Bacterial Grazing Research Articles

Effects of long-term fertilization with contemporary Danish human urine, composted household waste and sewage sludge on soil nematode abundance and community structure

It is desirable to recycle the urban waste products human urine, composted household waste and sewage sludge as fertilizers to agricultural fields. This could minimize the use of NPK fertilizer, improve soil structure and store carbon. However, waste products may contain heavy metals, persistent organic pollutants (POP) and plastics, and there are concerns that long-term build-up of these substances will cause unwanted effects on soil health.Nematodes are ubiquitous and numerous in soil ecosystems. Abundance and community structure of soil nematodes can be used as indicators of soil health, as some species are vulnerable to pollution. There are well-developed methods for detecting environmental changes based on nematode community structure.At the long-term CRUCIAL field experiment, where alternative fertilizer products have been applied since 2003, we measured effects of long-term fertilization with human urine, composted household waste and sewage sludge on soil properties (pH, soil organic matter and nitrogen availability), abundance of soil microorganisms (bacteria, fungi, small protozoa and ciliates) and nematode trophic groups compared to plots with unfertilized, NPK and cattle manure treatment. Sampling and assessments were done three times during a growth season. Further, we assessed the composition of nematode communities using metabarcoding.Treatments with a high input of organic matter (cattle manure, composted household waste and sewage sludge) had high abundances of bacteria and thus bacterial grazers (small protozoa, ciliates, and bacterial feeding nematodes). We found a significant correlation between nematode community structure and pH and organic matter. We calculated the nematode Maturity Index 2–5 (pollution indicator) based on metabarcoding data, which did not differ significantly between the treatments.We conclude that long-term fertilization with different types of contemporary Danish urban waste products affects both soil properties and abundance of soil organisms, the latter largely reflecting the organic matter input of the fertilizer treatments. We found no adverse effect on nematode communities that could indicate pollution-induced stress on nematofauna or decreased soil fertility.

Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves.

SummaryThe purpose of this study was to survey the eukaryotic microbiome of two karst caves in the Valley and Ridge physiographic region of the Appalachian Mountains. Caves are known to harbour eukaryotic microbes but their very low densities and small cell size make them difficult to collect and identify. Microeukaryotes were surveyed using two methodologies, filtering water and submerging glass microscope slides mounted in periphytometers in cave pools. The periphyton sampling yielded 13.5 times more unique amplicon sequence variants (ASVs) than filtered water. The most abundant protist supergroup was Alveolata with large proportions of the ASVs belonging to dinoflagellate, ciliate and apicomplexan clades. The next most abundant were Rhizarians followed by Stramenopiles (diatoms and chrysophytes) and Ameobozoans. Very few of the ASVs, 1.5%, matched curated protist sequences with greater than 99% identity and only 2.5% could be identified from surface plankton samples collected in the same region. The overall composition of the eukaryotic microbiome appears to be a combination of bacterial grazers and parasitic species that could possibly survive underground as well as cells, cysts and spores probably transported from the surface.

Simultaneous Study of the Growth and Grazing Mortality Rates of Microbial Food Web Components in a Mediterranean Coastal Lagoon

The abundances of 17 cytometric groups encompassing four groups of bacteria, three groups of cyanobacteria, six groups of eukaryotic picophytoplankton (<2–3 µm), and four groups of small eukaryotic nanophytoplankton (between 3 and 6 µm) were studied in the Thau Lagoon across different seasonal conditions. Among them, the growth (µ) and mortality rates due to grazing (g) of 12 groups of bacteria, cyanobacteria, and eukaryotic pico- and nanophytoplankton were simultaneously studied in the Thau Lagoon via four dilution experiments across different seasonal conditions. The abundances of heterotrophic flagellates and ciliates and their potential predators were studied and linked to prey mortality. Bacteria were more active than phytoplankton and displayed the highest growth and grazing mortality rates. Most studied groups had g:µ ratios > 1, suggesting that predators efficiently grazed and transferred these preys. Surprisingly, the observed variations in predator abundance across seasons did not necessarily correspond with changes in grazing pressure. The significant positive relationship found between water temperature and bacterial grazing mortality rates and the reverse trend observed for larger eukaryotic prey suggested that warmer water increases small prokaryote transfer to higher trophic levels but disadvantages larger eukaryotic prey transfer.

