Divergence of feeding channels within the soil food web determined by ecosystem type

Understanding trophic linkages within the soil food web (SFW) is hampered by its opacity, diversity, and limited niche adaptation. We need to expand our insight between the feeding guilds of fauna and not just count biodiversity. The soil fauna drive nutrient cycling and play a pivotal, but little understood role within both the carbon (C) and nitrogen (N) cycles that may be ecosystem dependent. Here, we define the structure of the SFW in two habitats (grassland and woodland) on the same soil type and test the hypothesis that land management would alter the SFW in these habitats. To do this, we census the community structure and use stable isotope analysis to establish the pathway of C and N through each trophic level within the ecosystems. Stable isotope ratios of C and N from all invertebrates were used as a proxy for trophic niche, and community‐wide metrics were obtained. Our empirically derived C/N ratios differed from those previously reported, diverging from model predictions of global C and N cycling, which was unexpected. An assessment of the relative response of the different functional groups to the change from agricultural grassland to woodland was performed. This showed that abundance of herbivores, microbivores, and micropredators were stimulated, while omnivores and macropredators were inhibited in the grassland. Differences between stable isotope ratios and community‐wide metrics, highlighted habitats with similar taxa had different SFWs, using different basal resources, either driven by root or litter derived resources. Overall, we conclude that plant type can act as a top‐down driver of community functioning and that differing land management can impact on the whole SFW.     

Trophic interactions within the microbial food web in the South China Sea revealed by size-fractionation method

To define nanoflagellate-bacteria interactions and potential trophic levels within the microbial food web in the oligotrophic South China Sea, we conducted fourteen size-fractionation experiments in which seawater was filtered through 1, 2, 5, 10, 20, 60, and 200 μm membranes or meshes and the growth of four groups of picoplankton, Prochlorococcus, Synechococcus, high DNA heterotrophic bacteria, and low DNA heterotrophic bacteria were monitored in each filtrate after 24 hours of incubation. Removing grazers by filtration would relieve the grazing pressure on lower trophic levels which finally influenced the net growth rates of picoplankton. The growth patterns of Prochlorococcus and Synechococcus were similar, with higher growth rates in the < 1 μm or < 2 μm treatments, a second peak in the < 10 μm treatments and often a third peak in the < 200 μm treatments. The net growth rates of low DNA heterotrophic bacteria were little influenced by size-fractionation. Due to a subgroup of high DNA heterotrophic bacteria with larger size and higher DNA content which appeared to resist the grazing by < 5 μm nanoflagellates, the net growth rates of high DNA heterotrophic bacteria were higher in the < 2 μm or < 5 μm treatments with a second peak in the < 60 μm treatments. A general pattern of five potential trophic levels (< 2 μm, 2-5 μm, 5-10 μm, 10-60 μm, 60-200 μm) was revealed combining all the experiments, confirming the existence of multiple trophic levels within the microbial food web in the oligotrophic South China Sea.     

Trophic relationships in a tropical stream food web assessed by stable isotope analysis

1. Stable isotope analysis, coupled with dietary data from the literature, was used to investigate trophic patterns of freshwater fauna in a tropical stream food web (Guadeloupe, French West Indies).
2. Primary producers (biofilm, algae and plant detritus of terrestrial origin) showed distinct δ¹³C signatures, which allowed for a powerful discrimination of carbon sources. Both autochthonous (¹³C-enriched signatures) and allochthonous (¹³C-depleted signatures) resources enter the food web. The migrating behaviour of fishes and shrimps between marine and freshwater during their life cycles can be followed by carbon isotopes. Here, shrimp δ¹³C signatures were shown to shift from −16‰ (for juveniles under marine influence) to −24.7‰ (for adults in freshwater habitats). For resident species, δ¹³C values partly reflected the species' habitat preferences along the river continuum : species living in river mouths were ¹³C-enriched in comparison with those collected upstream.
3. Nitrogen isotopic ratios were also discriminating and defined three main trophic guilds among consumers. The δ¹⁵N values of herbivores/detritivores were 5.0–8.4‰, omnivores 8.8–10.2‰ and carnivores 11–12.7‰.
4. Mixing model equations were employed to calculate the possible range of contribution made by respective food sources to the diet of each species. The results revealed the importance of omnivorous species and the dependence of riverine biota on terrestrial subsidies, such as leaf detritus and fruits. Finally, the abundance of shrimps and their feeding habits placed in relief their key role in tropical freshwater food webs. Isotopic analysis provides a useful tool for assessing animal feeding patterns.     

