First insights into the living groundwater mycobiome of the terrestrial biogeosphere

Inclusion of database outgroups reduces false positives in fungal metabarcoding taxonomic assignments

Metabarcoding studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other nonfungal environmental sequences that are amplified during polymerase chain reaction (PCR) are inherently assigned taxonomy by these same databases, possibly leading to ambiguous nonfungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including nonfungal outgroups in a fungal taxonomic database to aid in detecting and removing these nontarget amplicons. We processed 15 publicly available fungal metabarcode data sets and discovered that roughly 40% of the reads from these studies were not fungal, although they were assigned as Fungus sp. when using a database without nonfungal outgroups. We discuss implications for metabarcoding studies and recommend assigning taxonomy using a database with outgroups to better detect these nonfungal amplicons.

A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China

Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive.

FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species

Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and Fun^Fun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.

Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO₂, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX₅₈) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO₂ were significantly related to microbial community composition, with CO₂ inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO₂ production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome

Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of ¹³C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a ¹³C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a ¹³C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.

IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.

Current cave monitoring practices, their variation and recommendations for future improvement in Europe: A synopsis from the 6th EuroSpeleo Protection Symposium

This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link

The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.

Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface

Microbial communities play a key role for central biogeochemical cycles in the subsurface. Little is known about whether short-term seasonal drought and rewetting events influence the dominant microbes involved in C- and N-cycles. Here, we applied metaproteomics at different subsurface sites in winter, summer and autumn from surface litter layer, seepage water at increasing subsoil depths and remote located groundwater from two wells within the Hainich Critical Zone Exploratory, Germany. We observed changes in the dominance of microbial families at subsurface sampling sites with increasing distances, i.e., Microcoleaceae dominated in topsoil seepage, while Candidatus Brocadiaceae dominated at deeper and more distant groundwater wells. Nitrifying bacteria showed a shift in dominance from drought to rewetting events from summer by Nitrosomandaceae to autumn by Candidatus Brocadiaceae. We further observed that the reductive pentose phosphate pathway was a prominent CO2-fixation strategy, dominated by Woeseiaceae in wet early winter, which decreased under drought conditions and changed to a dominance of Sphingobacteriaceae under rewetting conditions. This study shows that increasing subsurface sites and rewetting event after drought alter the dominances of key subsurface microbes. This helps to predict the consequences of annual seasonal dynamics on the nutrient cycling microbes that contribute to ecosystem functioning.

Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests

Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T.macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.

Fungi in aquatic ecosystems

Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.

Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater

Groundwater ecosystems face the challenge of energy limitation due to the absence of light-driven primary production. Lack of space and low oxygen availability might further contribute to generally assumed low food web complexity. Chemolithoautotrophy provides additional input of carbon within the subsurface, however, we still do not understand how abundances of chemolithoautotrophs, differences in surface carbon input, and oxygen availability control subsurface food web complexity. Using a molecular approach, we aimed to disentangle the different levels of potential trophic interactions in oligotrophic groundwater along a hillslope setting of alternating mixed carbonate-/siliciclastic bedrock with contrasting hydrochemical conditions and hotspots of chemolithoautotrophy. Across all sites, groundwater harbored diverse protist communities including Ciliophora, Cercozoa, Centroheliozoa, and Amoebozoa but correlations with hydrochemical parameters were less pronounced for eukaryotes compared to bacteria. Ciliophora-affiliated reads dominated the eukaryotic data sets across all sites. DNA-based evidence for the presence of metazoan top predators such as Cyclopoida (Arthropoda) and Stenostomidae (Platyhelminthes) was only found at wells where abundances of functional genes associated with chemolithoautotrophy were 10-100 times higher compared to wells without indications of these top predators. At wells closer to recharge areas with presumably increased inputs of soil-derived substances and biota, fungi accounted for up to 85% of the metazoan-curated eukaryotic sequence data, together with a low potential for chemolithoautotrophy. Although we did not directly observe higher organisms, our results point to the existence of complex food webs with several trophic levels in oligotrophic groundwater. Chemolithoautotrophy appears to provide strong support to more complex trophic interactions, feeding in additional biomass produced by light-independent CO₂-fixation.

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors

Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%–40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.