Dominant marine heterotrophic flagellates are adapted to natural planktonic bacterial abundances.

SummaryGrazing controls bacterial abundances and composition in many ecosystems. In marine systems, heterotrophic flagellates (HFs) are important predators. Assemblages of HFs are primarily formed by species still uncultured; therefore, many aspects of their trophic behaviour are poorly known. Here, we assessed the functional response of the whole assemblage and of four taxa grown in an unamended seawater incubation. We used fluorescently labelled bacteria to create a prey gradient of two orders of magnitude in abundance and estimated ingestion rates. Natural HFs had a half‐saturation constant of 6.7 × 105 prey ml−1, a value lower than that of cultured flagellates and within the range of marine planktonic bacterial abundances. Minorisa minuta was well adapted to low prey abundances and very efficient in ingesting bacteria. MAST‐4 and MAST‐7 were also well adapted to the typical marine abundances but less voracious. In contrast, Paraphysomonas imperforata, a typical cultured species, did not achieve ingestion rate saturation even at the highest prey concentration assayed. Our study, beside to set the basis for the fundamental differences between cultured and uncultured bacterial grazers, indicate that the examined predator taxa have different functional responses, suggesting that they occupy distinct ecological niches according to their grazing strategies and prey preferences.

Oceanic heterotrophic flagellates are dominated by a few widespread taxa

AbstractMarine heterotrophic flagellates (HFs) form a diverse and ecologically relevant functional group of bacterial grazers and nutrient remineralizers in oceanic waters. Despite playing a crucial role in marine biogeochemical cycles, there is still a lack of information on which specific taxa dominate HF assemblages and what are their patterns of distribution in a global context. In the present work, we addressed this issue by analyzing amplicon sequencing data sets retrieved from samples taken in tropical and subtropical oceanic regions at depths from surface to 4000 m. Only a few dozens of widespread taxa, mostly affiliating to MAST clades, Picozoa, Bicosoecida and Chrysophyceae, seemed to dominate surface HF assemblages. The majority of these dominant HFs were present at relatively constant abundances, while others were influenced by temperature or displayed a patchy distribution. In the deep ocean, only a handful of taxa belonging to Bicosoecida and Chrysophyceae, together with Diplonemea and Kinetoplastida, explained most of the HF signal. Co‐occurrence networks between HF and prokaryotic taxa at the surface ocean revealed two main clusters influenced by temperature that did not seem to show specific patterns of interaction. However, some correlations emerged outside these thermal groups that could represent new prey–predator interactions. Overall, we identified the putatively most ecologically relevant HF taxa in the ocean, which become promising targets for further experimental and genomic studies.

Protist communities along freshwater–marine transition zones in Hudson Bay (Canada)

One of the most striking ecological divides on Earth is between marine and nearby freshwater environments, as relatively few taxa can move between the two. Microbial eukaryotes contribute to biogeochemical and energy cycling in both fresh and marine waters, with little species overlap between the two ecosystems. Arctic and sub-Arctic marine systems are relatively fresh compared to tropical and temperate systems, but details of microbial eukaryote communities along river-to-sea transitions are poorly known. To bridge this knowledge gap, we investigated three river-to-sea transitions (Nelson, Churchill, and Great Whale Rivers) in sub-Arctic Hudson Bay through 18S rRNA amplicon sequencing to identify microbial eukaryotes along the salinity and biogeochemical gradients. Salinity acted as the principal dispersal barrier preventing freshwater microorganisms from colonizing marine coastal waters, with microbial eukaryote communities of the three rivers clustering together. Just offshore, communities clustered by coastal regions associated with nutrient concentrations. Analysis of indicator species revealed that communities in the nitrate-depleted coastal water off the Churchill and Great Whale Rivers were dominated by heterotrophic taxa and small photosynthetic protists. In contrast, the Nelson offshore community was characterized by a high proportion of the diatom Rhizosolenia. A distinct community of heterotrophic protists was identified in the three estuarine transition zones, suggesting specialized estuarine communities. Such specialization was most marked in the Nelson River system that was sampled more intensely and showed estuarine circulation. The autochthonous community was composed of the bacterial grazers Katablepharis, Mataza, and Cryothecomonas, as well as brackish species of the diatoms Skeletonema and Thalassiosira. These findings suggest that flow regulation on the Nelson River that modifies estuarine circulation would affect estuarine community composition and distribution in the transition zone.

