Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte,Potamogeton crispus, in freshwater lakes

Ecological restoration enhanced the stability of epiphytic microbial food webs of submerged macrophytes: Insights from predation characteristics of epiphytic predators

The application of various submerged macrophytes for ecological restoration has gained increasing attention in urban lake ecosystems. The multitrophic microbial communities that colonized in various submerged macrophytes constitute microbial food webs through trophic cascade effects, which affect the biogeochemical cycles of the lake ecosystem and directly determine the effects of ecological restoration. Therefore, it is essential to reveal the diversity, composition, assembly processes, and stability of the microbial communities within epiphytic food webs of diverse submerged macrophytes under eutrophication and ecological restoration scenarios. In this study, we explored the epiphytic microbial food webs of Vallisneria natans and Hydrilla verticillata in both eutrophic and ecological restoration regions. The obtained results indicated that the two regions with different nutrient levels remarkably affected the diversity and composition of epiphytic multitrophic microbial communities of submerged macrophytes, among them, the community composition of epiphytic predators were more prone to change. Secondly, environmental filtering effects played a more important role in driving the community assembly of epiphytic predators than that of prey. Furthermore, the generality and intraguild predation of epiphytic predators were significantly improved within ecological restoration regions, which increased the stability of epiphytic microbial food webs. Additionally, compared with Hydrilla verticillata, the epiphytic microbial food webs of Vallisneria natans exhibited higher multitrophic diversity and higher network stability regardless of regions. Overall, this study focused on the role of the epiphytic microbial food webs of submerged macrophytes in ecological restoration and uncovered the potential of epiphytic predators to enhance the stability of microbial food webs, which may provide new insights into the development of ecological restoration strategies.

Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction

The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.

Interspecific Differences in Carbon and Nitrogen Metabolism and Leaf Epiphytic Bacteria among Three Submerged Macrophytes in Response to Elevated Ammonia Nitrogen Concentrations

Submerged macrophytes in eutrophic aquatic environments adapt to changes in ammonia nitrogen (NH4-N) levels by modifying their levels of free amino acids (FAAs) and soluble carbohydrates (SCs). As symbionts of submerged macrophytes, epiphytic bacteria have obvious host specificity. In the present study, the interspecific differences in the FAA and SC contents of Hydrilla verticillata (Linn. f.) Roylep, Vallisneria natans Hara and Chara braunii Gmelin and their leaf epiphytic bacterial communities were assessed in response to increased NH4-N concentrations. The results revealed that the response of the three submerged macrophytes to NH4-N stress involved the consumption of SCs and the production of FAAs. The NH4-N concentration had a greater impact on the variation in the FAA content, whereas the variation in the SC content was primarily influenced by the species. At the phylum level, the relative abundance of Nitrospirota on the leaves exhibited specific differences, with the order H. verticillata > V. natans > C. braunii. The dominant genera of epiphytic bacteria with denitrification effects on V. natans, H. verticillata and C. braunii leaves were Halomonas, Acinetobacter and Bacillus, respectively. When faced with NH4-N stress, the variation in epiphytic bacterial populations associated with ammonia oxidation and denitrification among submerged macrophytes could contribute to their divergent responses to heightened nitrogen levels.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms

Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.

Comparison of epiphytic and intestinal bacterial communities in freshwater snails (Bellamya aeruginosa) living on submerged plants

The combination of submerged plants and snails can combat eutrophication of freshwater systems by suppressing algal growth and assimilating nutrients. By consuming epiphytes, snails can benefit the growth of submerged plants. However, the efficiency of this phytoremediation strategy may depend on the microbes associated with the plants and snails. In this study, we compared the epiphytic bacterial communities on submerged plants (Vallisneria natans and Cabomba caroliniana) and intestinal bacterial communities of a snail, Bellamya aeruginosa, found on these plants using 16S rRNA gene sequencing. Epiphytic bacterial communities were similar between the two plant species and snails shared a high proportion of snail intestinal bacterial OTUs (75%) and genera (85%) with plants they grazed on. However, significant variations of Bray-Curtis distances differentiated epiphytic and intestinal bacterial communities. In addition, between the top 50 genera shared by intestinal and epiphytic bacterial communities, more Spearman correlations were detected within bacterial communities associated with snails than between communities associated with plants (190 vs. 143), and the correlations in epiphytic bacterial networks were more concentrated on certain genera, indicating they possessed distinct bacterial networks. This suggests the bacterial communities associated with snails do not depend strongly on the plant they graze on, which may be important for better understanding the role of snails in aquatic eco-restoration.

