The nutrient-load hypothesis: patterns of resource limitation and community structure driven by competition for nutrients and light

Effects of carbon limitation and carbon fertilization on karst lake-reservoir productivity

Nitrogen and phosphorus are universally recognized as limiting elements in the eutrophication processes affecting the majority of the world's lakes, reservoirs, and coastal ecosystems. However, despite extensive research spanning several decades, critical questions in eutrophication science remain unanswered. For example, there is still much to understand about the interactions between carbon limitation and ecosystem stability, and the availability of carbon components adds significant complexity to aquatic resource management. Mounting evidence suggests that aqueous CO2 could be a limiting factor, influencing the structure and succession of aquatic plant communities, especially in karstic lake and reservoir ecosystems. Moreover, the fertilization effect of aqueous CO2 has the potential to enhance carbon sequestration and phosphorus removal. Therefore, it is important to address these uncertainties to achieve multiple positive outcomes, including improved water quality and increased carbon sinks in karst lakes and reservoirs.

Phytoplankton stoichiometry along the salinity gradient under limited nutrient and light supply

Ongoing climate warming alters precipitation and water column stability, leading to salinity and nutrient supply changes in the euphotic zone of many coastal ecosystems and semi-enclosed seas. Changing salinity and nutrient conditions affect phytoplankton physiology by altering elemental ratios of carbon (C), nitrogen (N) and phosphorus (P). This study aimed to understand how salinity stress and resource acquisition affect phytoplankton stoichiometry. We incubated a phytoplankton polyculture composed of 10 species under different light, inorganic nutrient ratio and salinity levels. At the end of the incubation period, we measured particulate elemental composition (C, N and P), chlorophyll a and species abundances. The phytoplankton polyculture, dominated by Phaeodactylum tricornutum, accumulated more particulate organic carbon (POC) with increasing salinity. The low POC and low particulate C:N and C:P ratios toward 0 psu suggest that the hypoosmotic conditions highly affected primary production. The relative abundance of different species varied with salinity, and some species grew faster under low nutrient supply. Still, the dominant diatom regulated the overall POC of the polyculture, following the classic concept of the foundation species.

Chattonella marina blooms in a trophic gradient system: Interaction with environmental drivers

For coastal eutrophication, lots of studies focused on the influence from environmental factors, especially nitrogen and phosphorus, on algae blooms. The interaction between algae and environmental factors has been often ignored. Using Chattonella marina, a dominant species in marine algal blooms, we established a trophic gradient system that simulated C. marina blooms at three trophic levels: eutrophic, mesotrophic, and oligotrophic, and examined the life history patterns of C. marina and the interactions with environmental factors. Increased trophic levels influenced the growth potential of C. marina, while its unique cyst reproduction allowed it to thrive in nutrient-limited environments. Adequate nutrients caused changes in dissolved oxygen (DO) and pH led by C. marina, with the carbonate system playing a crucial role in regulating pH under nutrient-limited conditions. Limiting the growth of C. marina in areas with low nutrient by manipulating reactive silicate (SiO32-) availability may prove effective. Nitrate (NO3-) was the preferred nutrient for C. marina when its concentration exceeded that of ammonium (NH4+). Phosphorus played a crucial role in the growth and proliferation of C. marina, especially when other nutrients were scarce. The findings of this study may provide valuable insights into the effective management and prevention of algae blooms.

Colonial morphology weakens the response of different inorganic carbon uptake systems to CO2 levels in Microcystis population

