Distribution and diversity of fungi in freshwater sediments on a river catchment scale

Distribution Pattern and Assembly Process of Fungal Communities Along Altitude Gradient in Sediments of the Yellow River Basin

Microorganisms have a profound impact on the stability and ecological health of aquatic environments. Fungi, as important components of river ecosystems, play critical roles as decomposers and symbionts. A comprehensive understanding of the mechanisms underlying fungal community assembly is essential for the effective conservation and management of river ecosystems. However, the distribution patterns and assembly process of fungal communities along elevation gradients in river sediments remain poorly understood. In this study, ITS amplicon sequencing, a neutral community model, and a null model were employed to analyze the distribution patterns and assembly processes of fungal communities in sediments along the altitudinal gradient of the Yellow River. The results indicated that Ascomycota (47.79%) and Basidiomycota (15.68%) were identified as the dominant phyla in the sediments, collectively accounting for 63.47% of the total relative abundance of the community. In the three different altitudinal gradients, the fungal community diversity (Shannon) showed a gradually decreasing trend with increasing altitude. The co-line networks of fungal communities exhibited positive interactions and had more complex and compact networks in the sediments of the Tibetan Plateau area (YRA). Environmental factors in the sediments played an important role in shaping the structure of fungal communities, with lead (Pb), total nitrogen (TN), silt, and total organic carbon (TOC) being the main factors driving changes in community structure, contributing 15.5%, 12.3%, 10.7%, and 10.2%, respectively. In the community assembly process, deterministic processes were found to dominate, with homogenizing selection contributing the most (69.66%). These research results help us understand the distribution patterns of fungal communities along altitudinal gradients and the mechanisms of community assembly, and also provide a scientific basis for biodiversity conservation and the rational use of biological resources.

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03-3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5-99.6%) and Ascomycota (22.0-34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks.

Seasonal Variations of Sediment Fungal Community of a Shallow Lake in North China

Fungi play important roles in the process of material cycling and energy transfers in aquatic ecosystems. Yet, little is known about the fungal community in lake sediment. In this study, sediment samples from five habitat types in Baiyangdian Lake (BYD Lake) were collected across three seasons. High-throughput sequencing techniques were used to determine the compositions of fungal communities. Fungi are highly diverse in the sediment of BYD Lake, although some important fungi have not been accurately identified. The fungal diversity was highest in winter and lowest in summer, while there was no significant difference in species richness among sampling sites. The compositions of fungal community differed among seasons and habitats. Physicochemical properties of sediments were measured and the influence of the environmental factors on fungal communities were analyzed. Temperature, P, N, and heavy metals explained 48.98% of the variations of fungal communities across three seasons. Human activities have affected the species and biomass of fungi to some extent. Temperature is the most influential factor and negatively correlated to fungal diversity. Nutrients in different forms have different effects on shaping the fungal community. The effect of heavy metals is relatively low.

Insights into Some Onygenalean Fungi from Freshwater Sediments in Spain and Description of Novel Taxa

During the course of a project investigating culturable Ascomycota diversity from freshwater sediments in Spain, we isolated 63 strains of cycloheximide-resistant fungi belonging to the order Onygenales. These well-known ascomycetes, able to infect both humans and animals, are commonly found in terrestrial habitats, colonizing keratin-rich soils or dung. Little is known about their diversity in aquatic environments. Combining morphological features and sequence analyses of the ITS and LSU regions of the nrDNA, we identified 14 species distributed in the genera Aphanoascus, Arachniotus, Arthroderma, Arthropsis, Emmonsiellopsis, Gymnoascoideus, Leucothecium, Malbranchea, and Myriodontium. Furthermore, three novel species for the genus Malbranchea are proposed as M. echinulata sp. nov., M. irregularis sp. nov., and M. sinuata sp. nov. The new genera Albidomyces and Neoarthropsis are introduced based on Arachniotus albicans and Arthropsis hispanica, respectively. Neoarthropsis sexualis sp. nov. is characterized and differentiated morphologically from its counterpart by the production of a sexual morph. The novel family Neoarthropsidaceae is proposed for the genera Albidomyes, Apinisia, Arachnotheca, Myriodontium, and Neoarthropsis, based on their phylogenetic relationships and phenotypic and ecological traits. Pseudoamaurascopsis gen. nov. is introduced to accommodate P. spiralis sp. nov., a fungus with unclear taxonomy related to Amaurascopsis and Polytolypa. We traced the ecology and global distribution of the novel fungi through ITS environmental sequences deposited in the GlobalFungi database. Studying the fungal diversity from freshwater sediments not only contributes to filling gaps in the relationships and taxonomy of the Ascomycota but also gives us insights into the fungal community that might represent a putative risk to the health of animals and humans inhabiting or transient in aquatic environments.

