acidic owing to anthropogenic carbon dioxide emissions, the rate of carbonate production by fish will increase. This finding led to a widely reported misconception when the study was published that fish could offset ocean acidification, when in fact the opposite could well be the case, according to Wilson.Biomass calculations are also shedding light on another man-made impact on the environment, namely the acidification of the oceans…As he pointed out, the immediate effect of producing calcium carbonate, whether by fish or plankton, is an increase rather than decrease of ocean acidity, because alkaline calcium ions are removed from the water. The ultimate impact on oceanic pH thus depends on whether that carbonate redissolves so that the calcium ions are given back, or whether it sinks to the bottom, in which case the calcium ions are in effect taken out of circulation. In the latter case, the effect on fish or plankton metabolism would be a net increase in ocean acidity. “So yes, the question becomes what is the fate of that carbonate,” Wilson said.On this point Wilson has recently made progress with the finding that the carbonate produced by fish has a high magnesium content, which makes it more soluble. This means it could be that the fish carbonate dissolves in shallower waters than does some of the carbonate produced by plankton, thus keeping acidity down at lesser depths—at higher temperatures and lower pressures the capacity of the water to dissolve calcium salts is lower. However, the overall implications are rather ambiguous as they suggest that because fish probably tend to increase ocean acidity, overfishing could be said to be a good thing. But, as Wilson rightly pointed out, doing so would have a disastrous impact on the whole marine ecosystem.Biomass research has also focused on the effects of human activities on whole land-based ecosystems and food chains. These systems are governed essentially by Liebig''s law of the minimum, which states that the one fundamental resource or nutrient that is in shortest supply in a given place determines the rate of production. This resource could be oxygen, carbon dioxide, nitrogen, water, temperature, light, or even some of the minor nutrients.…trees should be photo-synthesizing about 12% faster than two centuries ago, given the 70 ppm increase in atmospheric carbon dioxide since the industrial revolutionA major human effort in agriculture has been to increase the nitrogen content of soil by adding fertilizers, whether organic or inorganic. This boosts crop growth, but the full impact on other organisms in the soil was poorly understood until a 2006 study led by Pete Manning at Imperial College in London, UK confirmed that soil nitrogen enrichment led to a biomass increase rippling out from plants across the whole ecosystem (Manning et al, 2006). “Higher plant biomass led to greater plant litter input to the soil, leading in turn to more fungal and bacterial biomass and a higher abundance of Collembola [springtails], which are primitive insects that feed on the fungal material,” Manning said. “Similar findings have now been seen in field experiments where a greater diversity of plant species has produced a higher plant biomass, and this has translated to increases in the biomass of both microbes and soil animals.”Other ecosystems have different limiting factors constraining biomass increase in line with Liebig''s law. In forests, for example, it has been shown that the rate of growth has already increased with elevated carbon dioxide levels. Evidence from field-grown trees suggests that a 300 parts per million (ppm) increase in atmospheric carbon dioxide levels boosts the rate of photosynthesis in trees by 60% (Norby et al, 1999). If correct, trees should be photosynthesizing about 12% faster than two centuries ago, given the 70 ppm increase in atmospheric carbon dioxide since the industrial revolution.…more biomass research is also important to direct policies that aim to mitigate the damage to ecosystems and biodiversityThe accumulating results from biomass research are helping scientists to understand the complex web of interactions in the global carbon cycle and the underlying food chains, and to identify the impact of human activities. But much more needs to be done to integrate the amassing knowledge into a more detailed picture of how carbon and other elements flow in individual ecosystems and then on to the whole biosphere. In the light of ongoing anthropogenic climate change and the ever increasing concentration of greenhouse gases in the atmosphere, more biomass research is also important to direct policies that aim to mitigate the damage to ecosystems and biodiversity.     