Ciliate community structure and interactions within the planktonic food web in two alpine lakes of contrasting transparency

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Trophic interactions within the microbial food web in a tropical floodplain lake (Laguna Bufeos, Bolivia)

Whether the primary role of bacterioplankton is to act as "remineralizers" of nutrients or as direct nutritional source for higher trophic levels will depend on factors controlling their production and abundance. In tropical lakes, low nutrient concentration is probably the main factor limiting bacterial growth, while grazing by microzooplankton is generally assumed to be the main loss factor for bacteria. Bottom-up and top-down regulation of microbial abundance was studied in six nutrient limitation and dilution gradient-size fractionation in situ experiments. Bacteria, heterotrophic nanoflagellates (HNF), ciliates and rotifers showed relatively low densities. Predation losses of HNF and ciliates accounted for a major part of their daily production, suggesting a top-down regulation of protistan populations by rotifers. Phosphorus was found to be strongly limiting for bacterial growth, whereas no response to enrichment with Nitrogen or DOC was detected. HNF were the major grazers on bacteria (g-0.43 d(-1)), the grazing coefficient increased when ciliates were added (g- 0.80 d(-1)) but decreased when rotifers were added (g- 0.23 d(-1)) probably due to nutrient recycling or top-down control of HNF and ciliates by rotifers.     

Trophic coupling within the microbial food web: a study with fine temporal resolution in a eutrophic freshwater ecosystem

• 1 The major components of the microbial food web (dissolved organic carbon, bacteria, protozoa, rotifers and algae) of Priest Pot, a small freshwater pond, were investigated over a period of 5 months. Water samples were collected from the epilimnion every 1–3 days.
• 2 Time series analysis helped identify the trophic relationships within the planktonic community. There were strong predator—prey relationships between both ciliates and large rotifers and the total nanoplankton, between rotifers and small ciliates and between the total microzooplankton community and phytoplankton. Small rotifers and small ciliates probably share the same food resources. The major bacterivores in the system could not be identified with our methods. However, our previous results point to a dominating role of nanoplanktonic (2–20 μm) heterotrophic protists as the main grazers of bacteria.
• 3 Rotifers are the major type of metazoan zooplankton in Priest Pot; crustacean zooplankton are absent from the community. Bacterial production probably reaches rotifers via a variety of pathways: there may be a three-step link from bacteria to bacterivorous nanoplankton, to ciliates and then to rotifers. Furthermore, a strong correlation between the nanoplankton and rotifers suggests a direct link between these components, implying a much shorter pathway. Some of the rotifers in the pond can graze directly on bacteria, and many of the larger planktonic organisms (large ciliates and rotifers) are algivores. The latter two predator—prey relationships suggest an efficient transfer of bacterial and primary production to higher trophic levels.

     

Plant species identity and diversity effects on different trophic levels of nematodes in the soil food web

Previous studies on biodiversity and soil food web composition have mentioned plant species identity, as well as plant species diversity as the main factors affecting the abundance and diversity of soil organisms. However, most studies have been carried out under limitations of time, space, or appropriate controls. In order to further examine the relation between plant species diversity and the soil food web, we conducted a three-year semi-field experiment in which eight plant species (4 forb and 4 grass species) were grown in monocultures and mixtures of two, four and eight plant species. In addition there were communities with 16 plant species. We analyzed the abundance and identity of the nematodes in soil and roots, including feeding groups from various trophic levels (primary and secondary consumers, carnivores, and omnivores) in the soil food web.
Plant species diversity and plant identity affected the diversity of nematodes. The effect of plant diversity was attributed to the complementarity in resource quality of the component plant species rather than to an increase in total resource quantity. The nematode diversity varied more between the different plant species than between different levels of plant species diversity, so that plant identity is more important than plant diversity. Nevertheless the nematode diversity in plant mixtures was higher than in any of the plant monocultures, due to the reduced dominance of the most abundant nematode taxa in the mixed plant communities. Plant species identity affected the abundances of the lower trophic consumer levels more than the higher trophic levels of nematodes. Plant species diversity and plant biomass did not affect nematode abundance. Our results, therefore, support the hypothesis that resource quality is more important than resource quantity for the diversity of soil food web components and that plant species identity is more important than plant diversity per se.     