Microflora communities which can convert digested sludge to biogas

ABSTRACT In the present study, we developed several microflora communities that utilize digested sludge (DS), the recalcitrant waste product of anaerobic digestion, as a substrate for biogas production with the aim of their future application to DS recycling. Strict enrichment with DS as the sole nutrient source was introduced to culture microbes from soil and herbivore dung samples; microflora communities promoting stable levels of biogas production were obtained. The average methane and hydrogen yield from soil-derived microflora were 4.86 and 0.94 ml per 1.0 g DS, respectively. Notably, two microflora communities enriched from a riverbank sediment produced 20.79 ml and 14.10 ml methane from 1.0 g DS. By contrast, the methane and hydrogen yield for herbivore dung-derived microfloras were on average 1.31 ml and 1.87 ml per 1.0 g DS, respectively. Potent hydrogen-biogas producers were obtained from rabbit (4.12 ml per 1.0 g DS), goat (3.16 ml per 1.0 g DS), and sheep dung (2.52 ml per 1.0 g DS). The cultured microflora communities included representatives from the eubacterial genera, Clostridiaceae and Eubacteriaceae together with several anaerobic genera. Pseudomonas spp. are found in the riverbank sediment-derived microfloras, suggesting that the floras employ syntrophic acetate oxidation and hydrogentrophic methanogenesis (SAO-HM) pathway for methane production. The methanogenic microflora communities were dominated by bacteria from the Methanobacteriaceae family and unclassified archaea. Moreover, ascomycetous fungi and protists were found, implying that they act as oxygen scavengers and bacterial grazers, respectively. Enzymatic analysis suggested that the microfloras hydrolyze DS via cellulase, chitinase, and protease activities.

Role of mixotrophic nanoflagellates in the Eastern Mediterranean microbial food web

In the oligotrophic, phosphorus (P)-limited Eastern Mediterranean Sea (EMS), grazing on heterotrophic bacteria (HB) by pigmented nanoflagellates (PNF) through mixotrophy is a significant source of bacterial mortality and is P-dependent. Heterotrophic nanoflagellates (HNF) are also important consumers of HB. However, there is still no conceptual framework describing the flows of carbon (C) and P through the EMS microbial food web that takes into account the mixotrophic behavior of PNF. In the present modelling study, we explore qualitatively the pathways of C- and P-flow through the HB-mixotrophic PNF-HNF link under varying availability of inorganic P. At low P availability, given the assumption that PNF can fulfill most of their P requirements through HB consumption when P-limited, model simulations show that PNF support bacterial production and P uptake by supplying HB with dissolved organic carbon (DOC), leading to a win-win stable scenario, with PNF holding a key role in P-transfer through the microbial food web. Conversely, increased P availability results in lower PNF grazing upon HB, amplifying the relative contribution of HNF to bacterial grazing. Based on our modelling study we propose a novel conceptual framework for bacteria-nanoflagellate interactions in the EMS, where PNF have the functional role of DOC primary producers and also share with HNF the functional role of bacterial consumers via mixotrophy. This alternative microbial loop operates in a Pdependent way. Our modelling study pinpoints the significance of the adaptive physiology of PNF for the functioning of the oligotrophic ecosystem of the EMS.

The grazing activity of Acrobeloides sp. drives phytate mineralisation within its trophic relationship with bacteria.