Engineering cellulolytic ability into bioprocessing organisms

Lignocellulosic biomass is an abundant renewable feedstock for sustainable production of commodities such as biofuels. The main technological barrier that prevents widespread utilization of this resource for production of commodity products is the lack of low-cost technologies to overcome the recalcitrance of lignocellulose. Organisms that hydrolyse the cellulose and hemicelluloses in biomass and produce a valuable product such as ethanol at a high rate and titre would significantly reduce the costs of current biomass conversion technologies. This would allow steps that are currently accomplished in different reactors, often by different organisms, to be combined in a consolidated bioprocess (CBP). The development of such organisms has focused on engineering naturally cellulolytic microorganisms to improve product-related properties or engineering non-cellulolytic organisms with high product yields to become cellulolytic. The latter is the focus of this review. While there is still no ideal organism to use in one-step biomass conversion, several candidates have been identified. These candidates are in various stages of development for establishment of a cellulolytic system or improvement of product-forming attributes. This review assesses the current state of the art for enabling non-cellulolytic organisms to grow on cellulosic substrates.     

The impact of extremophiles on structural genomics (and vice versa)

The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure. Thus, in the late 1990s, an international effort known as structural genomics (SG) was initiated, its primary goal to “fill sequence-structure space” by determining the 3D structures of representatives of all known protein families. This was to be achieved mainly by X-ray crystallography and it was estimated that at least 5,000 new structures would be required. While the proteins (genes) for SG have subsequently been derived from hundreds of different organisms, extremophiles and particularly thermophiles have been specifically targeted due to the increased stability and ease of handling of their proteins, relative to those from mesophiles. This review summarizes the significant impact that extremophiles and proteins derived from them have had on SG projects worldwide. To what extent SG has influenced the field of extremophile research is also discussed.     

Bermuda grass as feedstock for biofuel production: a review

Bermuda grass is a promising feedstock for the production of fuel ethanol in the Southern United States. This paper presents a review of the significant amount of research on the conversion of Bermuda grass to ethanol and a brief discussion on the factors affecting the biomass production in the field. The biggest challenge of biomass conversion comes from the recalcitrance of lignocellulose. A variety of chemical, physico-chemical, and biological pretreatment methods have been investigated to improve the digestibility of Bermuda grass with encouraging results reported. The subsequent enzymatic hydrolysis and fermentation steps have also been extensively studied and effectively optimized. It is expected that the development of genetic engineering technologies for the grass and fermenting organisms has the potential to greatly improve the economic viability of Bermuda grass-based fuel ethanol production systems. Other energy applications of Bermuda grass include anaerobic digestion for biogas generation and pyrolysis for syngas production.     