Carbon steady-state model of the planktonic food web of Lake Biwa, Japan

1. A steady‐state model of carbon flows was developed to describe the summer planktonic food web in the surface mixed‐layer of the North Basin in Lake Biwa, Japan. This model synthesised results from numerous studies on the plankton of Lake Biwa. 2. An inverse analysis procedure was used to estimate missing flow values in a manner consistent with known information. Network analysis was applied to characterise emergent properties of the resulting food web. 3. The system strongly relied on flows related to detrital particles. Whereas primary production was mainly by phytoplankton >20 μm, microzooplankton were active and mainly ingested detritus and bacteria. 4. The main emergent property of the system was strong recycling, through either direct ingestion of non‐living material by zooplankton, or ingestion of bacteria after degradation of detritus to release dissolved organic carbon.     

Bacterial diversity within the planktonic community of an artesian water supply

Culture and molecular methods were used to describe the planktonic bacterial diversity of an artesian water supply in rural Latah County, Idaho, within the drainage of a small perennial stream, Thorn Creek. The surrounding depth to groundwater at this location is thought to be significant (>100 m), and this transitional zone (basalt-granite) of the Palouse aquifer system is little studied. The water produced by this artesian source is consistent even in years of drought and is of high quality, both mineralogically and microbiologically. A culture-based analysis using 30 media types and four incubation temperatures demonstrated that several metabolic types were present in the water. 16S rRNA gene fragments amplified from the DNA of pooled cultured cells and from the DNA extracted from 1 L of the source water were compared using denaturing gradient gel electrophoresis. The results indicated that the two DNA samples did not have similar 16S rRNA gene compositions and that several uncultured phyla were present in the community DNA sample. These results indicated that large-scale culturing did not accurately represent the structure planktonic community. 16S rRNA gene sequences from 17 different genera were obtained from the community DNA sample; the most abundant were similar to Rhodoferax, Rhodobacter, and Polaromonas species. Sequences related to the Proteo bacteria, Bacteroidetes/Chlorobi, Firmicutes, and Acidobacterium/Fibrobacter divisions were also detected.     

Genetic diversity within the genus Pleurotus determined by random amplified polymorphism DNA (RAPD) analysis

Random amplified polymorphism DNA (RAPD) analysis was done to assess the diversity among 10 species of Pleurotus. Understanding of the pattern not only addresses questions concerning evolutionary process and the development of conservation strategies, but also a pre-requisite of the efficient use of genetic resources in breeding programme. The RAPD dendogram obtained by using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) programme were grouped into the investigated strains into five clusters. RAPD bands were scored as present (1) or absent (0) for all the Pleurotus isolate. Each band was assumed to represent a unique genetic locus. The pattern and extent of RAPD variation were analysed with respect to primer, polymorphic locus and isolate. Total number of amplified fragment and polymorphic fragment produced by 40 decamer primer was 229 and 226, respectively. Polymorphism percentage was 98.69. Ten primers; SBSA11, SBSA13, SBSA15, SBSA16, SBSA18, SBSA19, SBSA20, SBSB14, SBSB15 and SBSB17 were not amplified to the DNA from any of the isolate.     

