Seasonal dynamics of mycoplankton in the Yellow Sea reflect the combined effect of riverine inputs and hydrographic conditions

Microascaceae from the Marine Environment, with Descriptions of Six New Species

Most reported members of Microascaceae that have been reported originate from the terrestrial environment, where they act as saprobes or plant pathogens. However, our understanding of their species diversity and distribution in the marine environment remains vastly limited, with only 22 species in nine genera having been reported so far. A survey of the fungal diversity in intertidal areas of China's mainland has revealed the discovery of several Microascaceae strains from 14 marine algae and 15 sediment samples. Based on morphological characteristics and LSU-ITS-tef1-tub2 multilocus phylogeny using Bayesian inference and maximum likelihood methods, 48 strains were identified as 18 species belonging to six genera. Among these, six new species were discovered: Gamsia sedimenticola, Microascus algicola, M. gennadii, Scedosporium ellipsosporium, S. shenzhenensis, and S. sphaerospermum. Additionally, the worldwide distribution of the species within this family across various marine habitats was briefly reviewed and discussed. Our study expands the knowledge of species diversity and distribution of Microascaceae in the marine environment.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.

Seasonal and Spatial Dynamics of Fungal Diversity and Communities in the Intertidal Zones of Qingdao, China

Intertidal zones comprise diverse habitats and directly suffer from the influences of human activities. Nevertheless, the seasonal fluctuations in fungal diversity and community structure in these areas are not well comprehended. To address this gap, samples of seawater and sediment were collected seasonally from the estuary and swimming beaches of Qingdao's intertidal areas in China and were analyzed using a metabarcoding approach targeting ITS2 rDNA regions. Compared to the seawater community dominated by Ciliophora and Agaricomycetes, the sediment community was rather dominated by Dothideomycetes and Eurotiomycetes. Furthermore, the seawater community shifted with the seasons but not with the locations, while the sediment community shifted seasonally and spatially, with a specific trend showing that Cladosporium, Alternaria, and Aureobasidium occurred predominantly in the estuarine habitats during winter and in the beach habitats during spring. These spatiotemporal shifts in fungal communities' composition were supported by the PERMANOVA test and could be explained partially by the environmental variables checked, including temperature, salinity, and total organic carbon. Unexpectedly, the lowest fungal richness was observed in the summer sediments from two swimming beaches which were attracting a high influx of tourists during summer, leading to a significant anthropogenic influence. Predicted trophic modes of fungal taxa exhibited a seasonal pattern with an abundance of saprotrophic fungi in the summer sediments, positively correlating to the temperature, while the taxa affiliated with symbiotroph and pathotroph-saprotroph occurred abundantly in the winter and spring sediments, respectively. Our results demonstrate the space-time shifts in terms of the fungal community, as well as the trophic modes in the intertidal region, providing in-depth insights into the potential influence of environmental factors and human activity on intertidal mycobiomes.

Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters

Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.

Deterministic processes shape bacterial community assembly in a karst river across dry and wet seasons

Karst rivers are particularly vulnerable to bacterial pollution because immigrations are easily diffused from the surrounding environments due to their strong hydraulic connectivity. However, the assembly mechanism in shaping riverine bacterial biogeography is still poorly understood, especially for an ecosystem in the karst area. Here, 16S rRNA genes were used to explore the spatiotemporal and biogeographical patterns of bacterial communities from the Chishui River in the dry and wet seasons, and explore the impact of external immigration on the assembly of water bacterial communities. Our results showed clear spatiotemporal patterns of bacterial communities with a more pronounced seasonal rather than spatial fluctuation, which appeared to be dependent on seasonal-related environmental factors (e.g., temperature and turbidity). The bacterial communities exhibited a significant (p < 0.05) distance–decay pattern in both seasons, and they had a stronger distance–decay relationship in the dry season than in the wet season. However, most of the biomarkers of different external immigrations did not show significant (p > 0.05) distance–decay patterns along the Chishui river, implying that the biomarkers could be used as indicators of external immigration (e.g., OTU_125 and OTU_536). Also, the tributaries were the main external immigration (20.44–83.68%) for the Chishui River, while other terrestrial immigration (e.g., livestock, the soil of the cropland, brewing wastewater treatment plant, and sewages) showed relatively little influence, which could be due to the hydrodynamic conditions (e.g., fragile rock–soil system and hydrological structure) of the karst river. Additionally, the assembly of water bacterial communities in the Chishui river was governed by more determinism (50.7–85.7%) than stochasticity (14.3–49.3%) in both the dry and wet seasons. We demonstrated that the bacterial community’s substantial variations are largely shaped by deterministic processes, thereby providing a better understanding of spatiotemporal patterns and mechanisms of the bacterial community in karst river waters.

Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient

Evidence increasingly suggests planktonic fungi (or mycoplankton) play an important role in marine food webs and biogeochemical cycles. In order to better understand their ecological role and how oceanographic gradients from the coastal to open ocean shape the mycoplankton community, molecular approaches were used to study fungal dynamics along a repeatedly sampled, five-station transect beginning at the mouth of an estuary and continuing 87 km across the continental shelf to the oligotrophic waters at the boundary of the Sargasso Sea. Similar to patterns in chlorophyll a, fungal 18S rRNA gene abundance showed a sharp decrease from nearshore to offshore stations. While Shannon's diversity was not statistically different across the transect, nonmetric multidimensional scaling (NMDS) ordination revealed that fungal communities at the nearshore station were significantly different from those at other stations. Even though spatial gradients were consistently strong, the shelf mycoplankton were more similar to those of the offshore communities when temperature was high (>20°C) and while they shifted toward the nearshore communities when temperature was low (<19°C), suggesting a role for additional seasonal factors (such as temperature) in shaping mycoplankton distributions. However, overall phylotype distributions were patchy with few taxa observed at all stations and the majority observed at a single station with the nearshore station exhibiting the largest number of exclusive phylotypes. Overall, our findings revealed the patchy spatial distributions and distinct niche partitioning of mycoplankton populations across a nearshore to open ocean gradient, which improved our understanding of fungal ecology in coastal waters. IMPORTANCE Fungi are an important, but understudied, group of heterotrophic microbes in marine environments. Traditionally, fungi in the coastal ocean were largely assumed to be derived from terrestrial inputs. Yet here we find many fungal taxa are endemic to the open ocean environment but are rare or absent in nearshore waters, suggesting they are not washed into the ocean from the land. As observed for the bacterioplankton, coastal oceanographic gradients can function as habitat barriers to partition fungal communities. Compared to the bacterioplankton, however, the mycoplankton exhibit a much patchier distribution pattern, suggesting differential drivers and the potential for spatially/temporally limited habitats or strong density-dependent selection. Therefore, our results show that mycoplankton in the coastal ocean may play a significant but complementary role to that of the bacterioplankton.