Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient

Effects of Difenoconazole and Imidacloprid Seed Coatings on Soil Microbial Community Diversity and Ecological Function

Difenoconazole and imidacloprid are key components of seed-coating agents, which alter soil microbial community structure and function after application. Existing studies mainly focus on the environmental effects of their spraying application, while research on their impacts on the soil ecosystem when used as seed-coating agents is relatively limited. Through field experiments, this study systematically evaluated and compared the effects of difenoconazole and imidacloprid seed coatings on wheat rhizosphere soil microbial communities and ecological functions by measuring soil enzyme activities, employing 16S rRNA and ITS high-throughput sequencing technologies and predicting KEGG functional pathways. The results showed that imidacloprid and difenoconazole significantly reduced bacterial community diversity, particularly under the high-dosage difenoconazole treatment (0.18 g a.i./kg seed), with a 5.80% decrease in diversity by day 30. This treatment most strongly inhibited the phyla Bacteroidota and Myxococcota, with maximum reductions of 23.87% and 63.57%, respectively. However, the abundance of Actinobacteriota significantly increased, with a maximum increase of 38.53%. Additionally, fungal community diversity significantly increased under both difenoconazole and imidacloprid treatments. Both seed coatings significantly altered the microbial community structure from days 20 to 60, with recovery occurring by day 120. Furthermore, KEGG pathway analysis revealed that the high-dosage difenoconazole treatment (0.18 g a.i./kg seed) significantly activated functional pathways such as cell motility, signal transduction, and membrane transport, whereas the standard dosage (0.12 g a.i./kg seed) exhibited metabolic suppression. This study elucidates the dynamic impacts of seed-coating agent application on soil microbial communities, providing theoretical support for rational pesticide use and the optimization of agricultural strategies.

Shifts in Soil Fungal Community and Trophic Modes During Mangrove Ecosystem Restoration

Mangrove ecosystems are valuable coastal ecosystems; however, studies on the diversity and functional features of their soil fungal communities during restoration are limited. In this study, we examined fungal diversity and trophic modes across mudflat, young mangrove, and mature mangrove stages. We found that Ascomycota and Basidiomycota were the dominant phyla, with saprotrophs as the most abundant trophic mode. The abundance of the major phyla and trophic modes significantly varied across restoration stages. Although fungal alpha (α)-diversity remained stable among the stages, beta (β)-diversity showed significant differentiation. Spearman's analysis and partial Mantel tests revealed that total nitrogen and inorganic phosphorus significantly influenced the fungal α-diversity, whereas temperature and pH primarily shaped the fungal β-diversity. Total nitrogen and carbon were key factors affecting the trophic mode α-diversity, whereas total phosphorus and inorganic phosphorus were the main drivers of the trophic mode β-diversity. Variation partitioning analysis confirmed that nutrients, rather than soil properties, were the primary factors shaping fungal communities and trophic modes. Random forest analysis identified key bioindicators, including species such as Paraphyton cookei, and trophic modes such as saprotrophs, both of which were strongly influenced by soil carbon. These findings advance our understanding of fungal ecology in mangrove restoration.

Time-decay patterns and irregular disturbance: contrasting roles of abundant and rare microbial communities in dynamic coastal seawater

Microbial communities in coastal seas experience strong environmental disturbances, yet their response patterns, especially regarding differently abundant subcommunities, remain poorly understood. Here, through 16S rRNA gene amplicon sequencing, we investigated the diversity, time-decay pattern, and assembly process of abundant, conditionally rare taxa (CRT) and rare microbial subcommunities in temperate coastal waters over 60 consecutive weeks. The abundant (50.9%) and CRT (46.1%) communities each comprised approximately half of the planktonic community, while the CRT and rare communities contributed to the extremely high species diversity. Distinct temporal heterogeneity was observed among the three fractions and was associated with taxonomic level. The abundant subcommunity exhibited time-decay patterns at all taxonomic levels, while for CRT, the pattern was found only at finer levels. In contrast, variations of the rare community loosely followed a temporal rhythm and were largely confined within a specific taxonomic range, likely raised from turnovers among closely related taxa. Determinism dominated the community assembly of the abundant fraction, while the rare one was more controlled by stochasticity that may be related to pulse terrigenous inputs and anthropogenic disturbances. The rare subcommunity with narrow niche widths likely represented a stable repository to offer episodic specialists, while the abundant taxa that exhibited broader niche widths were considered the generalists in fluctuating environments. Our study revealed the distinct strategies that abundant and rare communities adopt to maintain community stability in temporal dynamics of prokaryotic plankton in the coastal seawater.