Differential responses of dominant and rare epiphytic bacteria from a submerged macrophyte to elevated CO2

Epiphytic bacteria develop complex interactions with their host macrophytes and play an important role in the ecological processes in freshwater habitats. However, how dominant and rare taxa respond to elevated atmospheric CO₂ remains unclear. A manipulated experiment was carried out to explore the effects of elevated CO₂ on the diversity or functional characteristics of leaf epiphytic dominant and rare bacteria from a submerged macrophyte. Three levels (high, medium, normal) of dissolved inorganic carbon (DIC) were applied to the overlying water. The physicochemical properties of the overlying water were measured. Elevated atmospheric CO₂ significantly decreased the pH and dissolved oxygen (DO) of overlying water. Proteobacteria, Cyanobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria are the dominant phyla of leaf epiphytic bacteria from Myriophyllum spicatum, occupying over 90% of the accumulated relative abundances. The aquatic DIC level and further pH significantly drove the epiphytic community composition differences among the three DIC levels. For dominant epiphytic bacteria, the functional potential of nutrient processes and mutualistic relationships were strongly affected by a high DIC level, while responses of rare epiphytic bacteria were more related to trace element processes, pathogens, and defense strategies under a high DIC level. Our results showed the responses of epiphytic bacteria to elevated CO₂ varied across dominant and rare taxa.

Community structure and function of epiphytic bacteria attached to three submerged macrophytes

In aquatic ecosystems, large amounts of epiphytic bacteria living on the leaf surfaces of submerged macrophytes play important roles in affecting plant growth and biogeochemical cycling. The restoration of different submerged macrophytes has been considered an effective measure to improve eutrophic lakes. However, the community ecology of epiphytic bacteria is far from well understood for different submerged macrophytes. In this study, we used quantitative PCR, 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structure and function of epiphytic bacteria in an aquatic ecosystem recovered by three submerged macrophytes (Hydrilla verticillata, Vallisneria natans and Potamogeton maackianus) during two growth periods. The results showed that the community compositions and functions of epiphytic bacterial communities on the submerged macrophyte hosts were different from those of the planktonic bacterial communities in the surrounding water. The alpha diversity of the epiphytic bacterial community was significantly higher in October than in July, and the community compositions and functions differed significantly in July and October. Among the three submerged macrophytes, the structures and functions of the epiphytic bacterial community exhibited obvious differences, and some specific taxa were enriched on the biofilms of the three plants. The alpha diversity and the abundance of functions related to nitrogen and phosphorus transformation were higher in the epiphytic bacteria of P. maackianus. In summary, these results provide clues for understanding the distribution and formation mechanisms of epiphytic bacteria on submerged macrophyte leaves and their roles in freshwater ecosystems.

Understanding the ecological processes governing hydrophyte-associated bacterial communities involved in hydrophyte growth and development

Maintaining hydrophyte growth has been a major focus of aquatic ecological research. The hydrophyte microbiome plays a key role in the growth and health of hydrophytes, but the ecological processes regulating the assembly and function of hydrophyte microbial communities remain unclear. This knowledge gap limits the efficacy of managing microbiomes to enhance the capacity of hydrophytes to restore the aquatic environment. Here, we sampled three typical hydrophytes (Ceratophyllum demersum, Nymphoides peltatum, and Potamogeton crispus) to study the ecological process governing hydrophyte-associated bacterial communities. The results demonstrated that hydrophyte-associated bacterial communities were affected more by the hydrophyte host species (HEEI = 2.40) than by the environment (HEEI = 1.00). The hydrophyte host species not only affected bacterial community assembly, but reduced the diversity and network complexity of the bacterial community relative to that of the environment. Furthermore, the core taxa of two hydrophytes were identified. Chryseobacterium was the core taxon of N. peltatum, and Burkholderia-Caballeronia-Paraburkholderia, Pseudolabrys, and Pajaroellobacter were the core taxa of P. crispus. The core taxa of P. crispus were closely related to potential denitrification-related functions of bacteria and revealed that P. crispus played a role in denitrification during aquatic ecological restoration. Overall, the results of this study highlight the need to develop approaches employing hydrophyte-associated bacteria to promote the development of hydrophytes, which will be essential for increasing the utility of hydrophyte microbiomes in the future and enhancing aquatic ecological restoration.