Rising atmospheric CO2 concentration negatively impacts aquatic ecosystems and may induce evolutionary changes in the CO2-concentrating mechanism (CCM) of cyanobacteria. As the most notorious freshwater cyanobacteria, Microcystis strains have high phenotypic plasticity to form colonies and blooms in lakes and reservoirs worldwide. However, phenotypic plasticity of Microcystis responses to elevated CO2 is still a major open question. Here, we studied how Microcystis strains with two genotype of inorganic carbon uptake systems, bicA and sbtA, and different colonial morphology response to 200 ppm, 400 ppm, and 800 ppm CO2 levels. The results revealed that sbtA genotypes showed significantly higher specific growth rates, Chl a concentration, and photosynthetic efficiency at 200 ppm CO2, whereas higher specific growth rates, Chl a concentration, and photosynthetic efficiency were found in bicA genotype at 800 ppm CO2. The highest values of specific growth rates, Chl a concentration, Fv/Fm, and maximal net photosynthesis (Pm) were observed in unicellular morphology, followed by small colony and large colonial morphology at all CO2 levels. The values of K0.5 (DIC), K0.5 (CO2), and K0.5 (HCO3-) in the large colonials increased with rising CO2 levels, but these values significantly decreased in the unicellular and small colonials. ANOSIM analysis indicated that colonial morphology reduced significantly inter-group differences between bicA and sbtA genotypes at all CO2 treatments. These results suggest that colonial morphology of Microcystis can weakens the response of different inorganic carbon uptake systems to CO2 levels. Moreover, phenotypic and genotypic plasticity is likely to broaden strongly the fitness of Microcystis from rising atmospheric CO2.

A new diatom-based multimetric index to assess lake ecological status

Eutrophication impairs lake ecosystems at a global scale. In this context, as benthic microalgae are well-established warnings for a large range of stressors, particularly nutrient enrichment, the Water Framework Directive required the development of diatom-based methods to monitor lake eutrophication. Here, we present the diatom-based index we developed for French lakes, named IBDL (Indice Biologique Diatomées en Lacs). Data were collected in 93 lakes from 2015 to 2020. A challenge arose from the discontinuous pressure gradient of our dataset, especially the low number of nutrient-impacted lakes. To analyze the data we opted for the so-called "Threshold Indicator Taxa ANalysis" method, which makes it possible to determine a list of "alert taxa." We obtained a multimetric index based on specific pressure gradients (Kjeldahl nitrogen, suspended matter, biological oxygen demand, and total phosphorous). Considering the European intercalibration process, the very good correlation between IBDL and the common metric (R2 from 0.52 to 0.87 according to the lake alkalinity type) makes us very confident in our ability to match future IBDL quality thresholds with European standards. The IBDL proved at last to be particularly relevant as it has a twofold interest: an excellent relationship with total phosphorus (R2 from 0.63 to 0.83 according to the lake alkalinity type) and a possible application to any lake metatype. Its complementarity with macrophyte-based indices moreover justifies the use of at least two primary producer components for lake ecological status classification.

Why do red tides occur frequently in some oligotrophic waters? Analysis of red tide evolution history in Mirs Bay, China and its implications

The process and management of red tide in oligotrophic waters are poorly understood as most studies on red tide were focused on eutrophic areas. In this study, 404 red tide events together with the historical water quality dynamics during 1991-2020 were investigated in an anthropogenically influenced bay in China - Mirs Bay, whose most region is oligotrophic except small inshore areas. Red tides of oligotrophic offshore accounted for 20 % of all. With the effective governmental management on inshore areas, concentration of PO₄ and DIN has been decreased to a low level (PO₄ <0.01 mg/L while DIN <0.1 mg/L) in the bay since about 2000. However, the reduction of nutrients was still accompanied by the frequent outbreaks of red tides, as well as a shift of dominant algae from diatoms to dinoflagellates, which might be due to the unbalanced nutrient reduction, such as N:P ratio fluctuation and organic nutrient increase. This shift might trigger more red tide events and even some super ones (long-duration or large-scale) in oligotrophic areas. Detailed analysis on red tide events combined with model simulation proved that the outbreak of red tide in Mirs Bay was caused by the joint contribution of nutrients and hydrodynamics. Nutrients of inshore area supported the red tides there, and with the help of physical conditions, red tides inshore could be transferred to offshore areas and then were likely to bloom again or be preyed to support blooms of other organisms. This study acknowledged that the reduction of both N and P either inorganic or organic nutrients was essential to control red tides, even in oligotrophic waters, but a balanced strategy considering the dual reduction of both nitrogen and phosphorus was of pivotal role to restore the health of coastal water systems disturbed by human.

