Prokaryotic communities adapted to microhabitats on the Indian lotus (Nelumbo nucifera) growing in the high-altitude urban Dal Lake.

doi:10.21203/rs.3.rs-1421588/v1

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Prokaryotic communities adapted to microhabitats on the Indian lotus (Nelumbo nucifera) growing in the high-altitude urban Dal Lake.

https://doi.org/10.21203/rs.3.rs-1421588/v1

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Indian lotus (Nelumbo nucifera) is one of the dominant aquatic plants cultivated in Dal Lake, situated at 1586 m above MSL in the northeast of Srinagar, Kashmir. Despite their economic and ecological role, the microbial communities associated with the lotus plant are still unexplored. In this study, we investigated prokaryotic communities harboured by different lotus microhabitats (roots, rhizome, leaves, flowers and fruits), lake water, and sediments using 16S rRNA gene amplicon sequencing. Overall, prokaryotic diversity decreased significantly on the lotus in comparison to the lake water and sediments. Among the microhabitats of lotus, roots and leaves harboured more diverse communities in comparison to rhizomes, fruits and flowers. A total of 98 genera were shared by lotus and the Dal Lake sediments and water. However, significant differences were found in their relative abundance, like Pseudomonas was the most dominant genus on most lotus microhabitats. On the other hand, Flavobacterium was highly abundant in the lake water, while a higher abundance of Acinetobacter was recorded in sediments. Additionally, significant differences were recorded in the proportion of several genera including Pseudomonas, Clostridium, Sphingomonas, Erwinia, Lactococcus, Rhizobium, Weissella, and Raoultella among the lotus microhabitats. Predicted functions of prokaryotic communities revealed a higher abundance of genes associated with nutrient uptake in the microhabitats of the lotus. This study offered first-hand information on the prokaryotic communities harboured by lotus plants and water and sediments of the Dal Lake and demonstrated the adaptation of diverse communities to microhabitats of lotus.

Phytomicrobiome

Nelumbo nucifera

Indian lotus

sediment

water

rhizosphere

Dal Lake is a postglacial, urban water body regarded as one of the most beautiful lakes in the world located between 34°6’N and 34°10’N latitude and 74°50’E and 74°54’E longitude in the middle of Kashmir Valley (Shah et al. 2014). This shallow, open-drainage lake is fed by Dachigam-Telbal Nallah (with the perennial flow), Dara Nallah along with several minor streams. The average annual inflow of the lake is around 292 million m³, with Telbal Nallah accounting for 80% of the total and 20% contributed by other sources (Bhat 2013). Long-term studies suggested a significant reduction in lake size, while the floating aquatic vegetation on the surface increased three-folds (Rashid et al. 2017). Anthropogenic activities such as the urbanization of the lake interiors, disposal of untreated household waste, and agriculture adversely affected the health of this pristine ecosystem (Rashid et al. 2017; Ahmad et al. 2020).

Indian lotus (Nelumbo nucifera) is an aquatic perennial herb, which grows in temperate and tropical climates like marshes and bogs, a floating anchored macrophyte growing in shallow lakes and ponds (Bhattacharjee and Lakshminarasimhan 2018; Gowthami et al. 2021). The plant possesses an anchored rhizome that contains numerous gas canals, mostly miss identified as the lotus stem (Matthews and Seymour 2010). Almost all parts of the lotus are used for various edible preparations. The rhizome of lotus (locally known as nadru) cultivated in the Dal Lake has high demand due to its unique taste and quality, which helps the farmers fetch a reasonable price in the markets and is the main driving force in its extensive cultivation in the lake. Leaves are used to wrap food and serve food as a plate due to their unique properties, such as super hydrophobicity and self-cleaning nature (Wang et al. 2009; Gowthami et al. 2021). Cultivating lotus is an important activity from both economic and ecological perspectives in the Dal Lake, as it is also known to remove pollutants (Mishra et al. 2009; Rasid et al. 2019).