Aquatic Macrophytes Are Associated With Variation in Biogeochemistry and Bacterial Assemblages of Mountain Lakes

In aquatic systems, microbes likely play critical roles in biogeochemical cycling and ecosystem processes, but much remains to be learned regarding microbial biogeography and ecology. The microbial ecology of mountain lakes is particularly understudied. We hypothesized that microbial distribution among lakes is shaped, in part, by aquatic plant communities and the biogeochemistry of the lake. Specifically, we investigated the associations of yellow water lilies (Nuphar polysepala) with the biogeochemistry and microbial assemblages within mountain lakes at two scales: within a single lake and among lakes within a mountain range. We first compared the biogeochemistry of lakes without water lilies to those colonized to varying degrees by water lilies. Lakes with >10% of the surface occupied by water lilies had lower pH and higher dissolved organic carbon than those without water lilies and had a different microbial composition. Notably, cyanobacteria were negatively associated with water lily presence, a result consistent with the past observation that macrophytes outcompete phytoplankton and can suppress cyanobacterial and algal blooms. To examine the influence of macrophytes on microbial distribution within a lake, we characterized microbial assemblages present on abaxial and adaxial water lily leaf surfaces and in the water column. Microbial diversity and composition varied among all three habitats, with the highest diversity of microbes observed on the adaxial side of leaves. Overall, this study suggests that water lilies influence the biogeochemistry and microbiology of mountains lakes.

Response of sediment and water microbial communities to submerged vegetations restoration in a shallow eutrophic lake

Submerged macrophytes are the main primary producers in shallow lakes and play an important role in structuring communities. Aquatic microbes are also an important component of aquatic ecosystems and play important roles in maintaining the health and stability of ecosystems. However, little is known about the interactions between macrophytes and microbes during the reintroduction of submerged vegetation. Here, we chose restored zones dominated by four different submerged vegetations and a bare zone in a shallow eutrophic lake to unveil the microbial diversity, composition and structure changes in sediment and water samples after submerged macrophytes were recovered for one and a half years (July 2019) and two years (April 2020). We found that the recovery of submerged vegetations decreased phosphorus content in water and sediments but increased nitrogen and carbon content in sediments. We observed that the transparency of water in the restored zones was significantly higher than that in the bare zone in July. The recovery of submerged vegetations significantly influenced the alpha diversity of bacterial communities in sediments, with higher values observed in restored zones than in bare zones, whereas no significant influence was found in the water samples. In July, the macrophyte species showed strong effects on the bacterial community composition in water and relatively little effect in sediment. However, a strong effect of the macrophyte species on the composition of bacterial communities in sediments was observed in April, which may be related to the decomposition of plant litter and the decay of detritus. Additionally, the dissimilarity of the sedimentary bacterial community may increase more slowly with environmental changes than the planktonic bacterial community dissimilarity. These results suggest that the large-scale restoration of aquatic macrophytes can not only improve water quality and change sediment characteristics but can also affect the diversity and compositions of bacterial communities, and these effects seem to be very long-lasting.