Negative effects of nitrogen override positive effects of phosphorus on grassland legumes worldwide

Anthropogenic nutrient enrichment is driving global biodiversity decline and modifying ecosystem functions. Theory suggests that plant functional types that fix atmospheric nitrogen have a competitive advantage in nitrogen-poor soils, but lose this advantage with increasing nitrogen supply. By contrast, the addition of phosphorus, potassium, and other nutrients may benefit such species in low-nutrient environments by enhancing their nitrogen-fixing capacity. We present a global-scale experiment confirming these predictions for nitrogen-fixing legumes (Fabaceae) across 45 grasslands on six continents. Nitrogen addition reduced legume cover, richness, and biomass, particularly in nitrogen-poor soils, while cover of non-nitrogen-fixing plants increased. The addition of phosphorous, potassium, and other nutrients enhanced legume abundance, but did not mitigate the negative effects of nitrogen addition. Increasing nitrogen supply thus has the potential to decrease the diversity and abundance of grassland legumes worldwide regardless of the availability of other nutrients, with consequences for biodiversity, food webs, ecosystem resilience, and genetic improvement of protein-rich agricultural plant species.

Interactive effect of water level and flushing rate on population dynamics of a harmful cyanobacterial species: Raphidiopsis raciborskii

Changes in water level and flushing rate directly affect to a large extent the biomass of harmful cyanobacteria, and drive the shift of phytoplankton composition between cyanobacteria dominance/non-dominance in eutrophic waters. Here, we gave a theoretical formula describing the combinational effect of water level and flushing rate on cyanobacterial biomass in eutrophic and well-mixed waters. We also formulated an equation predicting the water level and flushing rate at which cyanobacteria become non-dominating in such water columns. The formulae were confronted with field observations of a low-light adapted cyanobacterium in a large coastal reservoir of southern China. Our formulae demonstrate that water level and flushing rate have an interactive effect on the equilibrium biomass of low-light adapted cyanobacteria in mixed and turbid waters. The formulae were well fitted to the field observation of Raphidiopsis raciborskii population in the reservoir during four dry seasons. In agreement with the theoretical analysis, multiple regression analysis also showed that the interaction between water level and flushing rate is able to interpret the variation of R. raciborskii biomass in the water column. The two formulae are applicable for predicting the response of low-light adapted cyanobacteria to local climate change. Our findings have practical significance in designing measures against the dominance of low light-adapted cyanobacteria in reservoirs.

Resource Colimitation Drives Competition Between Phytoplankton and Bacteria in the Southern Ocean

Across the Southern Ocean, phytoplankton growth is governed by iron and light, while bacterial growth is regulated by iron and labile dissolved organic carbon (LDOC). We use a mechanistic model to examine how competition for iron between phytoplankton and bacteria responds to changes in iron, light, and LDOC. Consistent with experimental evidence, increasing iron and light encourages phytoplankton dominance, while increasing LDOC and decreasing light favors bacterial dominance. Under elevated LDOC, bacteria can outcompete phytoplankton for iron, most easily under lower iron. Simulations reveal that bacteria are major iron consumers and suggest that luxury storage plays a key role in competitive iron uptake. Under seasonal conditions typical of the Southern Ocean, sources of LDOC besides phytoplankton exudation modulate the strength of competitive interactions. Continued investigations on the competitive fitness of bacteria in driving changes in primary production in iron-limited systems will be invaluable in refining these results.

Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

Unabated Nitrogen Pollution Favors Growth of Toxic Cyanobacteria over Chlorophytes in Most Hypereutrophic Lakes

Human release of reactive nitrogen (N) to the environment has increased 10-fold since 1860 and is expected to increase by a further ∼75% by 2050. Much of this N enters phosphorus (P)-rich, eutrophic lakes in agricultural and urbanized watersheds. While N pollution of eutrophic lakes can promote toxic cyanobacterial growth, some cases of extreme N loading have led to the dominance of chlorophytes (green algae). As N loads required to shift communities from cyanobacterial to chlorophyte dominance are unclear, we experimentally tested phytoplankton responses to a gradient of N loading in a P-rich lake. Low-to-moderate doses (1-3 mg N L^-1 week^-1) promoted toxic cyanobacterial dominance and elevated concentrations of the hepatotoxin microcystin. Conversely, loads characteristic of pure urban or agricultural effluents (up to 18 mg N L^-1 week^-1) led to the dominance of chlorophytes over cyanobacteria and lower microcystin content. This indicates that N loads needed to sustain chlorophyte dominance are uncommon, likely restricted to select shallow lakes directly exposed to urban or agricultural effluents. As most N pollution regimes in P-rich lakes will favor toxic cyanobacterial dominance, restricting future N pollution will help curb further cyanobacterial dominance in lakes both directly and by constraining the capacity for future P loading and climate warming to drive cyanobacterial growth.