IMPORTANCE

The relative importance of rare and abundant taxa in microbial temporal patterns remains debated. Here, we identified taxonomically associated distinct diversity modes of abundant and rare subcommunities from a year-round time-series study in dynamic coastal seawater. We highlighted the significance of the rare subcommunity in maintaining community stability by serving as a repository to offer specialists driven by stochastic processes over time. The abundant subcommunity, by contrast, contributed mainly to temporal rhythmic variations. This study expands the current understanding of the temporal dynamics and stability of coastal microbial communities by revealing distinct variation patterns of subcommunities with different abundances.

Thermal sensitivity and niche plasticity of generalist and specialist leaf-endophytic bacteria in Mangrove Kandelia obovata

Leaf endospheres harbor diverse bacterial communities, comprising generalists and specialists, that profoundly affect ecosystem functions. However, the ecological dynamics of generalist and specialist leaf-endophytic bacteria and their responses to climate change remain poorly understood. We investigated the diversity and environmental responses of generalist and specialist bacteria within the leaf endosphere of mangroves across China. Our findings show a predominance of specialists in the mangrove leaf endosphere. Temperature is the key factor driving community dissimilarity in both groups, yet it negatively influences the alpha diversity. Soil nutritional factors, particularly phosphate for generalists and total organic carbon for specialists are critical in shaping the functional profiles. Interestingly, temperature has a limited impact on functional profiles. Stochastic processes govern community assembly in both bacterial groups, altering the β-nearest taxon indices as temperatures increase. Our findings indicate that the halophytic leaf endosphere favors microbial niche specialization, due to its unique microenvironment and discrete niches, showing thermal sensitivity in terms of the microbial community profile. This study provides insights into niche differentiation and environmental adaptation mechanisms of leaf endophytic microbes in woody halophytes in response to environmental perturbations.

Eutrophication-induced shifts cause diverse responses in the phoD community of a plateau freshwater lake

Eutrophication is a critical environmental challenge affecting lakes globally. Mitigating trophic level under endogenous phosphorus release is an unsolved problem in eutrophic lakes. However, understanding the dynamics and assembly of microbial communities encoding the alkaline phosphatase (phoD community) and their responses during trophic transitions in eutrophic lakes is limited. In this study, we compared the composition and assembly mechanisms of phoD communities in four seasons in the Yilong Lake, a shallow lake of the Yunnan-Guizhou Plateau. The lake exhibits slightly eutrophic conditions in summer and mesotrophic conditions in spring, autumn, and winter. By analyzing seasonal variations, we observed that during summer, the relative abundance of Pseudomonas in the water had the highest value, while the Shannon-Wiener index of phoD communities was lowest. Mantel tests showed an increased Bray-Curtis dissimilarity of phoD communities in the water with rising eutrophication, a trend not observed in sediment. Notably, eutrophication heightened the homogeneity selection governing the assembly of phoD communities in water. The co-occurrence networks showed that the OTUs in the summer exhibited closer interconnections than those in other seasons. Additionally, the topological parameters from networks indicated that eutrophication is poised to instigate changes and modulate the dynamics of the microbial phoD community, resulting in markedly distinct seasonal behaviors. pH was identified as a critical factor directly influencing phoD community diversity via partial least squares path modeling (PLS-PM). This study shed light on our understanding of the seasonal dynamics of phoD communities and their pivotal role in phosphorus cycling in eutrophic lakes.

Diversity and Distribution of Fungi in the Marine Sediments of Zhanjiang Bay, China

Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary-coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of high-throughput amplicon sequencing using the internal transcribed spacer (ITS) primers. Additionally, the FUNGuild database was employed to assess the potential functional traits of fungi. A total of 1242 ASV sequences, affiliated to 144 genera and five phyla, were identified. Ascomycota (68.97%) and Basidiomycota (6.41%) were the dominant fungal groups, together accounting for 75.38% of the total relative abundance of the fungal community. Significant differences were observed in the α-diversity indices (Shannon index and richness) and β-diversity of fungal communities across the three distinct salinity regions. The fungal molecular network exhibited primarily positive species interactions, with notable structural differences across salinity gradients. The low-salinity group had a large network with high modularity; the medium-salinity group a small, simple network with high centralization, and the high-salinity group a compact, moderately complex network. Symbiotrophs, saprotrophs, and pathotrophs, being the three trophic types with the highest proportions, were estimated based on ITS. A redundancy analysis (RDA) indicated that salinity was the primary factor influencing the distribution of Ascomycota communities, while the distributions of Basidiomycota, Chytridiomycota, Mucoromycota, and Rozellomycota were more strongly affected by environmental factors such as chlorophyll a, chemical oxygen demand (COD), pH, and temperature. Our work provides new scientific data on the diversity, composition, and distribution of fungal communities in Zhanjiang Bay, which helps to understand the biodiversity of fungi in the estuary-coast ecosystems.