Substrate type and plant phenolics influence epiphytic bacterial assembly during short-term succession

In natural ecosystems, large amounts of epiphytic bacteria live on the surfaces of submerged plants or non-biological substrates. Although it contributes greatly to host plant health or ecological functions in waters, little is known about the temporal dynamics and assembly mechanisms of epiphytic bacteria. To test whether host plant chemistry leads to divergent community dynamics, we investigated the fine scale temporal community successions of both epiphytic bacteria and the bacterioplankton of the surrounding water in two submerged plants and one non-biological artificial substance. We first observed differentiated epiphytic or surrounding water bacterial communities for different substrates in small spaces (approximately 1 m × 1 m). Selection played dominant roles in affecting the assembly of epiphytic bacteria in the high-phenolic plant Hydrilla verticillata, while for the artificial substance and the low-phenolic plant Vallisneria natans, drift and dispersal drove the assembly of both epiphytic bacteria and bacterioplankton. The higher selection may also contribute to higher turnover rates in both bacterioplankton and epiphytic communities of H. verticillata, with the latter changing drastically in approximately one week. Epiphytic bacteria in H. verticillata developed more complex networks with a higher proportion of positive links, suggesting that more intense interactions such as mutualism or facilitation may exist within epiphytic bacterial communities of the high-phenolic plant. Our results also implied that for the submerged macrophytes used in biological purification, the dynamics of epiphytic biofilm in the purification-related functional capacities might also be considered.

Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system

Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.

Effects of shading levels on the composition and co-occurrence patterns of bacterioplankton and epibiotic bacterial communities of Cabomba caroliniana

Epibiotic bacterial community colonized on the plant leaf plays important roles in promoting plant growth and nutrient absorption, but is sensitive to environmental changes. As one of the most important environmental factors affecting the growth of plants and photosynthetic microorganisms, light may affect the diversity, composition, and interactions of the epibiotic bacterial community. Submerged plants in the aquatic ecosystem may be more sensitive to light intensity variations compared to the terrestrial plants since they usually receive less light. However, the effects of light on the interactions between the submerged plants and their epibiotic microbial communities remain uncertain. Here we used the 16S rRNA gene high-throughput sequencing to investigate the diversity and composition of the bacterioplankton and epibiotic bacterial communities of the Cabomba caroliniana under four different shading levels. A total of 24 water and leaf samples were collected from the experimental microcosms near Lake Taihu. We found the epibiotic bacterial community possessed a higher diversity than that of the bacterioplankton community, although the alpha diversity of the bacterioplankton community was more susceptible to different levels of shading. SourceTracker analysis revealed that with the increase of shading, the colonization of bacterioplankton to epibiotic bacteria decreased. Network analysis showed that the bacterial community network at 50% shading level had the lowest modularity and highest clustering coefficient compared to the bacterial community networks of other shading levels. Our findings provided new understandings of the effects of different light intensities on the epibiotic bacterial communities of submerged macrophytes.

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China

Bacterial communities are sensitive to environmental fluctuations, and a better understanding of the relationships between bacterial community distribution and complex environmental conditions is important for the remediation of lake ecosystems. In this study, bacterial communities from 7 water and 7 sediment samples in 3 different regions (east, the hydrophyte-dominated region; north, the transitional region; west, the highly polluted region) of Lake Taihu were investigated via high-throughput sequencing. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the three lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The Shannon and Simpson values indicated that the diversity of bacterial communities in water was the highest in the eastern region, followed by the northern and western regions, while there was no significant difference in the bacterial community characteristics in sediments among lake regions. We found that the western lake region had the highest Cyanobacteria concentration (34.71%), suggesting that Cyanobacteria may have competitive advantages over the other bacterioplankton in water columns without plants. The abundances of Chlorobi detected in the water samples in the east (2.69%) and north (6.66%) were higher than those in the west because the high turbidity in the western lake region was unsuitable for the growth of Chlorobi. Nitrospirae (average 6.36%) and Chloroflexi (average 11.62%) were more common in the sediments than in the water of Lake Taihu, suggesting that the nutrient level of Lake Taihu sediment was higher than that of water bodies. Welch's t test revealed that there were significant differences in species abundance (such as Microcystis, Synechococcus, Flavobacterium, and hgcI_clade) among the different regions, except that the east was relatively similar to the north. Canonical correspondence analysis demonstrated that TN, TP, and DO showed significant effects on the relative abundance of the dominant bacterial genera in water, while TOC, TP, and TN were positively correlated with TOC, TP and TN. This study provides useful information for understanding the variation in the diversity of bacterial communities in different habitats of Lake Taihu.