Stable coexistence of equivalent nutrient competitors through niche differentiation in the light spectrum

Niche-based theories and the neutral theory of biodiversity differ in their predictions of how the species composition of natural communities will respond to changes in nutrient availability. This is an issue of major environmental relevance, as many ecosystems have experienced changes in nitrogen (N) and phosphorus (P) due to anthropogenic manipulation of nutrient loading. To understand how changes in N and P limitation may impact community structure, we conducted laboratory competition experiments using a multispecies phytoplankton community sampled from the North Sea. Results showed that picocyanobacteria (Cyanobium sp.) won the competition under N limitation, while picocyanobacteria and nonmotile nanophytoplankton (Nannochloropsis sp.) coexisted at equal abundances under P limitation. Additional experiments using isolated monocultures confirmed that Cyanobium sp. depleted N to lower levels than Nannochloropsis sp., but that both species had nearly identical P requirements, suggesting a potential for neutral coexistence under P-limited conditions. Pairwise competition experiments with the two isolates seemed to support the consistency of these results, but P limitation resulted in stable species coexistence irrespective of the initial conditions rather than the random drift of species abundances predicted by neutral theory. Comparison of the light absorption spectra indicates that coexistence of the two species was stabilized through differential use of the underwater light spectrum. Our results provide an interesting experimental example of modern coexistence theory, where species were equal competitors in one niche dimension but their competitive traits differed in other niche dimensions, thus enabling stable species coexistence on a single limiting nutrient through niche differentiation in the light spectrum.

Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta)

Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean_2014-2015 = 652 ± 179 μg chlorophyll a L^-1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.

Environmental characteristics in three seamount areas of the Tropical Western Pacific Ocean: Focusing on nutrients

Nutrients distribution and influencing factors in three seamount areas named Y3, M2 and C4 of the Tropical Western Pacific Ocean (TWPO) were investigated. Nutrients showed obvious uplifts around the three seamounts, consistent with the uplifts of isotherms and isohalines, indicating the existence of a bottom-up process of nutrients. Meanwhile, compared with the stations away from seamount and the reference stations in the TWPO, nutrients concentrations around seamount were much higher. Among the three seamounts, the average nutrients concentrations were highest in Y3, while they were lowest in C4. Moreover, compared with the obvious nitrogen limitation in Y3 and M2, the N:P (13.5:1) and Si:N (6.1:1) were closed to the Redfield ratio. The current-seamount interaction was the determining influencing factor on nutrients distribution, causing the hydrology dynamic changes such as uplifts and Taylor column. Meanwhile, T and S also affected nutrients distribution, especially nutrients and T showed significant negative correlations.

Nutrient Dependent Cross-Kingdom Interactions: Fungi and Bacteria From an Oligotrophic Desert Oasis

Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate potential in vitro interactions among fungi and bacteria isolated from a phosphorous oligotrophic aquatic system in the Cuatro Ciénegas Basin, Mexico, and to test the nutrients-based shifts. We assessed growth changes in bacteria (Aeromonas and Vibrio) and fungi (Coprinellus micaceus, Cladosporium sp., and Aspergillus niger) on co-cultures in relation to monocultures under diverse nutrient scenarios on Petri dishes. Interactions were explored using a network analysis, and a metabolome profiling for specific taxa. We identified nutrient-dependent patterns, as beneficial interactions dominated in low-nutrients media and antagonistic interactions dominated in rich media. This suggests that cross-kingdom synergistic interactions might favor microbial colonization and growth under low nutrient conditions, representing an adaptive trait to oligotrophic environments. Moreover, our findings agree with the stress-gradient hypothesis, since microbial interactions shifted from competition to cooperation as environmental stress (expressed as low nutrients) increased. At a functional level consistent differences were detected in the production of secondary metabolites, agreeing with plate bioassays. Our results based on culture experiments, provides evidence to understand the complexity of microbial dynamics and survival in phosphorous-depleted environments.