The phytomicrobiome is associated explicitly with plant parts and provides various services to benefit plants, like the availability of mineral nutrients and the control colonization of pathogens (Rahi 2017). In addition to these benefits to plants, the phytomicrobiome can also provide environment-friendly solutions to current challenges, for example, by degrading harmful chemicals and reducing the emission of greenhouse gasses (Hamonts et al. 2018; Ke et al. 2021). See Singh et al. (2021) for a review. Harnessing the potential of phytomicrobiome requires a detailed understanding of the composition of microbial communities (Macdonald and Singh, 2014; Hamonts et al. 2018). Multiple factors, including ecosystems (terrestrial or aquatic), host plant, microhabitats of the plant (roots, stems and leaves), and geographic location, can influence the phytomicrobiome. Most of the phytomicrobiome studies have focused on the terrestrial plants, and that too on the root microbiome, since most crop plants are of terrestrial origin and key function like nutrient uptake occurs through roots.

Contrary to this, several studies suggested the importance of microbial communities in all microhabitats of plants (Egamberdieva et al. 2017; Chen et al. 2021; Ke et al. 2021). Furthermore, the plants growing in the aquatic ecosystems have distinct microbial communities for above- and below-water compartments (Nielsen et al. 2001; Holmer and Laursen 2002; Shahid et al. 2020). Although lotus cultivation in the Dal Lake has both economic and ecological importance, the microbiology studies done so far were with the perspective of targeting diseased states in the lotus (Meeboon and Takamatsu 2015; Li et al. 2016; Chen and Kirschner 2017) and not to understand the overall structure of lotus microbiome. In the present study, we deciphered the composition of prokaryotic communities in water and sediment samples and root-to-fruits of lotus cultivated in the Dal Lake. We also used the microbiome data to predict the plausible functions of microbial communities harboured by lotus and the Dal Lake water and sediments.

2.1. Sample collection

Water and sediments, and lotus root, rhizome, flower, fruit and leaf samples were collected in the 50 ml falcon tube (Falcon™ 50mL Conical Centrifuge Tubes) and sterile sample collection bags from three sites of the Dal Lake. Samples were collected in triplicates from each site and pooled to make one composite sample for each site. The samples were stored in an icebox, transported to the laboratory, and processed immediately for DNA extraction.

2.2. DNA extraction for lake water and sediments, and plant parts

Total DNA was extracted from water and sediment samples using MoBio DNA Extraction Kit (MoBio Laboratories, Inc., USA). Before DNA extraction from sediments, the samples were homogenized under aseptic conditions, and 120 mg samples were transferred into the MoBio bead tubes and used for total DNA extraction. For water DNA extraction, 250 mL water was filtered through a 33 mm diameter sterile hydrophilic Polyethersulfone (PES) membrane filter with a 0.22 µm pore size (Merck, Millipore™, USA) using Merck laboratory filtration systems (Lab System 2). Subsequently, the filter was cut into small parts using sterile scalpel blade no. 4 (Himedia laboratories, India). Using sterile stainless steel pointed size forceps (Himedia laboratories, India), the filter parts were transferred into the MoBio bead tube and used for subsequent DNA extraction following the manufacturer’s instruction. For the plant samples, root and rhizome in 50 ml centrifuge tube, while fruit, flower and leaf in 500 ml sterile γ-irradiated Himedia disposable sterile bottles were submerged in the adequate phosphate buffer saline (PBS). The tubes were subjected to sonication for 60 seconds. The sonication process was repeated three times to get maximum microbial cells present on the plant parts into the PBS. The microbial cells containing PBS was filtered and processed as described for the Lake water samples. The yield and quality of the community DNA samples were checked on 0.8% agarose gel, and DNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Willingminton, USA). All the extracted DNA samples were stored at -20°C until further processing.