The microbial loop has been suggested as an alternative route for better utilization of phytate, a poorly available P source to plants. We hypothesized that bacterial grazer activity might dramatically enhance bacterial migration and proliferation, increasing the probability of phytate hydrolysis by bacterial phytases and, thus, phytate mineralization and release of free phosphate. We tested this hypothesis in a two-compartment system with a solid medium containing phytate or free phosphate as the source of P. Two bacterial species, B. subtilis 168 or Bradyrhizobium sp., with or without bacterial grazing nematodes belonging to Acrobeloides sp. previously fed on each of the bacterial species, were inoculated at a single point in the medium. Whatever the P source, nematode migration within both zones allowed the proliferation of bacteria. However, B. subtilis 168 was more efficient in using phytate than Bradyrhizobium sp. since the highest bacterial cell density and free phosphate concentrations were reached by Acrobeloides sp. fed on B. subtilis 168. The grazer activity seemed to be crucial to enhance phytate mineralization, despite Acrobeloides sp. showing a higher preference to feed on Bradyrhizobium sp. This study provides new insights into the effects of bacterial grazer activity on phytate mineralization.

Marine Bacteria Display Different Escape Mechanisms When Facing Their Protozoan Predators.

Free-living amoeba are members of microbial communities such as biofilms in terrestrial, fresh, and marine habitats. Although they are known to live in close association with bacteria in many ecosystems such as biofilms, they are considered to be major bacterial predators in many ecosystems. Little is known on the relationship between protozoa and marine bacteria in microbial communities, more precisely on how bacteria are able survive in environmental niches where these bacterial grazers also live. The objective of this work is to study the interaction between the axenized ubiquitous amoeba Acanthamoeba castellanii and four marine bacteria isolated from immersed biofilm, in order to evaluate if they would be all grazed upon by amoeba or if they would be able to survive in the presence of their predator. At a low bacteria-to-amoeba ratio, we show that each bacterium is phagocytized and follows a singular intracellular path within this host cell, which appears to delay or to prevent bacterial digestion. In particular, one of the bacteria was found in the amoeba nucleolar compartment whereas another strain was expelled from the amoeba in vesicles. We then looked at the fate of the bacteria grown in a higher bacteria-to-amoeba ratio, as a preformed mono- or multi-species biofilm in the presence of A. castellanii. We show that all biofilms were subjected to detachment from the surface in the presence of the amoeba or its supernatant. Overall, these results show that bacteria, when facing the same predator, exhibit a variety of escape mechanisms at the cellular and population level, when we could have expected a simple bacterial grazing. Therefore, this study unravels new insights into the survival of environmental bacteria when facing predators that they could encounter in the same microbial communities.

Spatial modeling and dynamics of organic matter biodegradation in the absence or presence of bacterivorous grazing

Biodegradation is a pivotal natural process for elemental recycling and preservation of an ecosystem. Mechanistic modeling of biodegradation has to keep track of chemical elements via stoichiometric theory, under which we propose and analyze a spatial movement model in the absence or presence of bacterivorous grazing. Sensitivity analysis shows that the organic matter degradation rate is most sensitive to the grazer’s death rate when the grazer is present and most sensitive to the bacterial death rate when the grazer is absent. Therefore, these two death rates are chosen as the primary parameters in the conditions of most mathematical theorems. The existence, stability and persistence of solutions are proven by applying linear stability analysis, local and global bifurcation theory, and the abstract persistence theory. Through numerical simulations, we obtain the transient and asymptotic dynamics and explore the effects of all parameters on the organic matter decomposition. Grazers either facilitate biodegradation or has no impact on biodegradation, which resolves the “decomposition–facilitation paradox” in the spatial context.

Bacterioplankton dynamics driven by interannual and spatial variation in diatom and dinoflagellate spring bloom communities in the Baltic Sea

AbstractIn parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting toward the co‐occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatoms are unknown. Here we explored the changes in bacterial communities and heterotrophic production during the spring bloom in four consecutive spring blooms across several sub‐basins of the Baltic Sea and related them to changes in environmental variables and in phytoplankton community structure. The taxonomic structure of bacterioplankton assemblages was partially explained by salinity and temperature but also linked to the phytoplankton community. Higher carbon biomass of the diatoms Achnanthes taeniata, Skeletonema marinoi, Thalassiosira levanderi, and Chaetoceros spp. was associated with more diverse bacterial communities dominated by copiotrophic bacteria (Flavobacteriia, Gammaproteobacteria, and Betaproteobacteria) and higher bacterial production. During dinoflagellate dominance, bacterial production was low and bacterial communities were dominated by Alphaproteobacteria, mainly SAR11. Our results suggest that increases in dinoflagellate abundance during the spring bloom will largely affect the structuring and functioning of the associated bacterial communities. This could decrease pelagic remineralization of organic matter and possibly affect the bacterial grazers communities.

