Diversity of protists and bacteria determines predation performance and stability

Species-specific predation determines the feeding impacts of six soil protist species on bacterial and eukaryotic prey

Predatory protists play a central role in nutrient cycling and are involved in other ecosystem functions by predating the microbiome. While most soil predatory protist species arguably are bacterivorous, some protist species can prey on eukaryotes. However, studies about soil protist feeding mainly focused on bacteria as prey and rarely tested both bacteria and eukaryotes as potential prey. In this study, we aimed to decipher soil predator-prey interactions of three amoebozoan and three heterolobosean soil protists and potential bacterial (Escherichia coli; 0.5-1.5 µm), fungal (Saccharomyces cerevisiae; 5-7 µm) and protist (Plasmodiophora brassicae; 3-5 µm) prey, either as individual prey or in all their combinations. We related protist performance (relative abundance) and prey consumption (qPCR) to the protist phylogenetic group and volume. We showed that for the six soil protist predators, the most suitable prey was E. coli, but some species also grew on P. brassicae or S. cerevisiae. While protist relative abundances and growth rates depended on prey type in a protist species-specific manner, phylogenetic groups and volume affected prey consumption. Yet we conclude that protist feeding patterns are mainly species-specific and that some known bacterivores might be more generalist than expected, even preying on eukaryotic plant pathogens such as P. brassicae.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

Mangrove sediments are environmental hotspots for pathogenic protists

Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.

Costs of being a diet generalist for the protist predator Dictyostelium discoideum

Consumers range from specialists that feed on few resources to generalists that feed on many. Generalism has the clear advantage of having more resources to exploit, but the costs that limit generalism are less clear. We explore two understudied costs of generalism in a generalist amoeba predator, Dictyostelium discoideum, feeding on naturally co-occurring bacterial prey. Both involve costs of combining prey that are suitable on their own. First, amoebas exhibit a reduction in growth rate when they switched to one species of prey bacteria from another compared to controls that experience only the second prey. The effect was consistent across all six tested species of bacteria. These switching costs typically disappear within a day, indicating adjustment to new prey bacteria. This suggests that these costs are physiological. Second, amoebas usually grow more slowly on mixtures of prey bacteria compared to the expectation based on their growth on single prey. There were clear mixing costs in three of the six tested prey mixtures, and none showed significant mixing benefits. These results support the idea that, although amoebas can consume a variety of prey, they must use partially different methods and thus must pay costs to handle multiple prey, either sequentially or simultaneously.

Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage

Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.

Protozoan predation as a driver of diversity and virulence in bacterial biofilms

Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a symbiotic or parasitic life-style. Biofilm formation is one such mechanism by which bacteria can survive predation. Structural and chemical components of biofilms enhance resistance to predation compared to their planktonic counterparts. Predation on biofilms gives rise to phenotypic and genetic heterogeneity in prey that leads to trade-offs in virulence in other eukaryotes. Recent advances, using molecular and genomics techniques, allow us to generate new information about the interactions of protozoa and biofilms of prey bacteria. This review presents the current state of the field on impacts of protozoan predation on biofilms. We provide an overview of newly gathered insights into (i) molecular mechanisms of predation resistance in biofilms, (ii) phenotypic and genetic diversification of prey bacteria, and (iii) evolution of virulence as a consequence of protozoan predation on biofilms.

The Effect of Protozoa Indigenous to Lakewater and Wastewater on Decay of Fecal Indicator Bacteria and Coliphage

Fecal indicator bacteria (FIB: Escherichia coli and enterococci) are used to assess recreational water quality. Viral indicators (i.e., somatic and F+ coliphage), could improve the prediction of viral pathogens in recreational waters, however, the impact of environmental factors, including the effect of predatory protozoa source, on their survival in water is poorly understood. We investigated the effect of lakewater or wastewater protozoa, on the decay (decreasing concentrations over time) of culturable FIB and coliphages under sunlight and shaded conditions. FIB decay was generally greater than the coliphages and was more rapid when indicators were exposed to lake vs. wastewater protozoa. F+ coliphage decay was the least affected by experimental variables. Somatic coliphage decayed fastest in the presence of wastewater protozoa and sunlight, though their decay under shaded conditions was-10-fold less than F+ after 14 days. The protozoa source consistently contributed significantly to the decay of FIB, and somatic, though not the F+ coliphage. Sunlight generally accelerated decay, and shade reduced somatic coliphage decay to the lowest level among all the indicators. Differential responses of FIB, somatic, and F+ coliphages to environmental factors support the need for studies that address the relationship between the decay of coliphages and viral pathogens under environmentally relevant conditions.

Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes

Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.

Distributional Pattern of Bacteria, Protists, and Diatoms in Ocean according to Water Depth in the Northern South China Sea

Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.

What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes

In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.

Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report)

Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.

Propagation of Recombinant Genes through Complex Microbiomes with Synthetic Mini-RP4 Plasmid Vectors

The promiscuous conjugation machinery of the Gram-negative plasmid RP4 has been reassembled in a minimized, highly transmissible vector for propagating genetically encoded traits through diverse types of naturally occurring microbial communities. To this end, the whole of the RP4-encoded transfer determinants (tra, mob genes, and origin of transfer oriT) was excised from their natural context, minimized, and recreated in the form of a streamlined DNA segment borne by an autoselective replicon. The resulting constructs (the pMATING series) could be self-transferred through a variety of prokaryotic and eukaryotic recipients employing such a rationally designed conjugal delivery device. Insertion of GFP reporter into pMATING exposed the value of this genetic tool for delivering heterologous genes to both specific mating partners and complex consortia (e.g., plant/soil rhizosphere). The results accredited the effective and functional transfer of the recombinant plasmids to a diversity of hosts. Yet the inspection of factors that limit interspecies DNA transfer in such scenarios uncovered type VI secretion systems as one of the factual barriers that check otherwise high conjugal frequencies of tested RP4 derivatives. We argue that the hereby presented programming of hyperpromiscuous gene transfer can become a phenomenal asset for the propagation of beneficial traits through various scales of the environmental microbiome.

Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities

With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.

Pedogenesis shapes predator-prey relationships within soil microbiomes

Pedogenesis determines soil physicochemical properties and many biodiversity facets, including belowground microbial bacteria and fungi. At the local scale, top-down predation by microbial protists regulates the soil microbiome, while the microbiome also affects protistan communities. However, it remains unknown how pedogenesis affects protistan communities and the potential protist-microbiome predator-prey relationships. With 435 soil samples representing different stages of pedogenesis ranging in soil age from centuries to millennia, we examined the influence of pedogenesis on the main protistan groups, and the interrelationships between protistan predators and microbial prey biomass. We revealed an enrichment in the diversity of total protists across pedogenesis and increasing richness of phototrophic protists in the medium compared with the early stages of pedogenesis. The richness of predatory protists accumulated throughout pedogenesis, which was more strongly determined by microbial biomass than environmental factors. Predator-prey associations were stronger in the young and the medium soils than in the older soils, likely because prey biomass accumulated in the latter and might be no longer limit predators. Together, our work provides evidence that pedogenesis shapes predatory protists differently than their prey, leading to shifts in predator-prey relationships. This knowledge is critical to better understand how soil food webs develop across soil development which might lead to changes in ecosystem functions.

Regulation of soil micro-foodwebs to root secondary metabolites in cultivated and wild licorice plants

The diversity of soil eukaryotes and micro-foodwebs are only partially understood. Moreover, how they affect secondary metabolites in plant roots under distinct soil environment is not well elucidated. By combining multiple statistical analyses and network constructions, variations in soil eukaryotic diversity, community assembly processes and potential associations of holistic microbiotas were investigated in the bulk and rhizosphere soils of cultivated and wild licorice, and their regulatory patterns for root secondary metabolites were elucidated. The protistan communities displayed lower alpha diversity, more varied beta diversity patterns, and higher stochastic processes, as compared with fungal communities. Soil fungi individually played a more essential role than soil protists in the regulation of root secondary metabolites. Furthermore, rhizosphere soil was associated with more complicated networks than bulk soil; and wild licorice was associated with more complicated networks than cultivated licorice. Specific responsive modules resulting from networks were essential for the regulation of root secondary metabolites and were mostly affected by edaphic properties. Moreover, these modules directly or indirectly regulated the root secondary metabolites to varying degrees in the presence of soil protists. This indicated that the secondary metabolites were affected by associations between protistan, fungal and bacterial groups, and not merely by individual types of microorganisms in agricultural ecosystems. This study provides insight into the responses of root secondary metabolites to different groups of soil eukaryotic diversity and micro-foodwebs. The results have implications for comprehensively understanding the characteristics of the separate and combined roles of microbiotas for environmental management of licorice plantation ecosystem.

Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria

Soil protists are essential but often overlooked in soil and could impact microbially driven element cycling in natural ecosystems. However, how protists influence heavy metal cycling in soil remains poorly understood. In this study, we used a model protist, Dictyostelium discoideum, to explore the effect of interactions between soil amoeba and metal-reducing bacteria on the reduction of soil Fe(III) and Cr(VI). We found that D. discoideum could preferentially prey on the Fe(III)-reducing bacterium Shewanella decolorationis S12 and significantly decrease its biomass. Surprisingly, this predation pressure also stimulated the activity of a single S. decolorationis S12 bacterium to reduce Fe(III) by enhancing the content of electron-transfer protein cyt c, intracellular ATP synthesis, and reactive oxygen species (e.g., H₂O₂). We also found that D. discoideum could not prey on the Cr(VI)-reducing bacterium Brevibacillus laterosporus. In contrast, B. laterosporus became edible to amoebae in the presence of S. decolorationis S12, and their Cr(VI) reduction ability decreased under amoeba predation pressure. This study provides direct evidence that protists can affect the Cr and Fe cycling via the elective predation pressure on the metal-reducing bacteria, broadening our horizons of predation of protists on soil metal cycling.

Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith's Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and ¹⁵N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N₂ fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and ¹⁵N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Particle foraging strategies promote microbial diversity in marine environments

Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.

Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices

Phagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.

Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota

Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.

Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility

Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co-occurrence networks constructed from time-series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate-specific subnetworks resembled autecological species-specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co-occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate-stressed ecosystems.

Impact of temperature on Legionella pneumophila, its protozoan host cells, and the microbial diversity of the biofilm community of a pilot cooling tower

Legionella pneumophila is a waterborne bacterium known for causing Legionnaires' Disease, a severe pneumonia. Cooling towers are a major source of outbreaks, since they provide ideal conditions for L. pneumophila growth and produce aerosols. In such systems, L. pneumophila typically grow inside protozoan hosts. Several abiotic factors such as water temperature, pipe material and disinfection regime affect the colonization of cooling towers by L. pneumophila. The local physical and biological factors promoting the growth of L. pneumophila in water systems and its spatial distribution are not well understood. Therefore, we built a lab-scale cooling tower to study the dynamics of L. pneumophila colonization in relationship to the resident microbiota and spatial distribution. The pilot was filled with water from an operating cooling tower harboring low levels of L. pneumophila. It was seeded with Vermamoeba vermiformis, a natural host of L. pneumophila, and then inoculated with L. pneumophila. After 92 days of operation, the pilot was disassembled, the water was collected, and biofilm was extracted from the pipes. The microbiome was studied using 16S rRNA and 18S rRNA genes amplicon sequencing. The communities of the water and of the biofilm were highly dissimilar. The relative abundance of Legionella in water samples reached up to 11% whereas abundance in the biofilm was extremely low (≤0.5%). In contrast, the host cells were mainly present in the biofilm. This suggests that L. pneumophila grows in host cells associated with biofilm and is then released back into the water following host cell lysis. In addition, water temperature shaped the bacterial and eukaryotic community of the biofilm, indicating that different parts of the systems may have different effects on Legionella growth.

