Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary

Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4+-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.

C:N:P stoichiometry of plant-soil-microbe in the secondary succession of zokor-made mounds on Qinghai-Tibet Plateau

The knowledge of ecological stoichiometry and stoichiometric homeostasis could contribute to exploring the balance of chemical elements in ecological recovery. However, it is largely unknown how the carbon (C), nitrogen (N), phosphorus (P), and stoichiometric characteristics in the plant-soil-microbe continuum system respond to the spontaneous secondary succession of degraded alpine grasslands. Therefore, we investigated the spontaneous secondary successional recovery of grasslands disturbed by zokor (Myospalax fontanierii) on the Qinghai-Tibetan Plateau, China, via a strategy of substituting space for time. Based on plant richness, biomass, and coverage, plant importance value was employed to assess the recovery degree of zokor-made mounds (ZMMs, large and bare patch areas constructed by zokors). Multiple statistical methods, including stoichiometric homeostatic model, network, and redundancy analysis, were conducted to decipher the stoichiometric patterns. The results indicated that plant C, C:N, and C:P increased with the recovery of ZMMs, contrary to the decrease of plant N and P. In addition, soil C, N, C:N, C:P, and N:P increased with the recovery degree, and the soil became relatively more N rich by increasing organic N under the revegetation of legumes. Meanwhile, soil microbial biomass C, N, and P increased with the recovery of ZMMs, but microbial biomass C:N:P ratios were highly constrained. Soil accessible inorganic nitrogen played an important role in driving plant and microbial nutrient and stoichiometry. Our results demonstrated that the different responses of C, N, and P contents in plant-soil-microbe lead to shifts in C:N:P stoichiometric ratio. Nevertheless, plants and soil microbes exhibited strong stoichiometric homeostasis. Collectively, our study provides new insight into biogeochemical responses to the successional recovery of degraded alpine grassland on the Qinghai-Tibetan Plateau from a stoichiometric perspective.

Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication

Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.

Both specific plant functional type loss and vegetation change influence litter metallic element release in an alpine treeline ecotone

Climate warming changes the plant community composition and biodiversity. Dominate species or plant functional types (PFTs) loss may influence alpine ecosystem processes, but much uncertainty remains. This study tested whether loss of specific PFTs and vegetation variation would impact the metallic element release of mixed litter in an alpine treeline ecotone. Six representative PFTs in the alpine ecosystem on the eastern Tibetan Plateau were selected. Litterbags were used to determine the release of potassium, calcium, magnesium, sodium, manganese, zinc, copper, iron, and aluminum from litter loss of specific PFTs after 669 days of decomposition in coniferous forest (CF) and alpine shrubland (AS). The results showed that potassium, sodium, magnesium, and copper were net released, while aluminum, iron, and manganese were accumulated after 669 days. Functional type mixtures promoted the release of potassium, sodium, aluminum, and zinc (synergistic effect), while inhibiting the release of calcium, magnesium, and iron (antagonistic effect). Further, loss of specific plant functional type significantly affected the aluminum and iron release rates and the relatively mixed effects of the potassium, aluminum, and iron release rates. The synergistic effects on potassium, sodium, and aluminum in AS were greater than those in CF, while the antagonistic effect of manganese release in AS was lower than that in CF. Therefore, increased altitude may further promote the synergistic effect of potassium, sodium, and aluminum release and alleviate the antagonistic effect of manganese in mixed litter. Finally, the initial stoichiometric ratios regulate the mixed effects of elemental release rates, with the nitrogen-related stoichiometric ratios playing the most important role. The regulation of elements release by stoichiometric ratios requires more in-depth and systematic studies, which will help us to understand the influence mechanism of decomposition more comprehensively.