Epiphytic bacterial community enhances arsenic uptake and reduction by Myriophyllum verticillatum

Microbes play an important role in the biotransformation of arsenic (As) speciation in various environments. Nevertheless, whether epiphytic bacteria that attached on submerged macrophytes have the potential to influence As speciation still remains unclear. In this study, sterile or nonsterile Myriophyllum verticillatum was cultured with arsenite (As(III)) or arsenate (As(V)) to investigate the impact of epiphytic bacterial community on As uptake, transformation, and efflux. Results showed that both sterile and nonsterile M. verticillatum did not display substantial As(III) oxidation, suggesting that neither M. verticillatum nor epiphytic bacterial community has the capacities of As(III) oxidation. However, sterile M. verticillatum exhibited capacity for As(V) reduction, and the presence of epiphytic bacterial community substantially enhanced the proportions of As(III) in the medium (from 39.91 to 98.44%), indicating that epiphytic bacterial community contributes significantly to As(V) reduction in the medium. The presence of epiphytic bacterial community elevated As accumulation (by up to 2.06-fold) in plants when exposed to As(V). Results also showed that epiphytic bacterial community contributed little to As(III) efflux. Quantitative PCR of As metabolism genes revealed the dominance of the respiratory As(V) reductase genes (arrA) in epiphytic bacterial community, which might play a significant role in As(V) reduction in aquatic environments. Phylogenetic analysis of the arrA genes revealed the widely distribution and diversity of As(V)-respiring bacteria. These results highlighted the substantial impact of the epiphytic bacterial community associated with submerged aquatic macrophytes on As biogeochemistry in wetland and water environments.

Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake

Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes' effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

Structural Variability and Functional Prediction in the Epiphytic Bacteria Assemblies of Myriophyllum spicatum

The underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly. In this study, we used two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment of Myriophyllum spicatum to examine the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was affected by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.). Moreover, plant status effected the assembly in priority to water. 16S rRNA gene sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the 'lottery process' in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.

Community composition and correlations between bacteria and algae within epiphytic biofilms on submerged macrophytes in a plateau lake, southwest China

Epiphytic biofilms are complex matrix-enclosed communities comprising large numbers of bacteria and algae, which play an important role in the biogeochemical cycles in aquatic systems. However, little is known about the correlations that occur between these communities or the relative impact of environmental factors on their composition. In this study, epiphytic biofilms on three different aquatic plants were sampled in a typical plateau lake (Caohai, southwest China) in July and November of 2018. Bacterial diversity was assessed using Miseq sequencing approaches and algal communities were assessed using light microscopy. Gammaproteobacteria (54.64%), Bacteroidetes (17.50%) and Firmicutes (13.99%) were the dominant bacterial taxa and Chlorophyta (47.62%), Bacillariophyta (28.57%) and Euglenophyta (19.05%) were the dominant algae. The alpha diversity values of the epiphytic bacterial and algal communities were greater during the macrophyte decline period (November) than during the growth period (July). Microbial community composition was significantly affected by abiotic factors (water temperature, NH₄⁺, pH or TP) and biotic factors (algae or bacteria). Interestingly, in July and November, the epiphytic algal community dissimilarity was stronger than that observed for bacterial community dissimilarity, suggesting that bacterial community dissimilarity may increase more slowly with environmental change than algal community dissimilarity. Furthermore, association network analysis revealed complex correlations between algal biomass and bacteria phylotype, and that 67.83% of correlations were positive and 32.17% were negative. This may indicate that facilitative correlations between algae and bacteria are predominant in epiphytic biofilms. These results provide new information on algal-bacterial correlations as well as the possible mechanisms that drive variations in the microbial community in epiphytic biofilms in freshwater lakes.