Diversity and coexistence are influenced by time-dependent species interactions in a predator-prey system

Although numerous studies show that communities are jointly influenced by predation and competitive interactions, few have resolved how temporal variability in these interactions influences community assembly and stability. Here, we addressed this challenge in experimental microbial microcosms by employing empirical dynamic modelling tools to: (1) detect causal interactions between prey species in the absence and presence of a predator; (2) quantify the time-varying strength of these interactions and (3) explore stability in the resulting communities. Our findings show that predators boost the number of causal interactions among community members, and lead to reduced dynamic stability, but higher coexistence among prey species. These results correspond to time-varying changes in species interactions, including emergence of morphological characteristics that appeared to reduce predation, and indirectly facilitate growth of predator-susceptible species. Jointly, our findings suggest that careful consideration of both context and time may be necessary to predict and explain outcomes in multi-trophic systems.

The global-scale distributions of soil protists and their contributions to belowground systems

Protists are ubiquitous in soil, where they are key contributors to nutrient cycling and energy transfer. However, protists have received far less attention than other components of the soil microbiome. We used amplicon sequencing of soils from 180 locations across six continents to investigate the ecological preferences of protists and their functional contributions to belowground systems. We complemented these analyses with shotgun metagenomic sequencing of 46 soils to validate the identities of the more abundant protist lineages. We found that most soils are dominated by consumers, although parasites and phototrophs are particularly abundant in tropical and arid ecosystems, respectively. The best predictors of protist composition (primarily annual precipitation) are fundamentally distinct from those shaping bacterial and archaeal communities (namely, soil pH). Some protists and bacteria co-occur globally, highlighting the potential importance of these largely undescribed belowground interactions. Together, this study allowed us to identify the most abundant and ubiquitous protists living in soil, with our work providing a cross-ecosystem perspective on the factors structuring soil protist communities and their likely contributions to soil functioning.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

The dialogue between protozoa and bacteria in a microfluidic device

In nature, protozoa play a major role in controlling bacterial populations. This paper proposes a microfluidic device for the study of protozoa behaviors change due to their chemotactic response in the presence of bacterial cells. A three-channel microfluidic device was designed using a nitrocellulose membrane into which channels were cut using a laser cutter. The membrane was sandwiched between two glass slides; a Euglena suspension was then allowed to flow through the central channel. The two side channels were filled with either, 0.1% peptone as a negative control, or a Listeria suspension respectively. The membrane design prevented direct interaction but allowed Euglena cells to detect Listeria cells as secretions diffused through the nitrocellulose membrane. A significant number of Euglena cells migrated toward the chambers near the bacterial cells, indicating a positive chemotactic response of Euglena toward chemical cues released from Listeria cells. Filtrates collected from Listeria suspension with a series of molecular weight cutoffs (3k, 10k and 100k) were examined in Euglena chemotaxis tests. Euglena cells were attracted to all filtrates collected from the membrane filtration with different molecular weight cutoffs, suggesting small molecules from Listeria might be the chemical cues to attract protozoa. Headspace volatile organic compounds (VOC) released from Listeria were collected, spiked to 0.1% peptone and tested as the chemotactic effectors. It was discovered that the Euglena cells responded quickly to Listeria VOCs including decanal, 3,5- dimethylbenzaldehyde, ethyl acetate, indicating bacterial VOCs were used by Euglena to track the location of bacteria.

Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations

Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland rainforest into rubber agroforest (jungle rubber), and rubber and oil palm plantations; typical agricultural systems in Sumatra, Indonesia. We identified 5,204 operational taxonomic units (OTUs) at 97% identity threshold of protists from 32 sites. Protists species richness was similar in rainforest, jungle rubber and oil palm plantations but significantly lower in rubber plantations. After standardization, 4,219 OTUs were assigned to five trophic groups, and inspected for effects of land-use change, and potential biotic and abiotic driving factors. The most abundant trophic group was phagotrophs (52%), followed by animal parasites (29%), photoautotrophs (12%), plant parasites (1%), and symbionts (<1%). However, the relative abundance and OTU richness of phagotrophs and photoautotrophs increased significantly with increasing land-use intensity. This was similar, but less pronounced, for the relative abundance of symbionts. Animal and plant parasites decreased significantly in abundance and species richness with increasing land-use intensity. Community compositions and factors affecting the structure of individual trophic groups differed between land-use systems. Parasites were presumably mainly driven by the abundance and species richness of their hosts, while phagotrophs by changes in soil pH and increase in Gram-positive bacteria, and photoautotrophs by light availability. Overall, the results show that relative species richness, relative abundance, and community composition of individual trophic groups of protists in tropical lowland rainforest significantly differ from that in converted ecosystems. This is likely associated with changes in ecosystem functioning. The study provides novel insight into protist communities and their changes with land-use intensity in tropical lowland ecosystems. We show, that trophic groups of protists are powerful indicators reflecting changes in the functioning of ecosystems with conversion of rainforest into monoculture plantations.