Decadal Changes of Organic Carbon, Nitrogen, and Acidity of Austrian Forest Soils

Repeated soil surveys provide opportunities to quantify the effect of long-term environmental change. In recent decades, the topics of forest soil acidification as a consequence of acidic deposition, the enrichment of forest ecosystems with nitrogen, and the loss of carbon due to climate change have been discussed. We used two forest soil surveys that were 20 years apart, in order to establish the direction and magnitude of changes in soil carbon, nitrogen, and soil acidity. Soils have been initially sampled in the late 1980s. The plots were revisited twenty years later. Archived soil samples from the first survey were reanalyzed with the same protocol as the new samples. We found changes in the stocks of soil organic carbon, soil nitrogen, and soil pH. However, the changes were inconsistent. In general, as many sites have gained soil organic carbon, as sites have lost carbon. Most soils have been slightly enriched with nitrogen. The soil pH has not changed significantly. We conclude that changes in the evaluated soil chemical properties are mainly driven by forest management activities and ensuing forest stand dynamics, and atmospheric deposition. We have no convincing evidence that climate change effects have already changed the soil organic carbon stock, irrespective of bedrock type.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

Effects of tree species and topography on soil and microbial biomass stoichiometry in Funiu Mountain, China

BACKGROUND

Soil and microbial biomass stoichiometry plays an important role in understanding nutrient cycling in terrestrial ecosystems. However, studies on soil and microbial biomass stoichiometry in forests are rare. This study investigated the effect of tree species and topographic factors on the ecological stoichiometry of soil and soil microbial biomass.

METHODS

Three types of forest stands (Quercus variabilis, Larix principis-ruprechtii, and Cotinus coggygria Scop.) in the Beiru River basin of Funiu Mountain were analyzed in September 2018. Six slope positions (sunny bottom slope, sunny middle slope, sunny top slope, shady bottom slope, shady middle slope, and shady top slope) were selected, and the total number of sampling plots was 108. The stoichiometric indices of soil and microbial biomass were determined.

RESULTS

At a depth of 0-10 cm, the soil organic C contents in different stands followed the order of C. coggygria (27.7 ± 5.2 g/kg) > Q. variabilis (24.5 ± 4.9 g/kg) > L. principis-ruprechtii (20.8 ± 4.3 g/kg) (P < 0.05). The soil organic C contents at depths of 0-10 cm with different slope aspects and at different slope positions also showed significant differences (P < 0.05). The highest MBC content was observed at the slope bottom (1002 ± 157 mg/kg), whereas the lowest was observed at the slope top (641 ± 98.3 mg/kg). Redundancy analysis showed that the contribution of tree species to these differences was 57.1%, whereas that of topographical factors was 36.2%.

CONCLUSIONS

Tree species more significantly affected soil nutrients and microbial biomass C, N and P than did topographic factors.

Hyperspectral Inversion of Phragmites Communis Carbon, Nitrogen, and Phosphorus Stoichiometry Using Three Models

Studying the stoichiometric characteristics of plant C, N, and P is an effective way of understanding plant survival and adaptation strategies. In this study, 60 fixed plots and 120 random plots were set up in a reed-swamp wetland, and the canopy spectral data were collected in order to analyze the stoichiometric characteristics of C, N, and P across all four seasons. Three machine models (random forest, RF; support vector machine, SVM; and back propagation neural network, BPNN) were used to study the stoichiometric characteristics of these elements via hyperspectral inversion. The results showed significant differences in these characteristics across seasons. The RF model had the highest prediction accuracy concerning the stoichiometric properties of C, N, and P. The R2 of the four-season models was greater than 0.88, 0.95, 0.97, and 0.92, respectively. According to the root mean square error (RMSE) results, the model error of total C (TC) inversion is the smallest, and that of C/N inversion is the largest. The SVM yielded poor predictive results for the stoichiometric properties of C, N, and P. The R2 of the four-season models was greater than 0.82, 0.81, 0.81, and 0.70, respectively. According to RMSE results, the model error of TC inversion is the smallest, and that of C/P inversion is the largest. The BPNN yielded high stoichiometric prediction accuracy. The R2 of the four-season models was greater than 0.87, 0.96, 0.84, and 0.90, respectively. According to RMSE results, the model error of TC inversion is the smallest, and that of C/P inversion is the largest. The accuracy and stability of the results were verified by comprehensive analysis. The RF model showed the greatest prediction stability, followed by the BPNN and then the SVM models. The results indicate that the accuracy and stability of the RF model were the highest. Hyperspectral data can be used to accurately invert the stoichiometric characteristics of C, N, and P in wetland plants. It provides a scientific basis for the long-term dynamic monitoring of plant stoichiometry through hyperspectral data in the future.

