A glance into the black box: Novel species-specific quantitative real-time PCR assays to disentangle aquatic hyphomycete community composition

Fungal identity mediates the impacts of multiple stressors on freshwater ecosystems

Predicting how multiple anthropogenic stressors affect natural ecosystems is a major challenge in ecology. Freshwater ecosystems are threatened worldwide by multiple co-occurring stressors, which can affect aquatic biodiversity, ecosystem functioning and human wellbeing. In stream ecosystems, aquatic fungi play a crucial role in global biogeochemical cycles and food web dynamics, therefore, assessing the functional consequences of fungal biodiversity loss under multiple stressors is crucial. Here, a microcosm approach was used to investigate the effects of multiple stressors (increased temperature and nutrients, drying, and biodiversity loss) on three ecosystem processes: organic matter decomposition, fungal reproduction, and fungal biomass accrual. Net effects of stressors were antagonistic for organic matter decomposition, but additive for fungal reproduction and biomass accrual. Net effects of biodiversity were mainly positive for all processes, even under stress, demonstrating that diversity assures the maintenance of ecosystem processes. Fungal species displayed distinct contributions to each ecosystem process. Furthermore, species with negligible contributions under control conditions changed their role under stress, either enhancing or impairing the communities' performance, emphasizing the importance of fungal species identity. Our study highlights that distinct fungal species have different sensitivities to environmental variability and have different influence on the overall performance of the community. Therefore, preserving high fungal diversity is crucial to maintain fungal species with key ecosystem functions within aquatic communities in face of environmental change.

Microbial community history and leaf species shape bottom-up effects in a freshwater shredding amphipod

Arable land use and the associated application of agrochemicals can affect local freshwater communities with consequences for the entire ecosystem. For instance, the structure and function of leaf-associated microbial communities can be affected by pesticides, such as fungicides. Additionally, the leaf species on which these microbial communities grow reflects another environmental filter for community structure. These factors and their interaction may jointly modify leaves' nutritional quality for higher trophic levels. To test this assumption, we studied the structure of leaf-associated microbial communities with distinct exposure histories (pristine [P] vs vineyard run off [V]) colonising two leaf species (black alder, European beech, and a mixture thereof). By offering these differently colonised leaves as food to males and females of the leaf-shredding amphipod Gammarus fossarum (Crustacea; Amphipoda) we assessed for potential bottom-up effects. The growth rate, feeding rate, faeces production and neutral lipid fatty acid profile of the amphipod served as response variable in a 2 × 3 × 2-factorial test design over 21d. A clear separation of community history (P vs V), leaf species and an interaction between the two factors was observed for the leaf-associated aquatic hyphomycete (i.e., fungal) community. Sensitive fungal species were reduced by up to 70 % in the V- compared to P-community. Gammarus' growth rate, feeding rate and faeces production were affected by the factor leaf species. Growth was negatively affected when Gammarus were fed with beech leaves only, whereas the impact of alder and the mixture of both leaf species was sex-specific. Overall, this study highlights that leaf species identity had a more substantial impact on gammarids relative to the microbial community itself. Furthermore, the sex-specificity of the observed effects (excluding fatty acid profile, which was only measured for male) questions the procedure of earlier studies, that is using either only one sex or not being able to differentiate between males and females. However, these results need additional verification to support a reliable extrapolation.

Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming

Heterotrophic microbial decomposers colonize submerged leaf litter in close spatial proximity to periphytic algae that exude labile organic carbon during photosynthesis. These exudates are conjectured to affect microbial decomposers' abundance, resulting in a stimulated (positive priming) or reduced (negative priming) leaf litter decomposition. Yet, the occurrence, direction, and intensity of priming associated with leaf material of differing recalcitrance remains poorly tested. To assess priming, we submerged leaf litter of differing recalcitrance (Alnus glutinosa [alder; less recalcitrant] and Fagus sylvatica [beech; more recalcitrant]) in microcosms and quantified bacterial, fungal, and diatom abundance as well as leaf litter decomposition over 30 days in absence and presence of light. Diatoms did not affect beech decomposition but reduced alder decomposition by 20% and alder-associated fungal abundance by 40% in the treatments including all microbial groups and light, thus showing negative priming. These results suggest that alder-associated heterotrophs acquired energy from diatom exudates rather than from leaf litter. Moreover, it is suggested that these heterotrophs have channeled energy to alternative (reproductive) pathways that may modify energy and nutrient availability for the remaining food web and result in carbon pools protected from decomposition in light-exposed stream sections.

Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection

Milk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.

Environmentally relevant fungicide levels modify fungal community composition and interactions but not functioning

Aquatic hyphomycetes (AHs), a group of saprotrophic fungi adapted to submerged leaf litter, play key functional roles in stream ecosystems as decomposers and food source for higher trophic levels. Fungicides, controlling fungal pathogens, target evolutionary conserved molecular processes in fungi and contaminate streams via their use in agricultural and urban landscapes. Thus fungicides pose a risk to AHs and the functions they provide. To investigate the impacts of fungicide exposure on the composition and functioning of AH communities, we exposed four AH species in monocultures and mixed cultures to increasing fungicide concentrations (0, 5, 50, 500, and 2500 μg/L). We assessed the biomass of each species via quantitative real-time PCR. Moreover, leaf decomposition was investigated. In monocultures, none of the species was affected at environmentally relevant fungicide levels (5 and 50 μg/L). The two most tolerant species were able to colonize and decompose leaves even at very high fungicide levels (≥500 μg/L), although less efficiently. In mixed cultures, changes in leaf decomposition reflected the response pattern of the species most tolerant in monocultures. Accordingly, the decomposition process may be safeguarded by tolerant species in combination with functional redundancy. In all fungicide treatments, however, sensitive species were displaced and interactions between fungi changed from complementarity to competition. As AH community composition determines leaves' nutritional quality for consumers, the data suggest that fungicide exposures rather induce bottom-up effects in food webs than impairments in leaf decomposition.