Long-term farming systems modulate multi-trophic responses

Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.

Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

BACKGROUND

Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes.

RESULTS

Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements.

CONCLUSIONS

A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.

Rhizosphere Protists Change Metabolite Profiles in Zea mays

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.

Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning-interplay between nanoflagellates and bacterioplankton

The importance of biodiversity effects on ecosystem functioning across trophic levels, especially via predatory-prey interactions, is receiving increased recognition. However, this topic has rarely been explored for marine microbes, even though microbial biodiversity contributes significantly to marine ecosystem function and energy flows. Here we examined diversity and biomass of bacteria (prey) and nanoflagellates (predators), as well as their effects on trophic transfer efficiency in the East China Sea. Specifically, we investigated: (i) predator diversity effects on prey biomass and trophic transfer efficiency (using the biomass ratio of predator/prey as a proxy), (ii) prey diversity effects on predator biomass and trophic transfer efficiency, and (iii) the relationship between predator and prey diversity. We found higher prey diversity enhanced both diversity and biomass of predators, as well as trophic transfer efficiency, which may arise from more balanced diet and/or enhanced niche complementarity owing to higher prey diversity. By contrast, no clear effect was detected for predator diversity on prey biomass and transfer efficiency. Notably, we found prey diversity effects on predator-prey interactions; whereas, we found no significant diversity effect on biomass within the same trophic level. Our findings highlight the importance of considering multi-trophic biodiversity effects on ecosystem functioning in natural ecosystems.

Interactions between predation and disturbances shape prey communities

Ecological disturbances are important drivers of biodiversity patterns. Many biodiversity studies rely on endpoint measurements instead of following the dynamics that lead to those outcomes and testing ecological drivers individually, often considering only a single trophic level. Manipulating multiple factors (biotic and abiotic) in controlled settings and measuring multiple descriptors of multi-trophic communities could enlighten our understanding of the context dependency of ecological disturbances. Using model microbial communities, we experimentally tested the effects of imposed disturbances (i.e. increased dilution simulating density-independent mortality as press or pulse disturbances coupled with resource deprivation) on bacterial abundance, diversity and community structure in the absence or presence of a protist predator. We monitored the communities immediately before and after imposing the disturbance and four days after resuming the pre-disturbance dilution regime to infer resistance and recovery properties. The results highlight that bacterial abundance, diversity and community composition were more affected by predation than by disturbance type, resource loss or the interaction of these factors. Predator abundance was strongly affected by the type of disturbance imposed, causing temporary relief of predation pressure. Importantly, prey community composition differed significantly at different phases, emphasizing that endpoint measurements are insufficient for understanding the recovery of communities.

Killing the killer: predation between protists and predatory bacteria

Predation by microbes is one of the main drivers of bacterial mortality in the environment. In most ecosystems multiple micropredators compete at least partially for the same bacterial resource. Predatory interactions between these micropredators might lead to shifts within microbial communities. Integrating these interactions is therefore crucial for the understanding of ecosystem functioning. In this study, we investigated the predation between two groups of micropredators, i.e. phagotrophic protists and Bdellovibrio and like organisms (BALOs). BALOs are obligate predators of Gram-negative bacteria. We hypothesised that protists can prey upon BALOs despite the small size and high swimming speed of the latter, which makes them potentially hard to capture. Predation experiments including three protists, i.e. one filter feeder and two interception feeder, showed that BALOs are a relevant prey for these protists. The growth rate on BALOs differed for the respective protists. The filter feeding ciliate was growing equally well on the BALOs and on Escherichia coli, whereas the two flagellate species grew less well on the BALOs compared to E. coli. However, BALOs might not be a favourable food source in resource-rich environments as they are not enabling all protists to grow as much as on bacteria of bigger volume.