Competition for nutrients and light: testing advances in resource competition with a natural phytoplankton community

A key challenge in ecology is to understand how nutrients and light affect the biodiversity and community structure of phytoplankton and plant communities. According to resource competition models, ratios of limiting nutrients are major determinants of species composition. At high nutrient levels, however, species interactions may shift to competition for light, which might make nutrient ratios less relevant. The "nutrient-load hypothesis" merges these two perspectives, by extending the classic model of competition for two nutrients to include competition for light. Here, we test five key predictions of the nutrient-load hypothesis using multispecies competition experiments. A marine phytoplankton community sampled from the North Sea was inoculated in laboratory chemostats provided with different nitrogen (N) and phosphorus (P) loads to induce either single resource limitation or co-limitation of N, P, and light. Four of the five predictions were validated by the experiments. In particular, different resource limitations favored the dominance of different species. Increasing nutrient loads caused changes in phytoplankton species composition, even if the N:P ratio of the nutrient loads remained constant, by shifting the species interactions from competition for nutrients to competition for light. In all treatments, small species became dominant whereas larger species were competitively excluded, supporting the common view that small cell size provides a competitive advantage under resource-limited conditions. Contrary to expectation, all treatments led to coexistence of diatoms, cyanobacteria and green algae, resulting in a higher diversity of species than predicted by theory. Because the coexisting species comprised three phyla with different photosynthetic pigments, we speculate that niche differentiation in the light spectrum might play a role. Our results show that mechanistic resource competition models that integrate nutrient-based and light-based approaches provide an important step forward to understand and predict how changing nutrient loads affect community composition.

Trait selection and co-existence of phytoplankton in partially mixed systems: Trait based modelling and potential of an aggregated approach

Trait selection and co-existence in phytoplankton communities in partially mixed water columns is investigated using trait based modelling. In the models employed, trait selection results from phytoplankton competition for two limiting resources, light and nutrients. The study employs spatially resolved models, in which the phytoplankton community is represented as a large number of trait-groups characterized by fixed trait combinations (trade-offs). Results from the trait-group resolving model (RM) are compared to results from an aggregated trait based model with adaptive traits (AM). Differences in specific production resulting from a trade-off between the half saturation constants of light and nutrients are sufficient to support evolutionary stable co-existence confirming that co-existence does not require differences in resource consumption. If abiotic conditions lead to the selection of a single trait group in RM, AM provides excellent approximations of the development of total biomass, average community trait and trait variance in the phytoplankton community. However, if selection leads to bimodal trait distributions, e.g. to co-existence of two trait groups (or species), functionally important properties of the phytoplankton community cannot be adequately represented by the aggregated information provided by AM. Because the increase in variance due to the development of bimodal trait distributions cannot be distinguished from an increase in variance due to an increase in trait diversity, the development of trait variance in AM models is not a reliable measure of trait diversity. Furthermore, AM may not provide reliable simulations of trophic interactions if the performance of the consumers depends on the traits of their resources. However, AM may support exploration of the consequences of environmental conditions and of the parameterization of species for co-existence within communities.

Macrophyte Community Response to Nitrogen Loading and Thermal Stressors in Rapidly Flushed Mesocosm Systems

A mesocosm system was developed to simulate estuarine conditions characteristic of short water-residence time ecosystems of the Pacific Coast of North America, and used to evaluate the response of multiple macrophyte metrics to gradients of NO₃ loading and temperature. Replicated experiments found that few responses could be directly attributed to NO₃ loading up to 6 x ambient. Some response metrics exhibited weak relationships with nutrient loading but could not be resolved with available statistical power. While direct nutrient responses were found for some species-specific metrics (e.g. green macroalgal growth and biomass, tissue N%, etc.), many patterns were confounded with temperature. Temperature generally had a larger effect on response metrics than did nutrient load. Experimental macrophyte communities exhibited community shifts consistent with the predicted effects of nutrient loading at 20 °C, but there was no evidence of other eutrophication symptoms (phytoplankton blooms or hypoxia) due to the short system-residence time. The Z. marina Nutrient Pollution Index (NPI) tracked the NO₃ gradient at 10 °C, but exhibited no response at 20 °C, which may limit the utility of this metric in areas with marked thermal seasonality. Results suggest that teasing apart the influence of temperature and nutrients on the expression of eutrophication symptoms will require complex multi-stressor experiments and the use of indicators that are sensitive across a broad range of conditions.