PROCESSES OF ORGANIC PRODUCTION ON CORAL REEFS

1. The first quantitative studies of production on coral reefs were those of Sargent & Austin who showed that productivity on reefs was considerably higher than in surrounding waters. This high production occurred in spite of nutrient limitation and low productivity of offshore waters. Their conclusions have since been confirmed by numerous other workers in both the Atlantic and the Pacific. 2. Primary production on reefs has been studied by flow respirometry, measuring changes in oxygen or carbon dioxide concentrations in water flowing over reefs. Production of benthic organisms has also been measured in situ by light and dark bottle methods and by radioactive tracer techniques. Production values obtained by the various methods are not identical but their use in combination is to be recommended. 3. Rates of gross primary production on reefs vary between 300–5000 gC/m²/yr. These rates are higher than general oceanic values and as high as those of the most productive marine communities. 4. Sources of primary production include fleshy macrophytes, calcareous algae, filamentous algae on the coral skeletons or calcareous rock, marine grasses and the zooxanthellae within coral tissue. Production values from the various sources fall within the range of production of reefs as a whole. 5. Concentrations of nitrogen and phosphorus in waters flowing over reefs are consistently low. There is evidence to suggest that both these nutrients are recycled rapidly on the reef and that nitrogen is fixed by bacteria and primary producers. 6. In many instances the mass of detritus over coral reefs exceeds the biomass of zooplankton. While the quantitative significance of detritus as food for corals and other benthic organisms has not been evaluated, there is a growing body of evidence to show that this may be the key to understanding secondary production. 7. Opinions differ on the adequacy of zooplankton in satisfying the food requirements of corals and other benthic invertebrates on reefs. The weight of evidence suggests that while there is a removal of zooplankton by benthic organisms, the total biomass carried over the reef is too small to support the energy needs of secondary production. 8. Bacteria are a potential source of energy for secondary production on reefs and are implicated in nitrogen fixation, decomposition and biogeochemical cycling. 9. There is an abundance of sessile invertebrates other than corals on reefs but there are few quantitative data on their importance in secondary production. 10. The biomass of fish on reefs may be very high but the quantitative significance of grazing and predation is not fully established. 11. Studies on the growth of corals themselves have been based on measurements of skeletal accretion. These methods do not lead directly to estimates of reef organic production. Growth rates of corals vary considerably between and within species. 12. Estimates of reef growth have been made from measurements of coral growth and from the flux of calcium carbonate. There is less quantitative information on erosion caused by mechanical damage, by boring organisms and by human pollution. 13. Hydrographic factors influence growth and form of reefs and there is some evidence to show that production is enhanced by conservation of water in lagoonal areas.     

Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity. The untapped, staggering diversity of microbial organisms offers a wealth of potential resources for tackling medical, environmental, and energy challenges. Understanding microbial metabolism will be crucial to many of these potential applications. Thermodynamically-feasible metabolic reconstructions can be used, under some conditions, to predict the growth rate of certain microbes using constraint-based methods. While these reconstructions are powerful, they are still cumbersome to build and, because of the complexity of metabolic networks, it is hard for researchers to gain from these reconstructions an understanding of why a certain nutrient yields a given growth rate for a given microbe. Here, we present a simple model of biomass production that accurately reproduces the predictions of thermodynamically-feasible metabolic reconstructions. Our model makes use of only: i) a nutrient''s structure and function, ii) the presence of a small number of enzymes in the organism, and iii) the carbon flow in pathways that catabolize nutrients. When applied to test organisms, our model allows us to predict whether a nutrient can be a carbon source with an accuracy of about 90% with respect to in silico experiments. In addition, our model provides excellent predictions of whether a medium will produce more or less growth than another () and good predictions of the actual value of the in silico biomass production.     

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.     

Integrative Biological Hydrogen Production: An Overview

Biological hydrogen (H₂) production by dark and photo-fermentative organisms is a promising area of research for generating bioenergy. A large number of organisms have been widely studied for producing H₂ from diverse feeds, both as pure and as mixed cultures. However, their H₂ producing efficiencies have been found to vary (from 3 to 8 mol/mol hexose) with physiological conditions, type of organisms and composition of feed (starchy waste from sweet potato, wheat, cassava and algal biomass). The present review deals with the possibilities of enhancing H₂ production by integrating metabolic pathways of different organisms-dark fermentative bacteria (from cattle dung, activated sludge, Caldicellulosiruptor, Clostridium, Enterobacter, Lactobacillus, and Vibrio) and photo-fermentative bacteria (such as Rhodobacter, Rhodobium and Rhodopseudomonas). The emphasis has been laid on systems which are driven by undefined dark-fermentative cultures in combination with pure photo-fermentative bacterial cultures using biowaste as feed. Such an integrative approach may prove suitable for commercial applications on a large scale.     

Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation

With rising energy prices and concern over the environmental impact of fossil fuel consumption, the push to develop biomass derived fuels has increased significantly. Although most global carbon fixation occurs via the Calvin Benson Bassham cycle, there are currently five other known pathways for carbon fixation; the goal of this study was to determine the thermodynamic efficiencies of all six carbon fixation pathways for the production of biomass using flux balance analysis. The three chemotrophic pathways, the reductive acetyl-CoA pathway, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, were found to be more efficient than photoautotrophic carbon fixation pathways. However, as hydrogen is not freely available, the energetic cost of hydrogen production from sunlight was calculated and included in the overall energy demand, which results in a 5 fold increase in the energy demand of chemoautotrophic carbon fixation. Therefore, when the cost of hydrogen production is included, photoautotrophic pathways are more efficient. However, the energetic cost for the production of 12 metabolic precursors was found to vary widely across the different carbon fixation pathways; therefore, different pathways may be more efficient at producing products from a single precursor than others. The results of this study have significant impact on the selection or design of autotrophic organisms for biofuel or biochemical production. Overall biomass production from solar energy is most efficient in organisms using the reductive TCA cycle, however, products derived from one metabolic precursor may be more efficiently produced using other carbon fixation pathways.     

Succinate production in Escherichia coli

Succinate has been recognized as an important platform chemical that can be produced from biomass. While a number of organisms are capable of succinate production naturally, this review focuses on the engineering of Escherichia coli for the production of four-carbon dicarboxylic acid. Important features of a succinate production system are to achieve an optimal balance of reducing equivalents generated by consumption of the feedstock, while maximizing the amount of carbon channeled into the product. Aerobic and anaerobic production strains have been developed and applied to production from glucose and other abundant carbon sources. Metabolic engineering methods and strain evolution have been used and supplemented by the recent application of systems biology and in silico modeling tools to construct optimal production strains. The metabolic capacity of the production strain, the requirement for efficient recovery of succinate, and the reliability of the performance under scaleup are important in the overall process. The costs of the overall biorefinery-compatible process will determine the economic commercialization of succinate and its impact in larger chemical markets.     

Identification of Soil Microbes Capable of Utilizing Cellobiosan

Approximately 100 million tons of anhydrosugars, such as levoglucosan and cellobiosan, are produced through biomass burning every year. These sugars are also produced through fast pyrolysis, the controlled thermal depolymerization of biomass. While the microbial pathways associated with levoglucosan utilization have been characterized, there is little known about cellobiosan utilization. Here we describe the isolation and characterization of six cellobiosan-utilizing microbes from soil samples. Each of these organisms is capable of using both cellobiosan and levoglucosan as sole carbon source, though both minimal and rich media cellobiosan supported significantly higher biomass production than levoglucosan. Ribosomal sequencing was used to identify the closest reported match for these organisms: Sphingobacterium multivorum, Acinetobacter oleivorans JC3-1, Enterobacter sp SJZ-6, and Microbacterium sps FXJ8.207 and 203 and a fungal species Cryptococcus sp. The commercially-acquired Enterobacter cloacae DSM 16657 showed growth on levoglucosan and cellobiosan, supporting our isolate identification. Analysis of an existing database of 16S rRNA amplicons from Iowa soil samples confirmed the representation of our five bacterial isolates and four previously-reported levoglucosan-utilizing bacterial isolates in other soil samples and provided insight into their population distributions. Phylogenetic analysis of the 16S rRNA and 18S rRNA of strains previously reported to utilize levoglucosan and our newfound isolates showed that the organisms isolated in this study are distinct from previously described anhydrosugar-utilizing microbial species.     

Microorganism lipid droplets and biofuel development

Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech ‘factories’ to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581]     

Experimental evidence for the immediate impact of fertilization and irrigation upon the plant and invertebrate communities of mountain grasslands