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations

Ecosystem functionality depends on interactions among populations, of the same or different taxa, and these are not just the sum of pairwise interactions. Thus, know-how of the social interactions occurring in mixed-populations are of high interest, however they are commonly unknown due to the limitations posed in tagging each population. The limitations include costs/time in tediously fluorescent tagging, and the number of different fluorescent tags. Tag-free strategies exist, such as high-throughput sequencing, but ultimately both strategies require the use of expensive machinery. Our work appoints social behaviors on individual strains in mixed-populations, offering a web-tool (BSocialhttp://m4m.ugr.es/BSocial.html) for analyzing the community framework. Our quick and cheap approach includes the periodic monitoring of optical density (OD) from a full combinatorial testing of individual strains, where number of generations and growth rate are determined. The BSocial analyses then enable us to determine how the addition/absence of a particular species affects the net productivity of a microbial community and use this to select productive combinations, i.e., designate their social effect on a general community. Positive, neutral, or negative assignations are applied to describe the social behavior within the community by comparing fitness effects of the community against the individual strain. The usefulness of this tool for selection of optimal inoculum in biofilm-based methyl tert-butyl ether (MTBE) bioremediation was demonstrated. The studied model uses seven bacterial strains with diverse MTBE degradation/growth capacities. Full combinatorial testing of seven individual strains (triplicate tests of 127 combinations) were implemented, along with MTBE degradation as the desired function. Sole observation of highest species fitness did not render the best functional outcome, and only when strains with positive and neutral social assignations were mixed (Rhodococcus ruber EE6, Agrobacterium sp. MS2 and Paenibacillus etheri SH7), was this obtained. Furthermore, the use of positive and neutral strains in all its combinations had a significant higher degradation mean (x1.75) than exclusive negative strain combinations. Thus, social microbial processes benefit bioremediation more than negative social microbial combinations. The BSocial webtool is a great contributor to the study of social interactions in bioremediation processes, and may be used in other natural or synthetic habitat studies.

The combined effects of biotic and abiotic stress on species richness and connectance

Food web structure and species richness are both subject to biotic (e.g. predation pressure and resource limitation) and abiotic stress (e.g. environmental change). We investigated the combined effects of both types of stress on richness and connectance, and on their relationship, in a predator-prey system. To this end, we developed a mathematical two trophic level food-web model to investigate the effects of biotic and abiotic stress on food web connectance and species richness. We found negative effects of top-down and bottom-up control on prey and predator richness, respectively. Effects of top-down and bottom-up control were stronger when initial connectance was high and low, respectively. Bottom-up control could either aggravate or buffer negative effects of top-down control. Abiotic stress affecting predator richness had positive indirect effects on prey richness, but only when initial connectance was low. However, no indirect effects on predator richness were observed following direct effects on prey richness. Top-down and bottom-up control selected for weakly connected prey and highly connected predators, thereby decreasing and increasing connectance, respectively. Our simulations suggest a broad range of negative and positive richness-connectance relationships, thereby revisiting the often found negative relationship between richness and connectance in food webs. Our results suggest that (1) initial food-web connectance strongly influences the effects of biotic stress on richness and the occurrence of indirect effects on richness; and (2) the shape of the richness-connectance relationship depends on the type of biotic stress.

Prey size diversity hinders biomass trophic transfer and predator size diversity promotes it in planktonic communities

Body size exerts multiple effects on plankton food-web interactions. However, the influence of size structure on trophic transfer remains poorly quantified in the field. Here, we examine how the size diversity of prey (nano-microplankton) and predators (mesozooplankton) influence trophic transfer efficiency (using biomass ratio as a proxy) in natural marine ecosystems. Our results support previous studies on single trophic levels: transfer efficiency decreases with increasing prey size diversity and is enhanced with greater predator size diversity. We further show that communities with low nano-microplankton size diversity and high mesozooplankton size diversity tend to occur in warmer environments with low nutrient concentrations, thus promoting trophic transfer to higher trophic levels in those conditions. Moreover, we reveal an interactive effect of predator and prey size diversities: the positive effect of predator size diversity becomes influential when prey size diversity is high. Mechanistically, the negative effect of prey size diversity on trophic transfer may be explained by unicellular size-based metabolic constraints as well as trade-offs between growth and predation avoidance with size, whereas increasing predator size diversity may enhance diet niche partitioning and thus promote trophic transfer. These findings provide insights into size-based theories of ecosystem functioning, with implications for ecosystem predictive models.