The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

From Ecological Stoichiometry to Biochemical Composition: Variation in N and P Supply Alters Key Biosynthetic Rates in Marine Phytoplankton

One of the major challenges in ecological stoichiometry is to establish how environmental changes in resource availability may affect both the biochemical composition of organisms and the species composition of communities. This is a pressing issue in many coastal waters, where anthropogenic activities have caused large changes in riverine nutrient inputs. Here we investigate variation in the biochemical composition and synthesis of amino acids, fatty acids (FA), and carbohydrates in mixed phytoplankton communities sampled from the North Sea. The communities were cultured in chemostats supplied with different concentrations of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) to establish four different types of resource limitations. Diatoms dominated under N-limited, N+P limited and P-limited conditions. Cyanobacteria became dominant in one of the N-limited chemostats and green algae dominated in the one P-limited chemostat and under light-limited conditions. Changes in nutrient availability directly affected amino acid content, which was lowest under N and N+P limitation, higher under P-limitation and highest when light was the limiting factor. Storage carbohydrate content showed the opposite trend and storage FA content seemed to be co-dependent on community composition. The synthesis of essential amino acids was affected under N and N+P limitation, as the transformation from non-essential to essential amino acids decreased at DIN:DIP ≤ 6. The simple community structure and clearly identifiable nutrient limitations confirm and clarify previous field findings in the North Sea. Our results show that different phytoplankton groups are capable of adapting their key biosynthetic rates and hence their biochemical composition to different degrees when experiencing shifts in nutrient availability. This will have implications for phytoplankton growth, community structure, and the nutritional quality of phytoplankton as food for higher trophic levels.

Synergistic effect of elevated temperature, pCO2 and nutrients on marine biofilm

Natural marine biofilms provide signatures of the events that occur over a period of time and can be used as bioindicators of environmental changes. Hence, the effects of temperature (30 and 34°C), pCO2 (400 and 1500μatm) and nutrients (unenriched and enriched f/2 media) on the marine biofilm were evaluated using a 2×2×2 factorial design. In unenriched condition, acidification significantly increased the abundance of phytoperiphytes whereas reduced that of bacteria and it was vice versa in the enriched condition. Warming had significant negative effect on the abundance of both phytoperiphytes and bacteria, except in unenriched condition wherein it favoured bacterial growth. Synergistically, acidification and warming had deleterious effects resulting in further reduction in the abundance of both phytoperiphytes and bacteria, except in enriched condition wherein bacterial abundance increased. Such changes in biofilm communities in response to warming and acidification can have cascading effect on the subsequent build-up of macrofouling community.

Synthetic Ecology of Microbes: Mathematical Models and Applications

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

A preliminary and qualitative study of resource ratio theory to nitrifying lab-scale bioreactors

The incorporation of microbial diversity in design would ideally require predictive theory that would relate operational parameters to the numbers and distribution of taxa. Resource ratio-theory (RRT) might be one such theory. Based on Monod kinetics, it explains diversity in function of resource-ratio and richness. However, to be usable in biological engineered system, the growth parameters of all the bacteria under consideration and the resource supply and diffusion parameters for all the relevant nutrients should be determined. This is challenging, but plausible, at least for low diversity groups with simple resource requirements like the ammonia oxidizing bacteria (AOB). One of the major successes of RRT was its ability to explain the ‘paradox of enrichment’ which states that diversity first increases and then decreases with resource richness. Here, we demonstrate that this pattern can be seen in lab-scale-activated sludge reactors and parallel simulations that incorporate the principles of RRT in a floc-based system. High and low ammonia and oxygen were supplied to continuous flow bioreactors with resource conditions correlating with the composition and diversity of resident AOB communities based on AOB 16S rDNA clone libraries. Neither the experimental work nor the simulations are definitive proof for the application of RRT in this context. However, it is sufficient evidence that such approach might work and justify a more rigorous investigation.