Grazing effect of flagellates on bacteria in response to phosphate addition in the oligotrophic Cretan Sea, NE Mediterranean.

The planktonic food web in the oligotrophic Mediterranean Sea is dominated by small-sized (<20μm) microbes, with nanoflagellates being the major bacterial grazers and the main participants in nutrient cycling. Phosphate is a key nutrient in the P-limited Cretan Sea (NE Mediterranean) and P-availability can affect its trophic dynamics. Here, we examined the grazing potential of heterotrophic (HF) and pigmented (PF) nanoflagellates as a response mechanism to phosphate amendment. Flagellate grazing effect on bacteria was quantified in P-amended nutrient-depleted water from the Cretan Sea over the course of 4 days using microcosm experiments. P-addition positively affected HF abundance, while PF abundance remained unchanged. At the community level, P-addition had a negative effect on PF bacterial removal rates. In the control, PF-grazing rate was significantly higher than that of HF throughout the experiment. Pigment analysis showed no changes in phytoplankton community composition as a result of P-addition, indicating that PF grazing rate declined as a physiological response of the cells. The present study emphasizes the dominant grazing role of PF under P-depleted conditions and reveals that during the late stratified season PF respond to P-addition by lowering their grazing rates, enhancing the relative importance of bacterial removal by HF.

Multivariate control of heterotrophic bacterial abundance and zooplankton grazing in Labrador fjords (northeastern Canada)

This study was conducted in 4 Labrador fjords (Nachvak, Saglek, Okak, and Anaktalak) during the summers of 2007 and 2013, early fall 2010, and late fall 2009. Our results show that water temperature combined with the availability of nutrients and organic substrates are the main abiotic factors controlling the abundance of heterotrophic bacteria in Labrador fjords. Bacterivory also played a crucial role, with heterotrophic bacteria exerting a significant bottom-up control on the abundance of heterotrophic nanoflagellates (r = 0.35, p &lt; 0.05) and ciliates (r = 0.70, p &lt; 0.01). During summer 2013, the intrinsic phytoplankton growth rate varied between &lt;0 and 0.64 d-1, with a mean value of 0.36 d-1. The herbivory rate was highly variable, ranging from 0.01 to 0.86 d-1, with a mean value of 0.31 d-1. Grazing mortality was 6-fold higher than phytoplankton growth rate. Mean phytoplankton growth and herbivory rates in Labrador fjords were comparable to the Barents and Bering seas. The intrinsic growth rate of total heterotrophic bacteria ranged between &lt;0 and 0.68 d-1, with a mean value of 0.30 d-1. Bacterivory varied from 0.01 to 0.95 d-1, with a mean of 0.30 d-1. Mortality due to grazing was up to 2.3 times higher than total bacterial growth rate. This study improves our understanding of the factors influencing the dynamics of heterotrophic bacteria and indicates that herbivory and bacterivory exert substantial control on microbial communities in Labrador fjords.

Micro-food web interactions involving bacteria, nematodes, and mycorrhiza enhance tree P nutrition in a high P-sorbing soil amended with phytate

Phytate is considered a poorly available plant P source but proved to be useful for particular soil bacteria strains. In soil-free conditions, it has been shown that bacteria locked up the mineralized phosphorus from phytate whereas bacterial grazers like nematodes were able to deliver P to plants. Here, we aimed to determine if the interactions between phytate-mineralizing bacteria, bacterial grazer nematodes, and mycorrhizal fungi could increase plant P acquisition from phytate in high P-adsorbing soils. Pinus pinaster was grown in a Cambisol supplemented with phytate. Plants, whether associated or not associated with the ectomycorrhizal fungus Hebeloma cylindrosporum, were either inoculated or not inoculated with the phytase-releasing bacteria Bacillus subtilis and the bacterial-feeding nematode Rhabditis sp. After 100 days, the dual inoculation of bacteria and nematodes significantly increased net plant P accumulation. We observed that, on average, mycorrhizal plants accumulated more P in their shoots than non-mycorrhizal plants. However, the highest plant P acquisition efficiency was found when the three soil organisms were present in the P. pinaster rhizosphere. We conclude that, in a highly inorganic P-fixing soil, plant P acquisition from phytate strongly depends on the grazing of phytate-mineralizing bacteria. Our results confirm the importance of the soil microbial loop to improve plant P nutrition from phytate, which should be considered a route to improve the utilization of this source of poorly available P by plants.