Influence of epiphytic bacteria on arsenic metabolism in Hydrilla verticillata

Microbial assemblages such as biofilms around aquatic plants play a major role in arsenic (As) cycling, which has often been overlooked in previous studies. In this study, arsenite (As(III))-oxidizing, arsenate (As(V))-reducing and As(III)-methylating bacteria were found to coexist in the phyllosphere of Hydrilla verticillata, and their relative activities were shown to determine As speciation, accumulation and efflux. When exposed to As(III), As(III) oxidation was not observed in treatment H(III)-B, whereas treatment H(III)+B showed a significant As(III) oxidation ability, thereby indicating that epiphytic bacteria displayed a substantial As(III) oxidation ability. When exposed to As(V), the medium only contained 5.89% As(III) after 48 h of treatment H(V)-B, while an As(III) content of 86.72% was observed after treatment H(V)+B, thereby indicating that the elevated As(III) in the medium probably originated from As(V) reduction by epiphytic bacteria. Our data also indicated that oxidizing bacteria decreased the As accumulation (by approximately 64.44% compared with that of treatment H(III)-B) in plants, while reducing bacteria played a critical role in increasing As accumulation (by approximately 3.31-fold compared with that of treatment H(V)-B) in plants. Regardless of whether As(III) or As(V) was supplied, As(III) was dominant in the plant tissue (over 75%). Furthermore, the presence of epiphytic bacteria enhanced As efflux by approximately 9-fold. Metagenomic analysis revealed highly diverse As metabolism genes in epiphytic bacterial community, particularly those related to energetic metabolism (aioAB), and As resistance (arsABCR, acr3, arsM). Phylogenetic analysis of As metabolism genes revealed evidence of both vertical inheritance and horizontal gene transfer, which might have contributed to the evolution of the As metabolism genes. Taken together, our research suggested that the diversity of As metabolism genes in epiphytic bacterial community is associated with aquatic submerged macrophytes which may play an important role in As biogeochemistry in aquatic environments.

Effect of plant-based carbon source supplements on denitrification of synthetic wastewater: focus on the microbiology

The effects of plant-based carbon source addition on wastewater NO₃^--N removal and the involved microorganisms, especially denitrifying bacteria, were investigated. A synthetic wastewater (NO₃^--N, 15 mg/L) was treated through the batch experiment, which included three inoculation cycles (7 days/cycle), and was conducted at 25 °C. Four natural plant substrates, namely, rice straw (RS), wheat straw (WS), ryegrass (RG), and reed (RD), were used as carbon sources and supplemented at the rate of 1% (w/v). The results showed that both RS and WS performed well in promoting NO₃^--N removal (79.55-97.07%). While RG removed only 22.08% of NO₃^--N in the first cycle, the removal efficiency increased afterward (86.09-95.82%). Conversely, the NO₃^--N removal rate of RD decreased from 95.10 to 24.77% as a result of its low ability to supply carbon. With respect to the microorganisms, the RS treatment resulted in more bacteria and denitrifying genes such as narG, nirK, nirS, and norB than other treatments, while the highest number of nosZ gene copies was recorded in the WS treatment. Sequencing results revealed that Firmicutes (18.19-56.96%), Proteobacteria (38.82-74.80%), and Bacteroidetes (3.15-4.15%) were three dominant bacterial phyla for RS, WS, and RD treatments. Furthermore, the genera Enterobacter, Massilia, and Bacillus were the main denitrifying bacteria participating in the NO₃^--N removal. Furthermore, correlation analysis indicated that the denitrifying genus Sphingobacterium played an important role in enhancing nitrogen removal. This study suggested that RS is the superior plant-based carbon source for denitrifying bioreactors used in agricultural runoff treatment.

Habitat species pools shape algal and bacterial communities and their correlations

Understanding of community ecology is scale dependent. When the scale definition changes from subjectively defined "regional species pools" to "habitat species pools", heterogeneity differences occur for microbial communities. However, given the environmental gradients differences among habitats, responses of other organisms and interspecific correlations to habitat species pools may also be heterogeneous. This hypothesis is supported by our research about algal and bacterial communities among four different habitats in littoral zones. In our results, both the algal and bacterial community compositions varied along habitat species pools. Furthermore, at community level, significant correlation was only found between bacterioplankton and phytoplankton in pelagic habitat. And at individual level, the covariant trends between habitat generalists in algal and bacterial communities varied among habitats. Our results indicated that habitat-specific patterns can not only influence the habitat species pools, but also shape the interspecies interaction, and this should be considered in the further study of algae-bacterial correlation.