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake

The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH4+-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication

The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

Trophic level plays an enhanced role in shaping microbiota structure and assembly in lakes with decreased salinity on the Qinghai-Tibet and Inner Mongolia Plateaus

Plateau lakes characterized by salinization and eutrophication are essential aquatic ecosystems. A myriad of microorganisms serve as crucial biological resources in plateau lakes and drive the elemental cycles of these ecosystems. Currently, there is a paucity of knowledge regarding the impacts of salinization and eutrophication dynamics on the microbiota in plateau lakes. Here, high-throughput sequencing of the 16S ribosomal RNA genes (V4 region) was used to characterize microbial community structure and assembly in plateau lakes with different salinities and trophic levels. Water samples were collected at 191 sites across 24 lakes on the Qinghai-Tibet and Inner Mongolia Plateaus in northern China. The results showed that high salinity considerably reduced microbial alpha-diversity and niche breadth while increasing within-group similarity among various lake types. High salinity additionally decreased the complexity of microbial networks and enhanced network robustness. The assembly of microbial communities was primarily governed by deterministic processes in high-salinity and eutrophic low-salinity lakes. At decreased salinity, trophic level played a leading role in shaping microbial community structure, and the ecological processes shifted from deterministic processes driven by high salinity to eutrophication-driven deterministic processes. The biomarkers also varied from taxa adapted to high-salinity environments (e.g., Nanoarchaeaeota, Rhodothermia) to those suited for living in freshwater and low-salinity habitats (e.g., Alphaproteobacteria, Actinobacteria). In the case of eutrophication, Actinobacteria, Chloroflexi, and Cyanobacteria became the dominant taxa. Our findings indicate that decreased salinity enables trophic level to play an enhanced role in shaping microbial community structure and assembly in plateau lakes. This study enriches our knowledge about the ecological impacts of salinization and eutrophication in plateau lakes.

Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Structure and assembly process of fungal communities in the Yangtze River Estuary

Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater

The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.

Copper and temperature shaped abundant and rare community assembly respectively in the Yellow River

Untangling assembly and microbial interaction of abundant and rare microbiota in aquatic ecosystem is pivotal for understanding how community assembly respond to environmental variables and co-occurrence patterns. Here, we explored the assembly mechanisms, their drivers, and species co-occurrence of abundant and rare microbiomes in the Yellow River using 16S rRNA gene sequencing in Lanzhou, China. Here, abundant community was ubiquitous across all sites, whereas rare community was uneven distributed. The richness and community dissimilarity of rare taxa were significantly greater than those of abundant ones. Stochastic processes structured the rare community assembly in spring and winter, while deterministic processes shaped the abundant and rare community assembly in other seasons and all sites. Copper and water temperature mediated the balance between deterministic and stochastic processes of abundant and rare community, respectively. A few abundant taxa with closer relationships frequently occupied central positions and had a great effect on other co-occurrences in the network, while the majority of keystone microbiota were rare microbiome and played a considerable part in maintaining the network structure. Our study provides some ecological proposals for water quality management and ecological stability of the Yellow River. KEY POINTS: • Deterministic process dominated abundant and rare community assembly. • Cu and TW mediated the balance of abundant and rare community assembly respectively. • Abundant taxa had a greater effect on other co-occurrences in the network.

Novel insights in seasonal dynamics and co-existence patterns of phytoplankton and micro-eukaryotes in drinking water reservoir, Northwest China: DNA data and ecological model

Although associations between phytoplankton and micro-eukaryotes have been studied in aquatic ecosystems, there are still knowledge gaps in comprehending their dynamics and interactions in drinking water reservoirs. Here, the seasonal dynamics of phytoplankton and micro-eukaryotic diversities and their co-existence patterns were studied in a drinking water reservoir, Northwest China. The highest phytoplankton diversity was observed in summer, and Chlorella sp. that belongs to Chlorophyta was the most abundant genus. The highest eukaryotic diversity was also detected in summer, and Rimostrombidium sp. that belongs to Ciliophora was the most dominant genus. Mantel test showed that the phytoplankton diversity was significantly correlated with ammonia nitrogen (r = 0.561, p = 0.001) and dissolved organic carbon (r = 0.267, p = 0.017), while the eukaryotic diversity was significantly associated with ammonia nitrogen (r = 0.265, p = 0.034) and temperature (r = 0.208, p = 0.046). PLS-PM (Partial Least Squares Path Modeling) further revealed that nutrients (P < 0.01) significantly affected the phytoplankton diversity, while nutrients (P < 0.01) and temperature (P < 0.01) significantly influenced the eukaryotic diversity. Co-occurrence network displayed the primarily positive interactions (77.66% positive and 22.34% negative) between phytoplankton and micro-eukaryotes. These findings could deepen our understanding of interactions between phytoplankton and micro-eukaryotes and their driving factors under changing aquatic environments of drinking water reservoirs.