2.3. Preparation of 16S rRNA gene amplicon libraries and sequencing

The prokaryotic communities were analyzed using 16S rRNA amplicon sequencing via the Illumina-Miseq platform. PCR amplification was performed using the primer set 515F (5’ CCTACGGGNGGCWGCAG 3’) and 806R (5’ GACTACHVGGGTATCTAATCC 3’) that selectively amplified the V4 region of the 16S rRNA gene. Template and library preparation was carried out according to the manufacturer’s protocol (Illumina, USA). The sequencing of multiplexed 16S rDNA amplicon libraries was performed on the Illumina Miseq platform using paired-end 2 x 250 bp chemistry. Multiplexing of the equimolar concentration of DNA was carried out to generate at least 0.1 million (1 lakh) reads for each sample.

2.4. Bioinformatics and statistical analysis

Assembly of forward and reverse reads for each sample was carried out using FLASH (Magoč and Salzberg 2011). Microbial diversity analysis was done using a standard QIIME (v1.8.0) pipeline (Caporaso et al. 2010) on the high-quality sequences. A closed reference-based OTU picking approach was used to cluster reads into Operational Taxonomic Units (OTUs) at 97% sequence similarity using UCLUST (Edgar 2010) algorithm and SILVA database for the further downstream analysis. Representative sequences (repset) from each OTU were selected for taxonomic assignment. Beta diversity (PCoA) was carried out using the scientific data analysis tool PAST3 (Hammer 2001). Detection of the differentially abundant Phyla and genera across the samples was done using analysis of variance (ANOVA) in GraphPad Prism ver. 9.0.

The functional potentials of the prokaryotic communities were predicted using an R package i.e., Tax4Fun (Aßhauer et al. 2015). It uses taxonomic information based on the 16S rRNA gene sequence and KEGG database to predict functional potentials of the prokaryotic communities. Analysis of differential abundance of functional potentials across different sample groups (including plant parts, lake water, and lake sediment sample) was done based on ANOVA. The genera and predicted genes with a significant difference in their relative abundance (p < 0.05), were plotted in a heatmap matrix in an R package pheatmap (version 1.0.12). Venn diagrams were constructed using an online tool developed by Van de Peer Lab (https://www.vandepeerlab.org/?q=tools/venn-diagrams).

3.1. Sequencing results and diversity analyses

Overall, a total of 16,51,507 sequences were generated in the study. Quality filtered sequences (n = 12,93,594) were assigned to 6,876 OTUs, belonging to 58 phyla. Values for goods coverage were more than 0.97% for all the samples. A significant decline in all alpha-diversity indices except Simpson was noted for lotus plants in comparison to the water and sediments of the Dal Lake (Fig. 1). No such differences were observed in alpha-diversity indices except observed ASVs among the microhabitats of the lotus plant (Fig. S1). Beta diversity analysis using Bray NMDS plot showed unique clustering of the Dal Lake water and sediments and lotus microhabitats (Fig. 2). The above water lotus parts including leaf, flower and fruit along with rhizomes are placed on the positive side of axis 1, while lotus roots are placed on the negative side of axis 1 with sediments and water of the Dal Lake.

3.2. Prokaryotic community structure and differential abundance analysis

Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia, Acidobacteria, Cyanobacteria, Chloroflexi, Nitrospirae, Thaumarchaeota and Planctomycetes represented more than 95% of the prokaryotic communities across the sample groups (Fig. 3 and Table S1). Proteobacteria was the most dominant phylum across all the samples except lotus leaves and represent more than 90% of the total prokaryotes in the fruit and flower samples. Members of the phylum Firmicutes dominated the prokaryotic communities on the leaves, and represent more than 10% of the total prokaryotes in the roots and rhizomes of lotus and sediments of the Dal Lake. Likewise, Actinobacteria makes approximately 20% of the prokaryotic communities in the waters and ≈ 8% in the sediments of the Dal Lake, while less than 0.5% in lotus plants. Additionally, more than 15% proportion of the prokaryotic communities in the water and sediments of the Dal Lake consists of Bacteroidetes. The proportion of Lokiarchaeota, Deferribacteres, Hadesarchaea, Cyanobacteria and Bathyarchaeota was less than 1.0% for all the samples and sediments harboured the highest abundance of these phyla.