The response of montane and subalpine hay meadow plant and arthropod communities to the application of liquid manure and aerial irrigation – two novel, rapidly spreading management practices – remains poorly understood, which hampers the formulation of best practice management recommendations for both hay production and biodiversity preservation. In these nutrient-poor mountain grasslands, a moderate management regime could enhance overall conditions for biodiversity. This study experimentally assessed, at the site scale, among low-input montane and subalpine meadows, the short-term effects (1 year) of a moderate intensification (slurry fertilization: 26.7–53.3 kg N·ha⁻¹·year⁻¹; irrigation with sprinklers: 20 mm·week⁻¹; singly or combined together) on plant species richness, vegetation structure, hay production, and arthropod abundance and biomass in the inner European Alps (Valais, SW Switzerland). Results show that (1) montane and subalpine hay meadow ecological communities respond very rapidly to an intensification of management practices; (2) on a short-term basis, a moderate intensification of very low-input hay meadows has positive effects on plant species richness, vegetation structure, hay production, and arthropod abundance and biomass; (3) vegetation structure is likely to be the key factor limiting arthropod abundance and biomass. Our ongoing experiments will in the longer term identify which level of management intensity achieves an optimal balance between biodiversity and hay production.     

Evidence for phenotypic plasticity in the Antarctic extremophile Chlamydomonas raudensis Ettl. UWO 241

Life in extreme environments poses unique challenges to photosynthetic organisms. The ability for an extremophilic green alga and its genetic and mesophilic equivalent to acclimate to changes in their environment was examined to determine the extent of their phenotypic plasticities. The Antarctic extremophile Chlamydomonas raudensis Ettl. UWO 241 (UWO) was isolated from an ice-covered lake in Antarctica, whereas its mesophilic counterpart C. raudensis Ettl. SAG 49.72 (SAG) was isolated from a meadow pool in the Czech Republic. The effects of changes in temperature and salinity on growth, morphology, and photochemistry were examined in the two strains. Differential acclimative responses were observed in UWO which include a wider salinity range for growth, and broader temperature- and salt-induced fluctuations in F(v)/F(m), relative to SAG. Furthermore, the redox state of the photosynthetic electron transport chain, measured as 1-q(P), was modulated in the extremophile whereas this was not observed in the mesophile. Interestingly, it is shown for the first time that SAG is similar to UWO in that it is unable to undergo state transitions. The different natural histories of these two strains exert different evolutionary pressures and, consequently, different abilities for acclimation, an important component of phenotypic plasticity. In contrast to SAG, UWO relied on a redox sensing and signalling system under the growth conditions used in this study. It is proposed that growth and adaptation of UWO under a stressful and extreme environment poises this extremophile for better success under changing environmental conditions.     

Relationships among salinity, egg size, embryonic development, and larval biomass in the estuarine crab Chasmagnathus granulata Dana, 1851

We studied interrelationships between initial egg size and biomass, duration of embryogenesis at different salinities, and initial larval biomass in an estuarine crab, Chasmagnathus granulata. Ovigerous females were maintained at three different salinities (15‰, 20‰ and 32‰); initial egg size (mean diameter), biomass (dry weight, carbon and nitrogen) as well as changes in egg size, embryonic development duration, and initial larval biomass were measured.

Initial egg size varied significantly among broods from different females maintained under identical environmental conditions. Eggs from females maintained at 15‰ had on average higher biomass and larger diameter. We hypothesise that this is a plastic response to salinity, which may have an adaptive value, i.e. it may increase the survivorship during postembryonic development. The degree of change in egg diameter during the embryonic development depended on salinity: eggs in a late developmental stage were at 15‰ significantly larger and had smaller increment than those incubated at higher salinities. Development duration was longer at 15‰, but this was significant only for the intermediate embryonic stages. Initial larval biomass depended on initial egg size and on biomass loss during embryogenesis. Larvae with high initial biomass originated either from those eggs that had, already from egg laying, a high initial biomass (reflecting individual variability under identical conditions), or from those developing at a high salinity (32‰), where embryonic biomass losses were generally minimum. Our results show that both individual variability in the provisioning of eggs with yolk and the salinity prevailing during the embryonic development are important factors causing variability in the initial larval biomass of C. granulata, and thus, in early larval survival and growth.     