Integrating spatial and temporal variability into the analysis of fish food web linkages in Tijuana Estuary

Our understanding of fish feeding interactions at Tijuana Estuary was improved by incorporating estimates of spatial and temporal variability into diet analyses. We examined the stomach contents of 7 dominant species (n=579 total fish) collected between 1994 and 1999. General feeding patterns pooled over time produced a basic food web consisting of 3 major trophic levels: (1) primary consumers (Atherinops affinis, Mugil cephalus) that ingested substantial amounts of plant material and detritus; (2) benthic carnivores (Clevelandia ios, Hypsopsetta guttulata, Gillichthys mirabilis, and Fundulus parvipinnis) that ingested high numbers of calanoid copepods and exotic amphipods (Grandidierella japonica); and (3) piscivores (Paralichthys californicus and Leptocottus armatus) that often preyed on smaller gobiids. Similarity-based groupings of individual species' diets were identified using nonmetric multidimensional scaling to characterize their variability within and between species, and in space and time. This allowed us identify major dietary shifts and recognize events (i.e., modified prey abundance during 1997–98 El Ni no floods) that likely caused these shifts.     

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.     

Marine viral ecology: incorporation of bacteriophage into the microbial planktonic food web paradigm

In the decade since the microbial loop was defined by Azam etat. (Mar. Ecol. Prog. Ser., 59, 1–17, 1983), the importanceof the interaction between microbial organisms and the largerplanktonic animals has been a subject of controversy. Untilrecently, grazing was considered to be the major fate of bacterialproduction. Now, however, viruses are seen to have an importantrole in microbial processes. We describe how growth and recyclingparameters affect the transfer of bacterial production througha microbial loop model that includes viruses. The loop is veryinefficient for all reasonable conditions, but its relativeimportance as a source of mesozooplankton nutrition is variable.The model demonstrates that in mesotrophic coastal waters, themicrobial loop is unlikely to supply more than a minor componentof mesozooplankton nutrition, a proposition that is supportedby accumulating evidence. For oligotrophic pelagic waters, themodel indicates that in the absence of viruses the microbialloop, despite its low efficiency, may provide an important resourcefor mesozooplankton. Bacterial production, without viral mortality,is also relatively important in the case of direct exploitationby salps. Under these conditions, bacteria account for 10–30%of mesozooplankton nutrition. With high levels of bacteriophageactivity, zooplankton production is generally reduced by 5–15%.We thus conclude that bactenophages could significantly affectmesozooplanktonic and, hence, exploitable marine production. ¹Present address: CSIRO Division of Fisheries, GPO Box 1538,Hobart, Tasmania 7001, Australia ²Present address: Resource Protection Division, Parks and WildlifeDepartment, 3000 1H 35 South, Suite 320, Austin, TX 78704, USA     

Trophic coupling of the microbial and the classical food web in Lake Baikal,Siberia

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Mixing an enclosed, 1300m3 water column: effects on the planktonic food web

The nutrient, phytoplankton, and zooplankton dynamics in threeenclosed water columns (1300 m³) are described. Two of the enclosureswere mixed using a bubbling chamber at depth. Young chum salmon(Oncorhynchus keta) were added to one of the mixed enclosuresand the unmixed enclosure. No other manipulations were imposed.Copepods appeared in large numbers (e.g. especially Pseudocalanusminutus s.l. and Paracalanus parvus) and population growth rateswere estimated. Ctenophora did not appear in large numbers despitepresumably ideal food environments; it is suggested that inone enclosure this is a consequence of fish predation on thectenophores. The fish experienced high mortalities and low growthrates presumably due to unsuitable prey size. Weekly collectionsof sediment permitted isolation of two major sediment contributors,the first from phytoplankton sinking and the second from biogenkfallout associated with herbivore production. It was found thatthe more oligotrophic enclosure (unmixed) experienced proportionallyhigher utilization of organic carbon. Some of these resultsare explained by our data while others require more sophisticatedexperimentation, both in the design of the containers and inthe types of observations.     

Multi-scale analysis on species diversity within a 40-ha old-growth temperate forest

In order to better explore the maintenance mechanisms of biodiversity,data collected from a 40-ha undisturbed Pinus forest were applied to the Individual SpecieseArea Relationship model (ISAR) to determine distribution patterns for species richness.The ecological processes influencing species abundance distribution patterns were assessed by applying the same data set to five models:a LogNormal Model (LNM),a Broken Stick Model (BSM),a Zipf Model (ZM),a Niche Preemption Model (NPM),and a Neutral Model (NM).Each of the five models was used at six different sampling scales (10 m×10 m,20 m×20 m,40 m×40 m,60 m×60 m,80 m×80 m,and 100 m×100 m).Model outputs showed that:(1) Accumulators and neutral species strongly influenced species diversity,but the relative importance of the two types of species varied across spatial scales.(2) Distribution patterns of species abundance were best explained by the NPM at small scales (10 me20 m),whereas the NM was the best fit model at large spatial scales.(3) Species richness and abundance distribution patterns appeared to be driven by similar ecological processes.At small scales,the niche theory could be applied to describe species richness and abundance,while at larger scales the neutral theory was more applicable.     