Fungal-fungal and fungal-bacterial interactions in aquatic decomposer communities: bacteria promote fungal diversity

Fungi produce a variety of extracellular enzymes making recalcitrant substrates bioavailable. Thus, fungi are central for decomposition of dead organic matter such as leaf litter. Despite their ecological importance, our understanding of relationships between fungal species diversity and ecosystem functioning is limited, especially with regard to aquatic habitats. Moreover, fungal interactions with other groups of microorganisms such as bacteria are rarely investigated. This lack of information may be attributed to methodological limitations in tracking the biomass of individual fungal species in communities, impeding a detailed assessment of deviations from the overall performance expected from the sum of individual species' performances, so-called net diversity effects (NDEs). We used fungal species-specific biomolecular tools to target fungal-fungal and fungal-bacterial interactions on submerged leaves using four cosmopolitan aquatic fungal species and a stream microbial community dominated by bacteria. In microcosms, we experimentally manipulated fungal diversity and bacterial absence/presence and assessed functional performances and fungal community composition after 14 days of incubation. Fungal community data was used to evaluate NDEs on leaf colonization. The individual fungal species were functionally distinct and fungal cultures were on average more efficient than the bacterial culture. In absence of bacteria, NDEs correlated with growth rate (negatively) and genetic divergence (positively), but were predominantly negative, suggesting that higher fungal diversity led to a lower colonization success (niche overlap). In both absence and presence of bacteria, the overall functional performances of the communities were largely defined by their composition (i.e., no interactions at the functional level). In presence of bacteria, NDEs correlated with genetic divergence (positively) and were largely positive, suggesting higher fungal diversity stimulated colonization (niche complementarity). This stimulation may be driven by a bacteria-induced inhibition of fungal growth, alleviating competition among fungi. Resulting feedback loops eventually promote fungal coexistence and synergistic interactions. Nonetheless, overall functional performances are reduced compared to bacteria-free cultures. These findings highlight the necessity to conduct future studies, investigating biodiversity-ecosystem functioning relationships using artificial systems, without exclusion of key organisms naturally co-occurring in the compartment of interest. Otherwise, study outcomes might not reflect true ecological relationships and ultimately misguide conservation strategies.

The Fungicide Tebuconazole Confounds Concentrations of Molecular Biomarkers Estimating Fungal Biomass

Due to their ecological importance, fungi are suitable indicator organisms for anthropogenic stress. To estimate fungal biomass, the fungal membrane molecule ergosterol is often quantified as a proxy. Estimates based on ergosterol may, however, be distorted by exposure to demethylase inhibiting (DMI) fungicides, interfering with sterol synthesis. To test this hypothesis, we exposed ten fungal species to the DMI fungicide tebuconazole and measured concentrations of ergosterol and DNA per unit dry mass of the fungal hyphae. The latter served as alternative biomass proxy that is not specifically targeted by tebuconazole. Effects of tebuconazole on ergosterol concentrations were species-specific, while concentrations were on average reduced by 13%. In contrast, DNA concentrations were on average increased by 13%. We demonstrate that DMI fungicides - at close to field relevant levels - can distort fungal biomass estimation, complicating the use of this endpoint for environmental management.

Quantification of Major Bacteria and Yeast Species in Kefir Consortia by Multiplex TaqMan qPCR

Kefir grains are complex microbial systems of several groups of microorganisms. The identification and quantification of the microbial composition of milk kefirs was described in several studies, which provided an insight into the microbial consortia in this complex ecosystem. Nevertheless, the current methods for identification and quantification are not appropriate for deeper studies on kefir consortia, e.g., population dynamics and microbial interactions in kefir grains. This requires another sensitive and reliable quantitative method. Therefore, this study aims to develop multiplexed qPCR assays to specifically detect and quantify, as an example, several microorganisms of the milk kefir microbial community. Primer-probe sets, which target species-specific genes in six bacteria and five yeasts, were designed, and their sensitivity and specificity to the target species was analyzed in simplex as well as four multiplex qPCR assays. The self-designed multiplex assays were applied for the detection of target bacteria and yeast species in milk kefirs, in both, grain and beverage fractions. Detection of all target microorganisms in simplex and multiplex qPCR was achieved by good linearity, efficiency, repeatability and reproducibility in all assays. When the designed assays were applied on six kefirs, all target microorganisms were detected in different samples, but not all in one kefir sample. The two ubiquitous lactobacilli Lactobacillus kefiranofaciens and Lb. kefiri were present in all six kefirs studied, but were associated with different other yeasts and bacteria. Especially on the yeast community a significant diversity was observed. In general, multiplex TaqMan qPCR as developed here was proven to have high potential for specific identification of target microorganisms in kefir samples and for the first time, eleven target bacteria and yeasts of kefir microbiota were rapidly detected and quantified. This study, thus, provides a fast and reliable protocol for future studies on kefir and other similar microbial ecosystems.