Effects of grassland degradation on ecological stoichiometry of soil ecosystems on the Qinghai-Tibet Plateau

Grasslands across the world are being degraded due to the impacts of overgrazing and climate change. However, the influences of grassland degradation on carbon (C), nitrogen (N), and phosphorus (P) dynamics and stoichiometry in soil ecosystems are not well studied, especially at high elevations where ongoing climate change is most pronounced. Ecological stoichiometry facilitates understanding the biogeochemical cycles of multiple elements by studying their balance in ecological systems. This study sought to assess the responses of these soil elements to grassland degradation in the Qinghai Lake watershed on the Qinghai-Tibet Plateau (QTP), which has an average elevation of >4000 m and is experiencing serious grassland degradation due to its sensitivity and vulnerability to external disturbances. Substituting space for time, we quantified normalized difference vegetation index to gauge grassland degradation. C, N, and P concentrations and their molar ratios in soil and in soil microbial biomass were also measured. The results showed that grassland degradation decreased the concentrations of C and N, as well as the ratios of C:P and N:P in soil. The soil became relatively more P rich and thus N limitation is anticipated to be more apparent with grassland degradation. Moreover, C, N, and P concentrations in soil microbial biomass decreased with increased grassland degradation. C:N:P ratios of soil microbial biomass were highly constrained, suggesting that soil microorganisms exhibited a strong homeostatic behavior, while the variations of microbial biomass C:N:P ratios suggest changes in microbial activities and community structure. Overall, our study revealed that grassland degradation differentially affects soil C, N, and P, leading to decreased C:N and N:P in soil, as well as decreased C, N, and P concentrations in soil microbial biomass. This study provides insights from a stoichiometric perspective into microbial and biogeochemical responses of grassland ecosystems as they undergo degradation on the QTP.

Does plant community plasticity mediate microbial homeostasis?

Microbial homeostasis-constant microbial element ratios along resource gradients-is a core ecological tenet, yet not all systems display homeostasis. We suggest investigations of homeostasis mechanisms must also consider plant-microbial interactions. Specifically, we hypothesized that ecosystems with strong plant community plasticity to changing resources will have homeostatic microbial communities, with less microbial resource cost, because plants reduce variance in resource stoichiometry. Using long-term nutrient additions in two ecosystems with differing plant response, we fail to support our hypothesis because although homeostasis appears stronger in the system with stronger plant response, microbial mechanisms were also stronger. However, our conclusions were undermined by high heterogeneity in resources, which may be common in ecosystem-level studies, and methodological assumptions may be exacerbated by shifting plant communities. We propose our study as a starting point for further ecosystem-scale investigations, with higher replication to address microbial and soil variability, and improved insight into microbial assimilable resources.

Evaluating the stoichiometric trait distributions of cultured bacterial populations and uncultured microbial communities

We measured the stoichiometric trait distribution of cultured freshwater bacterial populations under different resource conditions and compared them to natural microbial communities sampled from three lakes. Trait distributions showed population differences among growth phases and community differences among lakes that would have been masked by only reporting the mean biomass value. The stoichiometric trait distribution of the environmental isolates changed with P availability, growth phase and genotype, with P availability having the strongest effect. The distribution of biomass ratios within each isolate growth experiment were the most constrained during the stages of rapid growth and commonly had unimodal distributions. In contrast to the population distributions, the distribution of N:P and C:P for a similar number of cells from each of the lake communities had narrower stoichiometric distributions and more commonly exhibited multiple modes. © 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.

Leaf Nitrogen and Phosphorus Stoichiometry of Cyclocarya paliurus across China

Leaf stoichiometry (nitrogen (N), phosphorus (P) and N:P ratio) is not only important for studying nutrient composition in forests, but also reflects plant biochemical adaptation to geographic and climate conditions. However, patterns of leaf stoichiometry and controlling factors are still unclear for most species. In this study, we determined leaf N and P stoichiometry and their relationship with soil properties, geographic and climate variables for Cyclocarya paliurus based on a nation-wide dataset from 30 natural populations in China. The mean values of N and P concentrations and N:P ratios were 9.57 mg g−1, 0.91 mg g−1 and 10.51, respectively, indicating that both leaf N and P concentrations in C. paliurus forests were lower than those of China and the global flora, and almost all populations were limited in N concentration. We found significant differences in leaf N and P concentrations and N:P ratios among the sampled C. paliurus populations. However, there were no significant correlations between soil properties (including organic C, total N and P concentrations) and leaf stoichiometry. The pattern of variation in leaf N concentration across the populations was positively correlated with latitude (24.46° N–32.42° N), but negatively correlated with mean annual temperature (MAT); meanwhile, leaf N concentration and N:P ratios were negatively correlated with mean temperature in January (MTmin) and mean annual frost-free period (MAF). Together, these results suggested that temperature-physiological stoichiometry with a latitudinal trend hold true at both global and regional levels. In addition, the relationships between leaf stoichiometry and climate variables provided information on how leaf stoichiometry of this species may respond to climate change.

A genomic perspective on stoichiometric regulation of soil carbon cycling

Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate-stoichiometry coupling in animal and plant communities.

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

Leaf N and P stoichiometry in relation to leaf shape and plant size for Quercus acutissima provenances across China

Plant stoichiometry in relation to the structure and function of biological systems has been investigated at multiple scales. However, few studies have focused on the roles of stoichiometry for a given species. In this study, we determined leaf N and P stoichiometry, leaf shape and plant size in three Quercus acutissima common gardens with different climatic and site conditions. In the three common gardens, leaf N and P stoichiometry was significantly correlated with leaf shape and plant size, suggesting that leaf N and P stoichiometry affects the morphological performance of the leaves and stem. The scaling slopes of the relationships between leaf N and P stoichiometry and leaf shape ranged from |0.12| to |1.00|, while the slopes of the relationships between leaf N and P stoichiometry and plant size ranged from |0.95| to |2.66|. These results suggest that non-functional tissues (stem) are more susceptible to leaf nutrition than functional tissues (leaves), and leaf stoichiometry is more important in the construction of non-functional tissues (stem). Between the northernmost and southernmost common gardens, leaf N and leaf width (W), N:P and stem height (H), and N:P and stem diameter (D) showed significant covariations, which indicates that leaf N and W, N:P and plant size exhibit similar plastic responses to environmental change.

The phosphorus release pathways and their mechanisms driven by organic carbon and nitrogen in sediments of eutrophic shallow lakes

To reveal phosphorus (P) release pathways from sediment and their mechanisms induced by organic matter enrichment, 116 sampling sites (including surface water and sediment) in 29 shallow lakes with different eutrophic degrees in Wuhan city, China, were investigated from July 2011 to November 2011. Empirical relationship and structural equation model indicated that the decomposition of total organic matter (TOM), including proteins (PRT), carbo-hydrates (CHO) and lipids (especially PRT) mediated by extracellular enzymes, accelerated the formation of anaerobic status. On the other hand, coupled nitrification-denitrification caused by ammonium (NH₄⁺-N) accumulation due to PRT decomposition further aggravated anaerobic status and nitrate removal in terms of the increase of dehydrogenase activity (DHA). As a consequence, ferric iron was reduced to ferrous iron and soluble reactive phosphorus (SRP) was released from iron-bound phosphorus (Fe(OOH)~P) in sediments. In addition, extracellular alkaline phosphatase can be induced by organic carbon and nitrogen on condition that the input of nitrogen (N) and carbon (C) exceeded by far that of P. Taken together, enrichment of N and C can result in P release through the formation of anaerobic status and alkaline phosphatase production. Hence, we indicated that a close coupling existed among C, N and P cycles.