Residues of pyrethroids and triazoles pesticides in water and sediment of certain Egyptian watercourses: assessing their influence on fungal diversity

Contamination of water and sediment with pyrethroids and triazoles residues can affect fungal diversity, and hence the aquatic system functioning. The aim of the present study is to investigate the effect of water and sediment contamination with pyrethroids and triazoles on fungal diversity. Water and sediment samples were seasonally collected along 2019 from water bodies representing Gharbeya and Qualubeya governorates. Concentrations of pyrethroids and triazoles were determined, and fungal species in water and sediment samples were molecularly identified. The results indicated that temperature and pH varied according to the season. Permethrin, deltamethrin, lambda-cyhalothrin and esfenvalerate showed the highest pyrethroids concentrations, whereas tetraconazole, tebuconazole and difenconazole were of the highest triazoles concentrations. Aspergillus niger was one of the most frequent species, in addition to Trichoderma capillare, Fusarium oxysporum, Penicillium commune and Penicillium polonicum. Principal component analysis indicated a positive correlation between temperature and different Aspergillus spp., and between pH and each of pyrethroids and triazoles. Moreover, a negative correlation was observed between triazoles and Trichoderma asperellum, Penicillium griseofulvum and Aspergillus fumigatus. In conclusion, contamination of water with pesticides affected fungal diversity. This disturbance in fungal assemblages might result in a reduction of some key organisms, or an increase and emergence of new pathogens.

Impact of environmental factors on diversity of fungi in sediments from the Shenzhen River Estuary

In this study, to explore the relationship between environmental factors and fungal diversity in the Shenzhen River ecosystem, multiple methods including chemical analysis, culture isolation, qPCR analysis of fungal ITS region and ITS-based Illumina next-generation-sequencing were integrated. A total of 115 isolates were finally isolated and could be classified into 23 genera. Top three abundant genera isolated were Meyerozyma (18 strains), Aspergillus (17 strains) and Penicillium (14 strains). Based on the Illumina sequencing approach, 829 OTUs were affiliated to seven phyla, 17 known classes, and 162 genera, indicating the Shenzhen estuary sediments are rich in fungal diversity. The major fungal genera were Meyerozyma, Trichoderma and Talaromyces. Environmental factors showed a gradient change in Shenzhen estuary, and fungal abundance was only significantly correlated with NH₄⁺. Shannon index was significantly correlated with pH and IC (P < 0.05). Principal coordinate analysis based on OTU level grouped into three clusters among sampling sites along with the IC and pH gradient. Functional guilds analysis suggests most of the fungi in this studying area were almost all saprotrophs, suggesting a large number of saprophytic fungi may play a significant role in the organic matter decomposition and nutrient cycling process. In summary, this study will deepen our understanding of fungi community in Shenzhen River ecosystem and their distribution and potential function shaped by environmental factors.

New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain

Penicillium species are common fungi found worldwide from diverse substrates, including soil, plant debris, food products and air. Their diversity in aquatic environments is still underexplored. With the aim to explore the fungal diversity in Spanish freshwater sediments, numerous Penicillium strains were isolated using various culture-dependent techniques. A preliminary sequence analysis of the β-tubulin (tub2) gene marker allowed us to identify several interesting species of Penicillium, which were later characterized phylogenetically with the barcodes recommended for species delimitation in the genus. Based on the multi-locus phylogeny of the internal transcribed spacer region (ITS) of the ribosomal DNA, and partial fragments of tub2, calmodulin (cmdA), and the RNA polymerase II largest subunit (rpb2) genes, in combination with phenotypic analyses, five novel species are described. These are P.ausonanum in sectionLanata-Divaricata, P.guarroi in sect.Gracilenta, P.irregulare in sect.Canescentia, P.sicoris in sect.Paradoxa and P.submersum in sect.Robsamsonia. The study of several isolates from samples collected in different locations resulted in the reinstatement of P.vaccaeorum into sectionCitrina. Finally, P.heteromorphum (sect.Exilicaulis) and P.tardochrysogenum (sect.Chrysogena) are reported, previously only known from Antarctica and China, respectively.

Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters

Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganism biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order are scarce. This study aims to fill this knowledge gap by a fungi-specific 18S ribosomal RNA (rRNA) gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of seventh stream order number). Using multivariate analyses and the quantitative process estimates (QPEs) method, questions (i) of how mycoplankton communities as part of the river continuum change along the transect, (ii) what factors, spatial and environmental, play a role, and (iii) what assembly processes, such as selection or dispersion, operate along the transect, were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response, for example, to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work so that fungi, as an important ecological organism group, can be integrated into models of, e.g., usage-balance considerations of rivers.

Biogeography and Diversity of Freshwater Bacteria on a River Catchment Scale

To illustrate how freshwater bacterial community changes with geographic gradient, we investigated the spatial changes of bacterial abundance and community structures from over 200 samples on a catchment scale in the Songhua River using heterotrophic plate counts, flow cytometry, denaturing gradient gel electrophoresis, and pyrosequencing analysis. The results showed that the mainstream had higher cultivable bacteria and total bacterial concentration than tributaries in the Songhua River catchment. Response model analysis demonstrated that the bacterial community exhibits a biogeographical signature even in an interconnected river network system, and the total bacterial concentration and biodiversity were significantly correlated to latitude (p < 0.001) and longitude (p < 0.001). Multivariate redundancy analysis indicated that temperature was the most important factor driving bacterial community structure in the Songhua River, which accounts for 35.30% variance of communities, then dissolved oxygen (17.60%), latitude (17.60%), longitude (11.80%), and pH (5.88%). High-throughput pyrosequencing revealed that at the phylum level, Proteobacteria was numerically dominant (89.6%) in river catchment, followed by Bacteroidetes (8.1%) and Cyanobacteria (1.2%). The overall results revealed that the bacterial community was driven by geographical distance regardless of the continuum of the river on a catchment scale.

Fungal Community as a Bioindicator to Reflect Anthropogenic Activities in a River Ecosystem

The fungal community interacts with the ambient environment and can be used as a bioindicator to reflect anthropogenic activities in aquatic ecosystems. Several studies have investigated the impact of anthropogenic activities on the fungal community and found that community diversity and composition are influenced by such activities. Here we combined chemical analysis of water properties and sequencing of fungal internal transcribed spacer regions to explore the relationship between water quality indices and fungal community diversity and composition in three river ecosystem areas along a gradient of anthropogenic disturbance (i.e., less-disturbed mountainous area, wastewater-discharge urban area, and pesticide and fertilizer used agricultural area). Results revealed that the level of anthropogenic activity was strongly correlated to water quality and mycoplankton community. The increase in organic carbon and nitrogen concentrations in water improved the relative abundance of Schizosaccharomyces, which could be used as a potential biomarker to reflect pollutant and nutrient discharge. We further applied a biofilm reactor using water from the three areas as influent to investigate the differences in fungal communities in the formed biofilms. Different community compositions were observed among the three areas, with the dominant fungal phyla in the biofilms found to be more sensitive to seasonal effects than those found in water. Finally, we determined whether the fungal community could recover following water quality restoration. Our biofilm reactor assay revealed that the recovery of fungal community would occur but need a long period of time. Thus, this study highlights the importance of preserving the original natural aquatic ecosystem.

Influence of water quality on diversity and composition of fungal communities in a tropical river

Freshwater fungi are key decomposers of organic material and play important roles in nutrient cycling, bio-remediation and ecosystem functioning. Although aquatic fungal communities respond to pollution, few studies have quantitatively assessed the effect of freshwater contamination on fungal diversity and composition; and knowledge is scarcer for tropical systems. Here we help fill this knowledge gap by studying a heavily-contaminated South American river spanning a biodiversity hotspot. We collected 30 water samples scattered across a quality gradient over two seasons and analyzed them using Terminal Restriction Fragment Length Polymorphisms (T-RFLP) coupled with 454 Pyrosequencing. Using T-RFLP we identified 451 and 442 Operational Taxonomy Units (OTUs) in the dry and rainy seasons respectively, whereas Pyrosequencing revealed 48,553 OTUs from which 11% were shared between seasons. Although 68% of all identified OTUs and 51% of all identified phyla remained unidentified, dominant fungal phyla included the Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Zygomycota and Neocallimastigomycota, while Calcarisporiella, Didymosphaeria, Mycosphaerella (Ascomycota) and Rhodotorula (Basidiomycota) were the most abundant genera. Fungal diversity was affected by pH and dissolved iron, while community composition was influenced by dissolved oxygen, pH, nitrate, biological oxygen demand, total aluminum, total organic carbon, total iron and seasonality. The presence of potentially pathogenic species was associated with high pH. Furthermore, geographic distance was positively associated with community dissimilarity, suggesting that local conditions allowed divergence among fungal communities. Overall, our findings raise potential concerns for human health and the functioning of tropical river ecosystems and they call for improved water sanitation systems.