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment

The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after 3 weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition.

Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community

N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria.

Depth of the biomass maximum affects the rules of resource competition in a water column

The theory of resource competition in spatially extended systems with resources and biomass fluxes is far from trivial. Here, we analyze the competition between two phytoplankton species for light and a nutrient in a weakly mixed water column. We develop a general framework for such an analysis and show that the competition outcome can be largely understood from a single parameter, the slope of the invasion threshold in the plane of resources. Using this approach, we show that the competition outcome crucially depends on the depth of the biomass maximum. Under eutrophic conditions, when the phytoplankton production peaks on the surface, species composition depends on the ratio of resource supplies, and the competition outcome follows the “classic” rule: coexistence is possible if each competitor has the greatest effect on its most limiting resource. By contrast, in oligotrophic systems, characterized by deep biomass maxima, the absolute level of resource supplies drives species composition, and coexistence becomes more feasible if each competitor mostly consumes its least limiting resource. Finally, when the production peaks in the subsurface, good nutrient competitors are favored. Our findings are supported by empirical data.

Biological control of toxic cyanobacteria by mixotrophic predators: an experimental test of intraguild predation theory

Intraguild predators both feed on and compete with their intraguild prey. In theory, intraguild predators can therefore be very effective as biological control agents of intraguild prey species, especially in productive environments. We investigated this hypothesis using the mixotrophic chrysophyte Ochromonas as intraguild predator and the harmful cyanobacterium Microcystis aeruginosa as its prey. Ochromonas can grow photoautotrophically, but can also graze efficiently on Microcystis. Hence, it competes with its prey for inorganic resources. We developed a mathematical model and parameterized it for our experimental food web. The model predicts dominance of Microcystis at low nutrient loads, coexistence of both species at intermediate nutrient loads, and dominance of Ochromonas but a strong decrease of Microcystis at high nutrient loads. We tested these theoretical predictions in chemostat experiments supplied with three different nitrogen concentrations. Ochromonas initially suppressed the Microcystis abundance by > 97% compared to the Microcystis monocultures. Thereafter, however, Microcystis gradually recovered to -20% of its monoculture abundance at low nitrogen loads, but to 50-60% at high nitrogen loads. Hence, Ochromonas largely lost control over the Microcystis population at high nitrogen loads. We explored several mechanisms that might explain this deviation from theoretical predictions, and found that intraspecific interference at high Ochromonas densities reduced their grazing rates on Microcystis. These results illustrate the potential of intraguild predation to control pest species, but also show that the effectiveness of their biological control can be reduced in productive environments.

Contrasting effects of rising CO2 on primary production and ecological stoichiometry at different nutrient levels

Although rising CO2 concentrations are thought to promote the growth and alter the carbon : nutrient stoichiometry of primary producers, several studies have reported conflicting results. To reconcile these contrasting results, we tested the following hypotheses: rising CO2 levels (1) will increase phytoplankton biomass more at high nutrient loads than at low nutrient loads, but (2) will increase their carbon : nutrient stoichiometry more at low than at high nutrient loads. We formulated a mathematical model to predict dynamic changes in phytoplankton population density, elemental stoichiometry and inorganic carbon chemistry in response to rising CO2 . The model was tested in chemostat experiments with the freshwater cyanobacterium Microcystis aeruginosa. The model predictions and experimental results confirmed the hypotheses. Our findings provide a novel theoretical framework to understand and predict effects of rising CO2 concentrations on primary producers and their nutritional quality as food for herbivores under different nutrient conditions.

Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis

Rising CO2 levels may act as an important selective factor on the CO2-concentrating mechanism (CCM) of cyanobacteria. We investigated genetic diversity in the CCM of Microcystis aeruginosa, a species producing harmful cyanobacterial blooms in many lakes worldwide. All 20 investigated Microcystis strains contained complete genes for two CO2 uptake systems, the ATP-dependent bicarbonate uptake system BCT1 and several carbonic anhydrases (CAs). However, 12 strains lacked either the high-flux bicarbonate transporter BicA or the high-affinity bicarbonate transporter SbtA. Both genes, bicA and sbtA, were located on the same operon, and the expression of this operon is most likely regulated by an additional LysR-type transcriptional regulator (CcmR2). Strains with only a small bicA fragment clustered together in the phylogenetic tree of sbtAB, and the bicA fragments were similar in strains isolated from different continents. This indicates that a common ancestor may first have lost most of its bicA gene and subsequently spread over the world. Growth experiments showed that strains with sbtA performed better at low inorganic carbon (Ci) conditions, whereas strains with bicA performed better at high Ci conditions. This offers an alternative explanation of previous competition experiments, as our results reveal that the competition at low CO2 levels was won by a specialist with only sbtA, whereas a generalist with both bicA and sbtA won at high CO2 levels. Hence, genetic and phenotypic variation in Ci uptake systems provide Microcystis with the potential for microevolutionary adaptation to changing CO2 conditions, with a selective advantage for bicA-containing strains in a high-CO2 world.

Fast detection of nutrient limitation in macroalgae and seagrass with nutrient-induced fluorescence

Background

Rapid determination of which nutrients limit the primary production of macroalgae and seagrasses is vital for understanding the impacts of eutrophication on marine and freshwater ecosystems. However, current methods to assess nutrient limitation are often cumbersome and time consuming. For phytoplankton, a rapid method has been described based on short-term changes in chlorophyll fluorescence upon nutrient addition, also known as Nutrient-Induced Fluorescence Transients (NIFTs). Thus far, though, the NIFT technique was not well suited for macroalgae and seagrasses.

Methodology & Principal Findings

We developed a new experimental setup so that the NIFT technique can be used to assess nutrient limitation of benthic macroalgae and seagrasses. We first tested the applicability of the technique on sea lettuce (Ulva lactuca) cultured in the laboratory on nutrient-enriched medium without either nitrogen or phosphorus. Addition of the limiting nutrient resulted in a characteristic change in the fluorescence signal, whereas addition of non-limiting nutrients did not yield a response. Next, we applied the NIFT technique to field samples of the encrusting fan-leaf alga Lobophora variegata, one of the key algal species often involved in the degradation of coral reef ecosystems. The results pointed at co-limitation of L. variegata by phosphorus and nitrogen, although it responded more strongly to phosphate than to nitrate and ammonium addition. For turtle grass (Thalassia testudinum) we found the opposite result, with a stronger NIFT response to nitrate and ammonium than to phosphate.

Conclusions & Significance

Our extension of the NIFT technique offers an easy and fast method (30–60 min per sample) to determine nutrient limitation of macroalgae and seagrasses. We successfully applied this technique to macroalgae on coral reef ecosystems and to seagrass in a tropical inner bay, and foresee wider application to other aquatic plants, and to other marine and freshwater ecosystems.

Dramatic changes in a phytoplankton community in response to local and global pressures: a 24-year survey of the river Loire (France)

The impact of climate change and of other anthropogenic pressures on the structure and composition of phytoplankton communities of large European rivers remains poorly documented. Here we report the findings of a study of the changes in the phytoplankton community of the middle segment of the river Loire over the past 24 years. An attempt is made to distinguish between the impact of changes acting at the local scale and that of those acting more globally. A dramatic reduction in phytoplankton abundance was observed, particularly in the mid -1990s; this was concomitant with an increase in the relative proportion of cyanobacteria. At the same time, the phytoplankton community displayed increasing richness and diversity, and little change in its size structure. All these changes seem to be related to local changes, in particular to the reduction in phosphorus concentrations, as well as to changes in climate, throughout modifications in the river discharge and water temperature. Interestingly, herbicide contamination also appeared to be of particular importance in explaining the unexpected increase in the proportion of cyanobacteria in the phytoplankton community after the 1990s. These findings suggest that combinations of numerous anthropogenic pressures acting at different spatial and temporal scales have led to a mix of predictable and unpredictable changes occurring in the phytoplankton community of the river Loire, with probable consequences for the trophic networks in this river.

Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery.