Microbial Food Chain Research Articles

Improvement of Biogas Production by Bioaugmentation

Biogas production technologies commonly involve the use of natural anaerobic consortia of microbes. The objective of this study was to elucidate the importance of hydrogen in this complex microbial food chain. Novel laboratory biogas reactor prototypes were designed and constructed. The fates of pure hydrogen-producing cultures of Caldicellulosiruptor saccharolyticus and Enterobacter cloacae were followed in time in thermophilic and mesophilic natural biogas-producing communities, respectively. Molecular biological techniques were applied to study the altered ecosystems. A systematic study in 5-litre CSTR digesters revealed that a key fermentation parameter in the maintenance of an altered population balance is the loading rate of total organic solids. Intensification of the biogas production was observed and the results corroborate that the enhanced biogas productivity is associated with the increased abundance of the hydrogen producers. Fermentation parameters did not indicate signs of failure in the biogas production process. Rational construction of more efficient and sustainable biogas-producing microbial consortia is proposed.

Above‐ and belowground linkages in Sphagnum peatland: climate warming affects plant‐microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands.

A Comparison of Nano – Scale X-Ray Microscopy and Scanning Transmission Electron Microscopy applied to TiO2 Nanoparticles in a Microbial Food Chain

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Testing the light : nutrient hypothesis in an oligotrophic boreal lake

Anthropogenic changes in the nitrogen (N), phosphorus (P), and carbon (C) cycles have altered nutrient concentrations and the light climate in freshwaters globally. These factors affect phytoplankton (PPr) and bacterial production (BP), which constitute the basal energy resource for higher trophic levels in the pelagic zone of lakes. The light : nutrient hypothesis (LNH) predicts that although basal production decreases at low light, seston C : nutrient ratios also decrease, thus increasing food quality for crustacean zooplankton and potentially offsetting the negative effects of reduced food availability. We tested the LNH in an oligotrophic boreal lake by manipulating N, P, C and reducing light, and measuring PPr, BP, seston C : nutrient ratios and zooplankton biomass in 32 mesocosms. Low light strongly reduced zooplankton biomass in contrast to LNH predictions. PPr did not decrease with low light as predicted by the LNH, however, the phytoplankton community shifted towards low light adapted, but potentially less edible phytoplankton species, such as colony forming Dinobryon (Chrysophyta) and gymnoid (Dinoflagellata) taxa, which were negatively correlated with zooplankton biomass. Seston C : nutrient ratios did not decrease with reduced light, possibly due to the high abundance of mixotrophic phytoplankton across treatments. BP decreased with low light and correlations between BP, bacterial biomass, ciliates and zooplankton suggest that bacteria may be coupled with zooplankton biomass. Thus, the LNH was inadequate when predicting changes in crustacean zooplankton biomass in this typical oligotrophic boreal system, where Daphnia is rare and mixotrophic phytoplankton are abundant. Instead, alternative explanations, such as changes in phytoplankton edibility and energy transferred through the microbial food chain may need investigation to explain reduced zooplankton biomass in low light treatments.

Sulfur, carbon, and nitrogen stable isotope ratios in soft tissues and trophic relationships of fish from the near-shore waters of the peter the great bay in the Sea of Japan

Stable isotope ratios of sulfur (34S/32S), carbon (13C/12C), and nitrogen (15N/14N) were analyzed in the soft tissues of 12 common species of fish from the near-shore waters of the Peter the Great Bay in the Sea of Japan. The average δ13C values of individual species varied from −20.7‰ for planktivorous fish to −16.8‰ for benthivorous fish, reflecting the growing relative contribution of benthic primary producers to fish nutrition. The majority of the various species representatives studied can be assigned to one trophic level, as indicated by their narrow range of δ15N values (9.9 to 12.6‰). Large interspecific variations were found in the sulfur stable isotope ratios of fish (the mean δ34S values ranged from 11.2 to 19.5‰). This is the result of the different contributions to fish nutrition of infaunal invertebrates that are depleted in 34S due to the microbial food chain of the bottom sediments.

Organic Carbon Degradation in Anoxic Organic-Rich Shelf Sediments: Biogeochemical Rates and Microbial Abundance

Identifying and explaining bottlenecks in organic carbon mineralization and the persistence of organic matter in marine sediments remain challenging. This study aims to illuminate the process of carbon flow between microorganisms involved in the sedimentary microbial food chain in anoxic, organic-rich sediments of the central Namibian upwelling system, using biogeochemical rate measurements and abundances of Bacteroidetes, Gammaproteobacteria, and sulfate-reducing bacteria at two sampling stations. Sulfate reduction rates decreased by three orders of magnitude in the top 20 cm at one sampling station (280 nmol cm−3 d−1 – 0.1 nmol cm−3 d−1) and by a factor of 7 at the second station (65 nmol cm−3 d−1 – 9.6 nmol cm−3 d−1). However, rates of enzymatic hydrolysis decreased by less than a factor of three at both sampling stations for the polysaccharides laminarin (23 nmol cm−3 d−1– 8 nmol cm−3 d−1 and 22 nmol cm−3 d−1– 10 nmol cm−3 d−1) and pullulan (11 nmol cm−3 d−1– 4 nmol cm−3 d−1 and 8 nmol cm−3 d−1– 6 nmol cm−3 d−1). Increasing imbalance between carbon turnover by hydrolysis and terminal oxidation with depth, the steep decrease in cell specific activity of sulfate reducing bacteria with depth, low concentrations of volatile fatty acids (less than 15 μM), and persistence of dissolved organic carbon, suggest decreasing bioavailability and substrate limitation with depth.

The effects of Anabaena spiroides exopolysaccharides on copper accumulation in an aquatic food chain

The influence of Anabaena spiroides exopolysaccharides (EPS) on copper speciation (total dissolved, particulate and free Cu 2+ ions) and bioavailability in aquatic organisms was investigated. Bacteria were used as the first trophic level, Paramecium caudatum (protozoan) as the second and the copepod cyclopoid Metacyclops mendocinus as the third level. The organisms were obtained from a freshwater reservoir and held under continuous laboratory controlled conditions. Freshwater media containing EPS excreted by A. spiroides (10 mg L −1) and copper (1.0 × 10 −6 mol L −1) were used for bacteria growth. Contamined bacteria were used as food source to protozoan, which was further furnished to copepods. The results showed a reduction of EPS concentration during bacteria growth and also a smaller copper accumulation by microorganisms in the presence of EPS. We concluded that A. spiroides exopolysaccharides have reduced copper entrance into the experimental aquatic microbial food chain.

How many consumer levels can survive in a chemotactic food chain?

We investigate the effect and the impact of predator-prey interactions, diffusivity and chemotaxis on the ability of survival of multiple consumer levels in a predator-prey microbial food chain. We aim at answering the question of how many consumer levels can survive from a dynamical system point of view. To solve this standing issue on food-chain length, first we construct a chemotactic food chain model. A priori bounds of the steady state populations are obtained. Then under certain sufficient conditions combining the effect of conversion efficiency, diffusivity and chemotaxis parameters, we derive the co-survival of all consumer levels, thus obtaining the food chain length of our model. Numerical simulations not only confirm our theoretical results, but also demonstrate the impact of conversion efficiency, diffusivity and chemotaxis behavior on the survival and stability of various consumer levels.

Natural DOM Affects Copper Speciation and Bioavailability to Bacteria and Ciliate

This study aimed to investigate the influence of natural dissolved organic materials (DOM) on copper speciation (total dissolved, particulate, and free Cu2+ ions) and bioavailability during a two-level experimental microbial food chain. Bacteria were used as the first trophic level, and Paramecium caudatum (protozoan) as the second. The organisms were obtained from a freshwater reservoir and kept under controlled laboratory conditions. Three experimental treatments were performed: exposure of the organisms to copper in the absence of DOM, exposure to DOM in the absence of copper, and exposure to both copper and DOM. Freshwater medium containing natural DOM and copper at a total dissolved concentration of 1.8 x 10(-6) mol L(-1) was furnished to bacteria, which was further used as food to the protozoan. The results showed that after bacterial growth, DOM concentration decreased as quantified by total organic carbon determinations. At the same time, free Cu2+ ions concentration increased in the medium. A lower copper concentration was detected in both microorganisms in the presence of DOM. We conclude that natural DOM reduced copper accumulation in the organisms on the first and second trophic levels, thus reducing the entrance of copper into the aquatic microbial food chain.

Microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor

Excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. The gravel contact oxidation reactor (GCOR) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. In order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in GCOR, a conventional activated sludge reactor (ASR) was studied as a comparison. The 16S rDNA library of the universal bacteria was constructed, Shannon's diversity index ( H) and Species evenness ( E) were calculated with distance-based operational taxonomic unit and richness (DOTUR) for microbial diversity. Real-time quantity PCR and optical microscope were used for absolute bacterial DNA concentration and eukarya identification, respectively. Meanwhile, the suspended solid index in GCOR and ASR was detected for assessing the excess sludge production. The results indicated that the most abundant bacteria in GCOR were those related to the β-Proteobacteria group, then γ-Proteobacteria and to Cytophaga-Flexibacter-Bacteriode (CFB). In the ASR samples major bacteria were in the closest match with γ-Proteobacteria, then β-Proteobacteria and CFB. Shannon's index ( H) was higher (3.41) for diversity of bacteria extracted from the carrier samples in GCOR than that (2.71) from the sludge sample in ASR. Species evenness ( E) for the isolates from GCOR and ASR samples was 0.97 and 0.96, respectively. Comparison of the universal bacteria population in GCOR and ASR shows that the total bacterial DNA concentration on the GCOR carriers were 8.98 × 10 5 μg/μl, twice that in ASR of 4.67 × 10 5 μg/μl under normal operation of two reactors. But the MLSS in GCOR was only 4.5 mg/L, 25 times less than that in ASR of 115.4 mg/L. The most representative eukarya were protozoa both in GCOR (15 no. per 20 ml) and in ASR (15 no. per 20 ml); the next abundant group was attachment plants 10 no. per 20 ml in GCOR and 4 no. per 20 ml in ASR, respectively. Rotifers and copepoda belonging to metazoan were only present in GCOR (8 no. per 20 ml for both rotifers and copepoda). The microbial diversity and population difference both in the GCOR carriers and ASR sludge indicated that the diverse microbes, a large amount of biomass forming longer microbial food chains attached on the carriers may be the main functions for the excess sludge reduction in GCOR.

Abstracts of Nippon Dojo-Hiryogaku Zasshi

Abstracts of Nippon Dojo-Hiryogaku Zasshi

Structure, biomass distribution and trophodynamics of the pelagic ecosystem in the Oyashio region, western subarctic Pacific

Biomass distribution and trophodynamics in the oceanic ecosystem in the Oyashio region are presented and analyzed, combining the seasonal data for plankton and micronekton collected at Site H since 1996 with data for nekton and other animals at higher trophic levels from various sources. The total biomass of biological components including bacteria, phytoplankton, microzooplankton, mesozooplankton, micronekton, fishes/squids and marine birds/mammals was 23 g C m−2, among which the most dominant component was mesozooplankton (34% of the total), followed by phytoplankton (28%), bacteria (15%) and microzooplankton (protozoans) (14%). The remainder (9%) was largely composed of micronekton and fish/squid. Marine mammals/birds are only a small fraction (0.14%) of the total biomass. Large/medium grazing copepods (Neocalaus spp., Eucalanus bungii and Metridia spp.) accounted for 77% of the mesozooplankton biomass. Based on information about diet composition, predators were assigned broadly into mean trophic level 3–4, and carbon flow through the grazing food chain was established based on the estimated annual production/food consumption balance of each trophic level. From the food chain scheme, ecological efficiencies as high as 24% were calculated for the primary/secondary production and 21% for the secondary/tertiary production. Biomass and production of bacteria were estimated as 1/10 of the respective values for phytoplankton at Site H, but the role of the microbial food chain remains unresolved in the present analysis. As keystone species in the oceanic Oyashio region, Neocalanus spp. are suggested as a vital link between primary production and production of pelagic fishes, mammals and birds.

Competition for inorganic and organic forms of nitrogen and phosphorous between phytoplankton and bacteria during an <i>Emiliania huxleyi</i> spring bloom

Abstract. Using 15N and 33P, we measured the turnover of organic and inorganic nitrogen (N) and phosphorus (P) substrates, and the partitioning of N and P from these sources into two size fractions of marine osmotrophs during the course of a phytoplankton bloom in a nutrient manipulated mesocosm. The larger size fraction (>0.8 μm), mainly consisting of the coccolithophorid Emiliania huxleyi, but also including an increasing amount of large particle-associated bacteria as the bloom proceeded, dominated uptake of the inorganic forms NH4+, NO3−, and PO43−. The uptake of N from leucine, and P from ATP and dissolved DNA, was initially dominated by the 0.8–0.2 μm size fraction, but shifted towards dominance by the >0.8 μm size fraction as the system turned to an increasing degree of N-deficiency. Normalizing uptake to biomass of phytoplankton and heterotrophic bacteria revealed that organisms in the 0.8–0.2 μm size fraction had higher specific affinity for leucine-N than those in the >0.8 μm size fraction when N was deficient, whereas the opposite was the case for NH4+. There was no such difference regarding the specific affinity for P substrates. Since heterotrophic bacteria seem to acquire N from organic compounds like leucine more efficiently than phytoplankton, our results suggest different structuring of the microbial food chain in N-limited relative to P-limited environments.

Methanogenesis in Marine Sediments

The anaerobic conversion of complex organic matter to CH(4) is an essential link in the global carbon cycle. In freshwater anaerobic environments, the organic matter is decomposed to CH(4) and CO(2) by a microbial food chain that terminates with methanogens that produce methane primarily by reduction of the methyl group of acetate and also reduction of CO(2). The process also occurs in marine environments, particularly those receiving large loads of organic matter, such as coastal sediments. The great majority of research on methanogens has focused on marine and freshwater CO(2)-reducing species, and freshwater acetate-utilizing species. Recent molecular, biochemical, bioinformatic, proteomic, and microarray analyses of the marine isolate Methanosarcina acetivorans has revealed that the pathway for acetate conversion to methane differs significantly from that in freshwater methanogens. Similar experimental approaches have also revealed striking contrasts with freshwater species for the pathway of CO-dependent CO(2) reduction to methane by M. acetivorans. The differences in both pathways reflect an adaptation by M. acetivorans to the marine environment.

Determination of food sources of marine invertebrates from a subtidal sand community using analyses of fatty acids and stable isotopes

The fatty acid compositions and stable isotope ratios of carbon, nitrogen, and sulfur were analyzed in the bivalve mollusks Mactra chinensis, Pandora pulchella, Felaniella usta, and Megangulus zyonoensis, the polychaete Chaetopterus cautus, and the main sources of organic matter in a subtidal sand bottom community in Vostok Bay (Sea of Japan). The fatty acid composition and stable isotope ratios of some bivalves is likely to be indicative of substantial inputs from benthic microalgae and an important role of microbial food chains. Only the filter-feeding polychaete C. cautus showed similarity in these characteristics to suspended particulate organic matter synthesized by phytoplankton. It is suggested that the contribution of benthic microalgae to the diet of a consumer organism, inferred solely from the carbon stable isotope analysis, can be significantly overestimated.

Rhizospheric influence on soil respiration and decomposition in a temperate Norway spruce stand

Assessments of terrestrial carbon fluxes require a thorough understanding of links between primary production, soil respiration and carbon loss through drainage. In this study, stem girdling was used to terminate autotrophic soil respiration including rhizosphere respiration and root exudation in a temperate Norway spruce stand. Rates of soil respiration and dissolved organic carbon (DOC) formation were measured in the second year after girdling, comparing an intact plant–rhizosphere continuum with an exclusive decomposer system. The molecular and isotopic composition of DOC in the soil solution was analysed with a coupled Py-GC/MS-C-IRMS system to distinguish between the carbon sources of dissolved carbon. Pyrolysis products were grouped according to their precursor origins: polysaccharides, proteins or of mixed origin (mainly derivates of lignins and proteins). When dead roots became available for decomposition, rates of heterotrophic soil respiration in girdling plots peaked at 6.5 μmol m −2 s −1, comparable to peak rates of total soil respiration (autotrophic and heterotrophic) in control plots, 6.1 μmol m −2 s −1. A significant response of soil respiration to temperature was found in control plots only, showing that an unlimiting supply of organic substrates for microbial respiration may mask any temperature effects. The enhanced decomposition in girdled plots was further supported by the isotopic composition of DOC in soil solution; all three precursor groups became isotopically enriched as the growing season progressed (polysaccharides by 2.3‰, proteins by 1.9‰, mixed origin group by 2.2‰). This indicates a trophic level shift due to incorporation of organic substrate into the microbial food chain. In the control plots’ mixed origin fraction, the isotopic composition changed over time from a signature resembling that of lignin (−28.9‰) to one similar of the protein fraction (−25.7‰). Significant temporal changes of structural DOC composition occurred in the girdling plots only. These results suggest that changes in the microbial community and in decomposition rates occurred in both girdled and control plots in the following ways: (i) increased substrate availability (dead roots) gave rise to generally enhanced performance of the decomposer community in girdled plots, (ii) root-derived exudates probably contributed to enhanced decomposition of recalcitrant lignin in the control plots and (iii) the structural composition of DOC seemed to be more a result of decomposition than of plant root exudation in all plots.

Activated Sludge Process Modification for Sludge Yield Reduction Using Pulp and Paper Wastewater

Implications of conventional activated sludge (CAS) process modification to a low sludge production (LSP) process have been studied for treating pulp and paper wastewaters. The activated sludge process is modified to a two-stage design to establish a microbial food chain that would result in reduced sludge production. The return activated sludge in the LSP process bypasses the first (dispersed growth) stage to be received only by the second (predatory) stage. The resulting once-through operation of the dispersed growth (DG) stage makes it potentially susceptible to bacterial washout under hydraulic shock conditions. A sensitivity analysis of the DG stage operation was performed by varying its hydraulic residence time. The experimental data revealed that the optimal DG stage hydraulic residence is between 3 and 5 h, with bacterial washout likely to be initiated within 2 h. Based on laboratory results, it appears that a well-designed LSP system is likely to be able to handle day-to-day variations in hydraulic and organic loading rates. The LSP process produced 36% less sludge than the CAS process while consuming approximately 25% more oxygen. The treatment performance of the two systems was comparable except that the LSP sludge had much better settling and dewatering properties.

Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community.

The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.

INDUCIBLE DEFENSES AND TROPHIC STRUCTURE

Resource edibility is a crucial factor in ecological theory on the relative importance of bottom-up and top-down control. Current theory explains trophic structure in terms of the relative abundance and succession of edible and inedible species across gradients of primary productivity. We argue that this explanation is incomplete owing to its focus on inedibility and the assumption that plants and herbivores have fixed defense levels. Consumer-induced defenses are an important source of variation in the vulnerability of prey and are prevalent in natural communities. Such induced defenses decrease per capita consumption rates of consumers but hardly ever result in complete inedibility. When defenses are inducible a prey population may consist of both undefended and defended individuals. Here we use food chain models with realistic parameter values to show that variation in consumption rates on different prey types causes a gradual instead of stepwise increase in the biomass of all trophic levels in response to enrichment. Such all-level responses have been observed in both aquatic and terrestrial ecosystems and in microbial food chains in the laboratory. We stress that, in addition to the known food web effects of interspecific variation in edibility, intraspecific variation in edibility is another form of within-trophic-level heterogeneity that also has such effects. We conclude that inducible defenses increase the relative importance of bottom-up control.

Competition between the rotifer Brachionus rotundiformis and the ciliate Euplotes vannus fed on two different algae

The ciliate Euplotes vannus is a common protozoan in mass cultures of rotifers, and rapid reproduction of E. vannus occasionally reduces the rotifer yield. We performed a competition experiment between the rotifer Brachionus rotundiformis and the ciliate E. vannus. The ciliate was inoculated at three stages of the rotifer growth curve: the lag phase, the logarithmic growth phase and the stationary phase. When feeding on the alga Tetraselmis tetrathele, the ciliate increased and the rotifer growth was suppressed. The interference with rotifer growth was stronger in the lag and stationary phases than in the logarithmic growth phase. In contrast, when feeding on the alga Nannochloropsis oculata, the ciliate did not increase and the rotifer growth was similar to the control. In addition to the competition experiments, 15N incorporation experiments were performed on the ciliate to investigate its food preference. The nitrogen incorporation rates (% of body nitrogen h −1) of the ciliate were 0.7% through dead algae and 1.9% through rotifer feces when using T. tetrathele, and 0.4% through dead algae and 3.4% through rotifer feces when using N. oculata. The incorporation rate through bacteria-free rotifer feces was about one-third that of normal rotifer feces. These results indicated that the ciliate did not incorporate algal nitrogen directly, but rather through the microbial food chain, from phytoplankton to rotifer feces to bacteria. E. vannus incorporated the nitrogen of N. oculata and grew for a short time but the growth was soon suppressed. This growth inhibition may be due to allelopathy of N. oculata for E. vannus. Consequently, we propose that periodic addition of N. oculata should control E. vannus, and that this technique of applying allelopathy should be more sustainable than conventional treatments.