Trophic complexity in aqueous systems: bacterial species richness and protistan predation regulate dissolved organic carbon and dissolved total nitrogen removal

Loading of water bodies with dissolved organic carbon (DOC) and dissolved total nitrogen (DTN) affects their integrity and functioning. Microbial interactions mitigate the negative effects of high nutrient loads in these ecosystems. Despite numerous studies on how biodiversity mediates ecosystem functions, whether and how diversity and complexity of microbial food webs (horizontal, vertical) and the underlying ecological mechanisms influence nutrient removal has barely been investigated. Using microbial microcosms accommodating systematic combinations of prey (bacteria) and predator (protists) species, we showed that increasing bacterial richness improved the extent and reliability of DOC and DTN removal. Bacterial diversity drove nutrient removal either due to species foraging physiology or functional redundancy, whereas protistan diversity affected nutrient removal through bacterial prey resource partitioning and changing nutrient balance in the system. Our results demonstrate that prey-predator diversity and trophic interactions interactively determine nutrient contents, thus implying the vital role of microbial trophic complexity as a biological buffer against DOC and DTN.

The influence of environmental factors on protistan microorganisms in grassland soils along a land-use gradient

In this study, we investigated the effect of land use intensity, soil parameters and vegetation on protistan communities in grassland soils. We performed qualitative (T-RFLP) and quantitative (qPCR) analyses using primers specifically targeting the 18S rRNA gene for all Eukarya and for two common flagellate groups, i.e. the Chrysophyceae and the Kinetoplastea. Both approaches were applied to extracted soil DNA and RNA, in order to distinguish between the potentially active protists (i.e. RNA pool) and the total protistan communities, including potentially inactive and encysted cells (i.e. DNA pool). Several environmental determinants such as site, soil parameters and vegetation had an impact on the T-RFLP community profiles and the abundance of the quantified 18S rRNA genes. Correlating factors often differed between quantitative (qPCR) and qualitative (T-RFLP) approaches. For instance the Chrysophyceae/Eukarya 18S rDNA ratio as determined by qPCR correlated with the C/N ratio, whereas the community composition based on T-RLFP analysis was not affected indicating that both methods taken together provide a more complete picture of the parameters driving protist diversity. Moreover, distinct T-RFs were obtained, which could serve as potential indicators for either active organisms or environmental conditions like water content. While site was the main determinant across all investigated exploratories, land use seemed to be of minor importance for structuring protist communities. The impact of other parameters differed between the target groups, e.g. Kinetoplastea reacted on changes to water content on all sites, whereas Chrysophyceae were only affected in the Schorfheide. Finally, in most cases different responses were observed on RNA- and DNA-level, respectively. Vegetation for instance influenced the two flagellate groups only at the DNA-level across all sites. Future studies should thus include different protistan groups and also distinguish between active and inactive cells, in order to reveal causal shifts in community composition and abundance in agriculturally used systems.

The extent of functional redundancy changes as species' roles shift in different environments

Assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. The exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. Using a microbial model system, we show that the relationship can vary depending on environmental conditions. Shapes suggesting functional redundancy in one environment can change, suggesting functional differences in another environment. We find that this change is due to shifting species roles and interactions. Species that are functionally redundant in one environment may become pivotal in another. Thus, caution is advised in drawing conclusions about functional redundancy based on a single environmental situation. It also implies that species richness is important because it provides a pool of species with potentially relevant traits. These species may turn out to be essential performers or partners in new interspecific interactions after environmental change. Therefore, our results challenge the generality of functional redundancy.