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

AbstractEnvironmental molecular sequencing has revealed an abundance of microorganisms that were previously unknown, mainly because most had not been cultured in the laboratory. Within this novel diversity, there are the uncultured MAST clades (MArine STramenopiles), which are major components of marine heterotrophic flagellates (HFs) thought to be active bacterial grazers. In this study, we investigated the gene expression of natural HFs in a mixed community where bacterivory was promoted. Using fluorescence in situ hybridization and 18S rDNA derived from metatranscriptomics, we followed the taxonomic dynamics during the incubation, and confirmed the increase in relative abundance of different MAST lineages. We then used single cell genomes of several MAST species to gain an insight into their most expressed genes, with a particular focus on genes related to phagocytosis. The genomes of MAST‐4A and MAST‐4B were the most represented in the metatranscriptomes, and we identified highly expressed genes of these two species involved in motility and cytoskeleton remodeling, as well as many lysosomal enzymes. Particularly relevant were the cathepsins, which are characteristic digestive enzymes of the phagolysosome and the rhodopsins, perhaps used for vacuole acidification. The combination of single cell genomics and metatranscriptomics gives insights on the phagocytic capacity of uncultured and ecologically relevant HF species.

Plant identity control on soil food web structure and C transfers under perennial bioenergy plantations

Conversion from arable cropping systems to perennial bioenergy crops is increasing across Europe to meet market energy demands, but our understanding of how this land use change is affecting below-ground diversity and C allocation remains limited. Here, we assessed the impact of conversion from arable cropland to Miscanthus and Short Rotation Coppice (SRC) willow in UK bioenergy commercial plantations on earthworm community structure and abundance. At this same location we then conducted an in-situ 13CO2 pulse-chase labelling experiment in the two bioenergy plantations to trace the fate of recently photosynthetically assimilated carbon into roots, bulk soil, soil microbial (PLFA) and earthworm communities. Results showed that land conversion from annual arable crops to both Miscanthus and SRC willow perennial bioenergy crops led to severe reductions of soil earthworm abundance and biomass. SRC willow had higher microbial biomass relative to Miscanthus, whereas Miscanthus provided a better habitat for a more functionally diverse earthworm community. Transfer of labile C compounds to soil pools was faster under Miscanthus supporting activity of bacterial grazers in the soil food chain, whereas a fungal-driven detrital decomposition processes dominated under SRC willow plantations. Taken together, these findings indicate that plant identity in land conversions have a strong influence not only on the abundance and structure of soil communities but also on which basal resources (root exudates, dead organic matter or microbial derived compounds) are preferentially consumed, and ultimately on the rates of mobilisation of these different C pools.

Novel biological method for controlling bacterial contaminants using the ciliate Colpoda sp. HSP-001 in open pond algal cultivation

Outdoor algal cultivation is frequently limited by bacterial contaminants. The aim of this study was to develop a biological control technique for removing bacterial contaminants using a small-size ciliate. During the cultivation of Chlorella sp. HS2 in a designed raceway pond, the bacterial population was significantly reduced by the ciliate strain. 18S rDNA analysis identified the ciliate as Colpoda sp. HSP-001. To verify selective bacterial grazing by the ciliate, an isolated phycospheric bacterium Microbacterium sp. was co-cultivated with Chlorella sp. HS2 while varying the ciliate cell concentrations. Colpoda sp. efficiently eliminated bacterial cells, whereas no algal grazing was observed by fluorescence microscopy. Based on the results, the utilization of Colpoda sp. HSP-001 in an outdoor algal cultivation system is a cost-effective strategy for controlling bacterial contamination without degrading the algal biomass.