Ammonium loading disturbed the microbial food webs in biofilms attached to submersed macrophyte Vallisneria natans

The knowledge about the impacts of ammonium loading on microbial food webs in biofilms attached to submersed macrophytes is limited. In the present study, Illumina sequencing method was employed to investigate bacterial and eukaryotic communities in biofilms attached to leaves of Vallisneria natans (V. natans) exposed to 1-16 mg L^-1 NH₄⁺-N for 10 days, and 8 mg L^-1 NH₄⁺-N for 21 days. Ammonium loading stimulated biofilms growth, enhanced the relative abundance of nitrifying genus Nitrospira and several denitrifying genera. Eukaryotic kingdom Metazoa, Viridiplantae, Chromista, Fungi and super group SARNU (Stramenopiles, Alveolata, Rhizaria, Nucleariidae and Fonticula group and unknown eukaryotes) were obtained. Relative abundance of Metazoa decreased with the increased ammonium concentration and exposure time. Redundancy analysis revealed that ammonium, dissolved oxygen (DO) and pH had a key role in determining microbial community structure. Network analyses revealed that there were complex interactions including feeding, parasitism and predatism among organism in biofilms, and the microbial food webs were disturbed by inhibiting metazoan growth but stimulating bacteria and algae growth. These results suggest that ammonium-disturbed microbial food webs in biofilms may contribute to the growth of biofilms and algae, and thus contribute to the decline of submersed macrophyte and provide "algal seeds" for the algae burst in water column. These data will be helpful in understanding the macrophytic region transform into algal region in water column polluted by ammonium.

Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu

Biofilms are often observed at the solid-water interface. The leaves of many floating macrophytes have characteristics of both terrestrial plants and submerged macrophytes, because, in general, their upper and lower surfaces are exposed to air and water, respectively. However, little is known about the biofilms attached to floating plants. We investigated biofilms attached to the leaves, stems and roots of the floating plants Nymphoides peltata (in summer and winter) and Trapa natans (in summer) in the Gonghu Bay of Lake Taihu. Bacteria and algae were major components of the biofilm on the leaves of the two species of plants. In addition, 454 pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the dominant phylum, followed by Bacteroidetes, Firmicutes, Chloroflexi, Acidobacteria, and Verrucomicrobia. Cluster analysis showed that bacterial communities from the same plant source were clustered into the same group. A total of 677 genera were detected, and 47 genera were shared by all samples. Nitrifiers, including Nitrosomonas, Nitrosococcus and Nitrospira were detected in this study. Seven denitrifying genes (napA, napG, nirS, nirK, cnorB, qnorB and nosZ) were used to detect the abundance of denitrifiers. Genes nirK, nirS cnorB and nosZ were the four most abundant genes in all samples. Our results demonstrated that cultivation of floating plants in water column could enlarge the area for biofilm growth, and biofilms might play an important role in denitrification in eutrophic water.

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake

To investigate the differences in the microbial community composition and assembly process in two lake zones (Meiliang Bay (MLB) and Xukou Bay (XKB) in Taihu Lake, China) with different nutrient loadings, water samples were collected. Both the 16S ribosomal RNA (rRNA) gene for the bacterial community and the 18S rRNA gene for the microeukaryote community were investigated using the Illumina second-generation sequencing platform (2 × 250 paired-end). The results indicated that both the bacterioplankton and microeukaryote community composition derived from the two lake zones were significantly different. Significantly higher operational taxonomic unit (OTU) richness (P < 0.01) and phylogenetic diversity (P < 0.05) were found for the bacterioplankton community of MLB. However, a comparable alpha diversity was found between the microeukaryote communities of MLB and XKB (P > 0.05). Environmental factors significantly affected the community compositions in XKB for both the bacterioplankton and microeukaryotes. However, they did not significantly influence the microbial community composition in MLB, except for a weak correlation between dissolved organic carbon (DOC) and the microeukaryote community. The microbial communities tended to be more phylogenetically clustered than expected by chance in the two lake zones. Moreover, the results of the phylogenetic structure suggest that deterministic processes played overwhelming roles in driving the assembly of both the bacterioplankton and microeukaryote community in XKB.