Taxonomic and Environmental Variability in the Elemental Composition and Stoichiometry of Individual Dinoflagellate and Diatom Cells from the NW Mediterranean Sea

Here we present, for the first time, the elemental concentration, including C, N and O, of single phytoplankton cells collected from the sea. Plankton elemental concentration and stoichiometry are key variables in phytoplankton ecophysiology and ocean biogeochemistry, and are used to link cells and ecosystems. However, most field studies rely on bulk techniques that overestimate carbon and nitrogen because the samples include organic matter other than plankton organisms. Here we used X-ray microanalysis (XRMA), a technique that, unlike bulk analyses, gives simultaneous quotas of C, N, O, Mg, Si, P, and S, in single-cell organisms that can be collected directly from the sea. We analysed the elemental composition of dinoflagellates and diatoms (largely Chaetoceros spp.) collected from different sites of the Catalan coast (NW Mediterranean Sea). As expected, a lower C content is found in our cells compared to historical values of cultured cells. Our results indicate that, except for Si and O in diatoms, the mass of all elements is not a constant fraction of cell volume but rather decreases with increasing cell volume. Also, diatoms are significantly less dense in all the measured elements, except Si, compared to dinoflagellates. The N:P ratio of both groups is higher than the Redfield ratio, as it is the N:P nutrient ratio in deep NW Mediterranean Sea waters (N:P = 20-23). The results suggest that the P requirement is highest for bacterioplankton, followed by dinoflagellates, and lowest for diatoms, giving them a clear ecological advantage in P-limited environments like the Mediterranean Sea. Finally, the P concentration of cells of the same genera but growing under different nutrient conditions was the same, suggesting that the P quota of these cells is at a critical level. Our results indicate that XRMA is an accurate technique to determine single cell elemental quotas and derived conversion factors used to understand and model ocean biogeochemical cycles.

The Role of Heterotrophic Microbial Communities in Estuarine C Budgets and the Biogeochemical C Cycle with Implications for Global Warming: Research Opportunities and Challenges

Estuaries are among the most productive and economically important marine ecosystems at the land-ocean interface and contribute significantly to exchange of CO2 with the atmosphere. Estuarine microbial communities are major links in the biogeochemical C cycle and flow of C in food webs from primary producers to higher consumers. Considerable attention has been given to bacteria and autotrophic eukaryotes in estuarine ecosystems, but less research has been devoted to the role of heterotrophic eukaryotic microbes. Current research is reviewed here on the role of heterotrophic eukaryotic microbes in C biogeochemistry and ecology of estuaries, with particular attention to C budgets, trophodynamics, and the metabolic fate of C in microbial communities. Some attention is given to the importance of these processes in climate change and global warming, especially in relation to sources and sinks of atmospheric CO2 , while also documenting the current paucity of research on the role of eukaryotic microbes that contribute to this larger question of C biogeochemistry and the environment. Some recommendations are made for future directions of research and opportunities of applying newer technologies and analytical approaches to a more refined analysis of the role of C in estuarine microbial community processes and the biogeochemical C cycle.

Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns

Carbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction-oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade-off between high nitrate and high organic carbon concentrations, and the even stronger trade-off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both microbial biomass stoichiometry and the availability of terminal electron acceptors. Because elements with multiple oxidation states (i.e. nitrogen, manganese, iron and sulphur) serve as both nutrients and sources of chemical energy in reduced environments, both assimilative demand and dissimilatory uses determine their concentrations across broad spatial gradients. Conceptual and quantitative models that integrate rather than independently examine thermodynamic, stoichiometric and evolutionary controls on biogeochemical cycling are essential for understanding local to global biogeochemical patterns.

Rhizosphere stoichiometry: are C : N : P ratios of plants, soils, and enzymes conserved at the plant species-level?

As a consequence of the tight linkages among soils, plants and microbes inhabiting the rhizosphere, we hypothesized that soil nutrient and microbial stoichiometry would differ among plant species and be correlated within plant rhizospheres. We assessed plant tissue carbon (C) : nitrogen (N) : phosphorus (P) ratios for eight species representing four different plant functional groups in a semiarid grassland during near-peak biomass. Using intact plant species-specific rhizospheres, we examined soil C : N : P, microbial biomass C : N, and soil enzyme C : N : P nutrient acquisition activities. We found that few of the plant species' rhizospheres demonstrated distinct stoichiometric properties from other plant species and unvegetated soil. Plant tissue nutrient ratios and components of below-ground rhizosphere stoichiometry predominantly differed between the C4 plant species Buchloe dactyloides and the legume Astragalus laxmannii. The rhizospheres under the C4 grass B. dactyloides exhibited relatively higher microbial C and lower soil N, indicative of distinct soil organic matter (SOM) decomposition and nutrient mineralization activities. Assessing the ecological stoichiometry among plant species' rhizospheres is a high-resolution tool useful for linking plant community composition to below-ground soil microbial and nutrient characteristics. By identifying how rhizospheres differ among plant species, we can better assess how plant-microbial interactions associated with ecosystem-level processes may be influenced by plant community shifts.

Eco-stoichiometric alterations in paddy soil ecosystem driven by phosphorus application

Agricultural fertilization may change processes of elemental biogeochemical cycles and alter the ecological function. Ecoenzymatic stoichiometric feature plays a critical role in global soil carbon (C) metabolism, driving element cycles, and mediating atmospheric composition in response to agricultural nutrient management. Despite the importance on crop growth, the role of phosphorous (P) in compliance with eco-stoichiometry on soil C and nitrogen (N) sequestration in the paddy field remains poorly understood in the context of climate change. Here, we collected soil samples from a field experiment after 6 years of chemical P application at a gradient of 0 (P-0), 30 (P-30), 60 (P-60), and 90 (P-90) kg ha⁻¹ in order to evaluate the role of P on stoichiometric properties in terms of soil chemical, microbial biomass, and eco-enzyme activities as well as greenhouse gas (GHG: CO₂, N₂O and CH₄) emissions. Continuous P input increased soil total organic C and N by 1.3–9.2% and 3%–13%, respectively. P input induced C and N limitations as indicated by the decreased ratio of C:P and N:P in the soil and microbial biomass. A synergistic mechanism among the ecoenzymatic stoichiometry, which regulated the ecological function of microbial C and N acquisition and were stoichiometrically related to P input, stimulated soil C and N sequestration in the paddy field. The lower emissions of N₂O and CH₄ under the higher P application (P-60 and P-90) in July and the insignificant difference in N₂O emission in August compared to P-30; however, continuous P input enhanced CO₂ fluxes for both samplings. There is a technical conflict for simultaneously regulating three types of GHGs in terms of the eco-stoichiometry mechanism under P fertilization. Thus, it is recommended that the P input in paddy fields not exceed 60 kg ha⁻¹ may maximize soil C sequestration, minimize P export, and guarantee grain yields.

Linking community size structure and ecosystem functioning using metabolic theory

Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change.

Differential nutrient limitation of soil microbial biomass and metabolic quotients (qCO2): is there a biological stoichiometry of soil microbes?

Background

Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils.

Methodology/Principal Findings

To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO₂ (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO₂) were most strongly associated with inorganic P availability.

Conclusions/Significance

Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.

Does microbial stoichiometry modulate eutrophication of aquatic ecosystems?

The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X-ray microanalysis to determine C : N : P ratios of individual prokaryotes from C-limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C : P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C : N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C : P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.

Stoichiometric flexibility as a regulator of carbon and nutrient cycling in terrestrial ecosystems under change

Ecosystems across the biosphere are subject to rapid changes in elemental balance and climatic regimes. A major force structuring ecological responses to these perturbations lies in the stoichiometric flexibility of systems - the ability to adjust their elemental balance whilst maintaining function. The potential for stoichiometric flexibility underscores the utility of the application of a framework highlighting the constraints and consequences of elemental mass balance and energy cycling in biological systems to address global change phenomena. Improvement in the modeling of ecological responses to disturbance requires the consideration of the stoichiometric flexibility of systems within and across relevant scales. Although a multitude of global change studies over various spatial and temporal scales exist, the explicit consideration of the role played by stoichiometric flexibility in linking micro-scale to macro-scale biogeochemical processes in terrestrial ecosystems remains relatively unexplored. Focusing on terrestrial systems under change, we discuss the mechanisms by which stoichiometric flexibility might be expressed and connected from organisms to ecosystems. We suggest that the transition from the expression of stoichiometric flexibility within individuals to the community and ecosystem scales is a key mechanism regulating the extent to which environmental perturbation may alter ecosystem carbon and nutrient cycling dynamics.