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments

Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi'an, China

Urban lakes play a vital role in the sustainable development of urbanized areas. In this freshwater ecosystem, massive microbial communities can drive the recycling of nutrients and regulate the water quality. However, water bacterial and fungal communities in the urban lakes are not well understood. In the present work, scanning electron microscopy (SEM) was combined with community level physiological profiles (CLPPs) and Illumina Miseq sequence techniques to determine the diversity and composition of the water bacterial and fungal community in three urban lakes, namely Xingqing lake (LX), Geming lake (LG) and Lianhu lake (LL), located in Xi’an City (Shaanxi Province, China). The results showed that these three lakes were eutrophic water bodies. The highest total nitrogen (TN) was observed in LL, with a value of 12.1 mg/L, which is 2 times higher than that of LG. The permanganate index (COD_Mn) concentrations were 21.6 mg/L, 35.4 mg/L and 28.8 mg/L in LG, LL and LX, respectively (p < 0.01). Based on the CLPPs test, the results demonstrated that water bacterial communities in the LL and LX urban lakes had higher carbon source utilization ability. A total of 62,742 and 55,346 high quality reads were grouped into 894 and 305 operational taxonomic units (OTUs) for bacterial and fungal communities, respectively. Water bacterial and fungal community was distributed across 14 and 6 phyla. The most common phyla were Proteobacteriaand Cyanobacteria. Cryptomycota was particularly dominant in LL, while Chytridiomycota and Entomophthormycota were the most abundant fungal phyla, accounting for 95% of the population in the LL and 56% in the LG. Heat map and redundancy analysis (RDA) highlighted the dramatic differences of water bacterial communities among three urban lakes. Meanwhile, the profiles of fungal communities were significantly correlated with the water quality parameters (e.g., COD_Mn and total nitrogen, TN). Several microbes (Legionella sp. and Streptococcus sp.) related to human diseases, such as infectious diseases, were also found. The results from this study provides useful information related to the water quality and microbial community compositions harbored in the aquatic ecosystems of urban lakes.

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile

Our study reports the diversity of culturable mycoplankton in the eastern South Pacific Ocean off Chile to contribute with novel knowledge on taxonomy of filamentous fungi isolated from distinct physicochemical and biological marine environments. We characterized spatial distribution of isolates, evaluated their viability and assessed the influence of organic substrate availability on fungal development. Thirty-nine Operational Taxonomic Units were identified from 99 fungal strains isolated from coastal and oceanic waters by using Automatic Barcode Gap Discovery. All Operational Taxonomic Units belonged to phylum Ascomycota and orders Eurotiales, Dothideales, Sordariales and Hypocreales, mainly Penicillium sp. (82%); 11 sequences did not match existing species in GenBank, suggesting occurrence of novel fungal taxa. Our results suggest that fungal communities in the South Pacific Ocean off Chile appear to thrive in a wide range of environmental conditions in the ocean and that substrate availability may be a factor influencing fungal viability in the ocean.

Spatio-Temporal Variations of High and Low Nucleic Acid Content Bacteria in an Exorheic River

Bacteria with high nucleic acid (HNA) and low nucleic acid (LNA) content are commonly observed in aquatic environments. To date, limited knowledge is available on their temporal and spatial variations in freshwater environments. Here an investigation of HNA and LNA bacterial abundance and their flow cytometric characteristics was conducted in an exorheic river (Haihe River, Northern China) over a one year period covering September (autumn) 2011, December (winter) 2011, April (spring) 2012, and July (summer) 2012. The results showed that LNA and HNA bacteria contributed similarly to the total bacterial abundance on both the spatial and temporal scale. The variability of HNA on abundance, fluorescence intensity (FL1) and side scatter (SSC) were more sensitive to environmental factors than that of LNA bacteria. Meanwhile, the relative distance of SSC between HNA and LNA was more variable than that of FL1. Multivariate analysis further demonstrated that the influence of geographical distance (reflected by the salinity gradient along river to ocean) and temporal changes (as temperature variation due to seasonal succession) on the patterns of LNA and HNA were stronger than the effects of nutrient conditions. Furthermore, the results demonstrated that the distribution of LNA and HNA bacteria, including the abundance, FL1 and SSC, was controlled by different variables. The results suggested that LNA and HNA bacteria might play different ecological roles in the exorheic river.

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR-DGGE

Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.