Trophic and non-trophic interactions in binary links affect carbon flow in the soil micro-food web

Soil organisms constitute multitrophic food webs, which are important determinants for nutrient and carbon flow through terrestrial systems. However, these complex interactions are not well understood, particular in the most cryptic compartment – the link between microorganisms and microfauna. The present study investigates binary trophic links between microbial prey and nematodes in a controlled semi-natural soil environment. A microcosm system with circulating airflow was filled with γ-irradiated arable soil (Luvisol), inoculated with 13C labelled microbial diet and nematode grazers, and incubated for 72 h. Signatures of 13C and CO2 evolved from microcosms, soil phospholipid fatty acids and nematode densities were determined. Except for the model nematode Caenorhabditis elegans, all organisms joint in the 12 different investigated binary links represent dominant taxa at the arable field site. Studied were the fungal grazers Aphelenchoides saprophilus and Aphelenchus sp. in combination with the fungi Chaetomium globosum, Aspergillus terreus or Cryptococcus terreus as well as the bacterial grazers C. elegans and Acrobeloides buetschlii in combination with the bacteria Pseudomonas putida, Kitasatospora sp. or Sphingomonas trueperi.The results assigned trophic and non-trophic interactions and considerable variation between binary links. The biomass decline of S. trueperi in presence of C. elegans as well as the increased release of 13C in links of C. globosum and A. terreus with Aphelenchus sp. and S. trueperi with A. buetschlii assign nematode grazing and thus a classical predator-prey system. Such direct trophic interactions can induce distinct C fluxes within a binary link as assigned by the increased density (i.e. biomass) of C. elegans when feeding on S. trueperi. In contrast, the numbers of Aphelenchus sp. declined when feeding on A. terreus, and thus reduced C flow to the next trophic level. Grazing can also foster C allocation in microbial biomass via compensatory growth, as indicated e.g. for the link of Aphelenchus sp. with the fungi C. globosum and A. terreus. While these diverse responses to grazing were to be expected, the use of CO2 and 13C measurements further revealed that non-trophic interactions shape C flux in a binary link, particularly in the bacterial channel. Besides the fungal link of C. terreus with Aphelenchus sp., non-trophic interactions were obvious for the bacterial links Kitasatospora sp. with C. elegans or A. buetschlii, and P. putida with A. buetschlii. The presence of nematodes caused a reduction in respiration (evolved CO2), thus a decline in microbial activity. The formation of chemical and/or morphological defense is likely a reason for that reduced prey activity. For further studies the inclusion of such non-trophic interactions is necessary to achieve realistic models for C flow through soil food webs.

Spatial and temporal distribution patterns of marine stramenopiles in Daya Bay, South China

Molecular surveys have revealed a surprisingly large novel diversity of heterotrophic nanoflagellates affiliated with MArine STramenopiles (MAST) in marine systems. It has been proved that MAST cells are globally distributed and efficient bacterial grazers, therefore playing indispensable roles on ecosystem functioning. Nevertheless, MAST organisms remain uncultured and data on distribution and trophic modes are limited. Here we investigated their composition and seasonal variability using Illumina high- throughput sequencing targeting 18S rDNA in Daya Bay. MAST accounted for 0.5% in winter and up to 2.1% in spring of total 18S rDNA sequences in the pico- nano fraction. Within MAST, sequences affiliated with eight groups (-1, -2, -3, -4, -6, -7, -8 and -12) were widely distributed in both seasons. On average, the most abundant groups were MAST-3 (45.8% of the total MAST sequences), MAST-1 (30.4%), MAST-2 (7.5%) and MAST-12 (6.3%). This study demonstrated some key physicochemical (water temperature and salinity) factors significantly explained MAST composition variations. As being potential bacterial predators, prey abundance as well as their quality were also responsible for shaping MAST spatial distribution and community structure. Given the importance of MAST function, this study contributes to broaden our understanding of the diversity and distribution of MAST community and helps refine hypotheses on their ecological characteristics.