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms

The current climate warming and eutrophication are known to interactively threaten freshwater biodiversity; however, the interactive effects on lacustrine bacterioplankton diversity remain to be determined. Here, we analyzed the spring bacterioplankton community composition (BCC) in 24 outdoor, flow-through mesocosms (mimicking shallow lake environments) under 3 temperature scenarios and 2 nutrient regimes. Our results revealed that neither long-term warming (8.5 years) nor nutrient enrichment had significant effects on bacterioplankton alpha diversity, whereas long-term enhanced warming (elevated 50% above the IPCC A2 climate scenario) and nutrient enrichment in combination increased bacterioplankton beta diversity. We also found that BCC shifted significantly under enhanced warming and nutrient-enriched conditions towards decreased relative abundances of Actinobacteria, Bacteroidetes and Betaproteobacteria, whereas the percentages of Cyanobacteria, total rare phyla and unclassified phyla significantly increased. Null-model tests indicated that deterministic processes played a more important role than stochastic processes in determining BCC. However, the relative importance of stochasticity, primarily ecological drift, was enhanced and contributed to the increased beta diversity of BCC under enhanced warming and nutrient-enriched conditions. Overall, our study suggests that the synergetic effects of warming and nutrient enrichment may result in high variability in the composition of bacterioplankton communities in lacustrine water bodies.

Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3–64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7–25.4%), Firmicutes (3.0–20.1%), Acidobacteria (2.7–15.7%), Actinobacteria (2.2–8.7%), Bacteroidetes (0.5–9.7%), and Verrucomicrobia (2.4–5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log₁₀ transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China

nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.

Phylogenetic structure of bacterial assemblages co-occurring with Ostreopsis cf. ovata bloom

Extensive blooms of the toxic epiphytic/benthic dinoflagellate Ostreopsis cf. ovata are being reported with increasing frequency and spatial distribution in temperate coastal regions including the Mediterranean. These blooms are of human and environmental health concern due to the production of isobaric palytoxin and a wide range of ovatoxins by Ostreopsis cf. ovata. Bacterial-microalgal interactions are important regulators in algal bloom dynamics and potentially toxin dynamics. This study investigated the bacterial assemblages co-occurring with O. cf. ovata (OA) and from ambient seawaters (SW) during the early and peak phases of bloom development in NW Adriatic Sea. Fractions of the bacterial assemblages co-occurring with O. cf. ovata (OA) and more closely associated to the mucilage layer (LA) embedding O. cf. ovata cells were also reported. In total, 14 bacterial phyla were detected by targeted 454 pyrosequencing of the 16S rRNA gene. The dominant bacterial phyla in the OA assemblages were Proteobacteria and Bacteroidetes; while at the class level, Alphaproteobacteria were the most abundant (83 and 66%, relative abundance, early and peak bloom phases), followed by Flavobacteria (7 and 19%, early and peak phases). Actinobacteria and Cyanobacteria were of minor importance (<5% of the relative bacterial abundance each). Gammaproteobacteria showed a notably presence in OA assemblage only at the early phase of the bloom (genus Haliea, 13%). The Alphaproteobacteria were predominately composed by the genera Ruegeria, Jannaschia and Erythrobacter which represented about half of the total phylotypes' contribution of OA at both early and peak phases of the O. cf. ovata bloom, suggesting interactions between this consortium and the microalga. Moreover, the highest contribution of Ruegeria (30% of the total phylotypes) was observed at the early phase of the bloom in LA assemblage. Microbial assemblages associated with the ambient seawaters while being also dominated by Alphaproteobacteria and Flavobacteria were partially distinct from those associated with O. cf. ovata due to the presence of genera almost not retrieved in the latter assemblages.

pH influences the importance of niche-related and neutral processes in lacustrine bacterioplankton assembly

pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.