Effects of a storm event on the structure of the pelagic food web with special emphasis on planktonic ciliates

Storm-induced changes in the water column structure and thepelagic food web were investigated by daily sampling duringa 3 week period (October 24 to November 10, 1988) at a permanentstation in the southern Kattegat (Denmark) Subsequent to a stormthe primary production increased and the size-distribution ofthe phytoplankton changed towards larger cells. Some componentsof the zooplankton community responded to the increase in potentialfood, either in terms of a functional response (copepods) orin terms of a numerical response (cladocera), whereas no changesin the populations of mixo- and heterotrophic aliates were evident.The dilates were not food limited since growth rates determinedin situ were comparable to maximum growth rates measured inthe laboratory. Calculations suggest that the total clearancecapacity of planktonic copepods (as fraction of water columncleared per unit time) was of the same magnitude as the measuredinstantaneous growth rates of the ciliates (0.55–0 85day^–1). Ciliate populations were therefore probably limitedby copepod predation. Ciliates, however, contributed only insignificantlyto the diets of copepods. Although the total zooplankton productionincreased by at least 30% subsequent to the storm (and thatof the copepods by 50%), the zooplankton community was unableto assimilate the entire increase in primary production. Therelative zooplankton (copepods, cladoceran and ciliates) grazingrate on the primary production decreased 30%, and the flow ofcarbon to biomass accumulation, other grazers and in particularsedimentation is predicted to have increased by 100% followingthe storm.     

Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments

To assess the extent of genotypic and phenotypic diversity within species of purple nonsulfur bacteria found in aquatic sediments, a total of 128 strains were directly isolated from agar plates that had been inoculated with sediment samples from Haren and De Biesbosch in The Netherlands. All isolates were initially characterized by BOX-PCR genomic DNA fingerprinting, and 60 distinct genotypes were identified. Analyses of 16S rRNA gene sequences of representatives of each genotype showed that five and eight different phylotypes of purple nonsulfur bacteria were obtained from the Haren and De Biesbosch sites, respectively. At the Haren site, 80.5% of the clones were Rhodopseudomonas palustris, whereas Rhodoferax fermentans and Rhodopseudomonas palustris were numerically dominant at the De Biesbosch site and constituted 45.9 and 34.4% of the isolates obtained, respectively. BOX-PCR genomic fingerprints showed that there was a high level of genotypic diversity within each of these species. The genomic fingerprints of Rhodopseudomonas palustris isolates were significantly different for isolates from the two sampling sites, suggesting that certain strains may be endemic to each sampling site. Not all Rhodopseudomonas palustris isolates could degrade benzoate, a feature that has previously been thought to be characteristic of the species. There were differences in the BOX-PCR genomic fingerprints and restriction fragment length polymorphisms of benzoate-coenzyme A ligase genes and form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes between benzoate-degrading and non-benzoate-degrading genotypes. The ability to distinguish these two Rhodopseudomonas palustris groups based on multiple genetic differences may reflect an incipient speciation event resulting from adaptive evolution to local environmental conditions.     

Effect of lipid reserves on individual carbon content of two planktonic freshwater copepod species

The effect of the variation of lipid droplet volume on individual carbon content was studied in two species of planktonic freshwater copepods, Eudiaptomus gracilis G.O. Sars and Thermocyclops oithonoides G.O. Sars. It was found, that when a multiple regression of carbon content on prosoma and lipid droplet volume instead of a simple regression of carbon content on prosoma volume was applied, the unexplainied variance of individual carbon content of Eudiaptomus gracilis could be reduced. However, the use of multiple regression on Thermocyclops oithonoides data did not lead to significantly higher coefficient of determination than was obtained by using a simple regression.