Structure of the Biotic Component in the Rybinsk Reservoir Ecosystem: Importance of Heterotrophic Bacteria (Review)

The total biomass of the biotic component of the ecosystem has been determined and the contribution of the main ecological groups—autotrophic and heterotrophic organisms from different habitats—to its formation has been estimated in a large plain meso-eutrophic reservoir (Rybinsk Reservoir, Upper Volga). Particular attention is paid to the role of heterotrophic bacteria in the structure and functioning of the biota in the reservoir. The total biomass of the biotic component of the ecosystem is 71536 t C, which is 5.2% of the total organic carbon in the reservoir. Higher aquatic plants make the largest contribution to the formation of the biomass in the reservoir. Their biomass, including epiphyton, was 6.0 and 1.9 times larger than the biomass of plankton and benthos, respectively. Heterotrophic bacteria, most of which inhabit bottom sediments, rank second in respect to their contribution to the total biomass. The comparison of the total primary production of all phototrophic organisms and the carbon demand of heterotrophic bacteria indicates the importance of allochthonous organic matter in the functioning of the reservoir ecosystem.     

Effects of grass species and grass growth on atmospheric nitrogen deposition to a bog ecosystem surrounded by intensive agricultural land use

We applied a ¹⁵N dilution technique called “Integrated Total Nitrogen Input” (ITNI) to quantify annual atmospheric N input into a peatland surrounded by intensive agricultural practices over a 2-year period. Grass species and grass growth effects on atmospheric N deposition were investigated using Lolium multiflorum and Eriophorum vaginatum and different levels of added N resulting in increased biomass production. Plant biomass production was positively correlated with atmospheric N uptake (up to 102.7 mg N pot⁻¹) when using Lolium multiflorum. In contrast, atmospheric N deposition to Eriophorum vaginatum did not show a clear dependency to produced biomass and ranged from 81.9 to 138.2 mg N pot⁻¹. Both species revealed a relationship between atmospheric N input and total biomass N contents. Airborne N deposition varied from about 24 to 55 kg N ha⁻¹ yr⁻¹. Partitioning of airborne N within the monitor system differed such that most of the deposited N was found in roots of Eriophorum vaginatum while the highest share was allocated in aboveground biomass of Lolium multiflorum. Compared to other approaches determining atmospheric N deposition, ITNI showed highest airborne N input and an up to fivefold exceedance of the ecosystem-specific critical load of 5–10 kg N ha⁻¹ yr⁻¹.     

Operation strategies for biohydrogen production with a high-rate anaerobic granular sludge bed bioreactor

Long-term operation for biohydrogen production with an efficient carrier-induced granular sludge bed (CIGSB) bioreactor had encountered problems with poor biomass retention at a low hydraulic retention (HRT) as well as poor mass-transfer efficiency at a high HRT or under a prolonged operation period. This work was undertaken to develop strategies enabling better biomass retention and mass-transfer efficiency of the CIGSB reactors. Supplementation of calcium ion was found to enhance mechanical strength of the granular sludge. Addition of 5.4–27.2 mg/l of Ca²⁺ also led to an over three-fold increase in biomass concentration and a nearly five-fold increase in the H₂ production rate (up to 5.1 l H₂/h/l). Two reflux strategies were utilized to enhance the mass-transfer efficiency of the CIGSB system. The liquid reflux (LR) strategy enhanced the H₂ production rate by 2.2-fold at an optimal liquid upflow velocity of 1.09 m/h, which also gave a maximal biomass concentration of ca. 22 g VSS/l. Similar optimal H₂ production rate was also obtained with the gas reflux (GR) strategy at a rate of 1.0–1.49 m/h, whereas the biomass concentration decreased to 2–7 g VSS/l and thereby the specific H₂ production rate was higher than that with LR. The operation strategies applied in this work were effective to allow stable and efficient H₂ production for nearly 100 days.