Genera level community analysis revealed a high abundance of Pseudomonas, Acinetobacter, Clostridium, Pantoea, Pectobacterium, Flavobacterium, Sphingomonas, Weissella, Rhizobium, Serratia, Polynucleobacter, Bacillus, Alpinimonas, Enterobacter, Pelosinus, Leuconostoc, Polaromonas and Dickeya across the samples (Fig. 4; Table S2). A significant difference was recorded in the abundance of 71 prokaryotic genera (ANOVA, p < 0.05). The relative abundance of Pseudomonas was consistently higher in lotus microhabitats, whereas water and sediments of the Dal Lake have increased Flavobacterium. Similarly, a high relative abundance of Clostridium was recorded in leaves, rhizomes and roots of lotus and sediments. A high relative abundance of Bacillus, Massilia, Geobacter and Arthrobacter was noted in the sediments of Dal Lake, in comparison to water and all microhabitats of lotus. The Dal Lake water exhibited a higher abundance of Polynucleobacter, Alpinimonas, Pseudarcicella, Luteolibacter and Opitutus. On the other hand, Pantoea, Pectobacterium, Serratia, Rhizobium, Sphingomonas, Weissella, Escherichia-Shigella, Enterobacter, Chryseobacterium, Xanthomonas, Leuconostoc, Lactococcus and Dickeya were present in higher proportions on one or more microhabitats of the lotus (Fig. 5). These genera were either absent or present in low proportions in the Dal Lake sediments and water.

3.3. Shared and unique microbial taxa

Overall, 98 genera were present across the lotus plant and, sediment and water of the Dal Lake (Fig. 6; Table S3). These core members of the communities consist of genera like Acinetobacter, Flavobacterium, Bacillus, Pseudomonas, Clostridium, Rhizobium, Sphingomonas, Polaromonas, Enterobacter, Pelosinus, Caulobacter, Brevundimonas, Novosphingobium, Hyphomicrobium, Weissella, Cryobacterium, Ruminococcaceae, Stenotrophomonas, Serratia, Hymenobacter, Dialister, Aeromonas, Pantoea, Escherichia-Shigella, Pectobacterium, Methylobacterium, Paracoccus, Psychrobacter, Klebsiella, Aquabacterium, Thauera and Cronobacter. Additionally, lotus and lake water exclusively shared 56 genera, while lake water and sediments shared 49 genera and lotus and lake sediments shared 38 genera. Sediments of the Dal Lake, exhibited 154 unique genera, comprising several uncultured bacteria and archaea, and genera such as Nitrosospira, Bryobacter, Arcticibacter, Gracilibacter, Oxobacter, Syntrophomonas, Anaerobacillus, Methanocella, Isosphaera, Lacibacter, Anaerovorax, Schlesneria, Singulisphaera, Steroidobacter, Symbiobacterium, Flavitalea and Methanosaeta. On the other hand, the Dal Lake water has 86 genera unique to sediments and lotus plants, while the lotus plant has only 34 unique genera. Among the microhabitats of the lotus plant, 18 genera including Pseudomonas, Acinetobacter, Clostridium, Sphingomonas, Methylobacterium, Rhizobium, and many members of Enterobacteriaceae such as Klebsiella, Escherichia-Shigella and Pantoea were found in all microhabitats making them the core of the lotus microbiome. Additionally, 48, 28, 20, 13 and 11 genera were exclusively present in the leaf, root, rhizome, flower and fruit, respectively.

3.4. Imputation of metabolic potentials of the prokaryotic communities

Predictive functional potential analysis showed that the abundance of different functional traits was significantly different among the lotus, and sediments and water of the Dal Lake (Fig. S2; Table S4). The communities of lotus plant microhabitats had functional features unique to the sediment and water of the Dal Lake and are clustered together in the heat map (Fig. S2). The relative abundance of several genes such as glutamine synthetase [EC:6.3.1.2] and glutamate synthase [EC:1.4.1.13], cobalt/nickel transport system permease protein, indolepyruvate ferredoxin oxidoreductase [EC:1.2.7.8], ferrous iron transport protein B and carbamoyl-phosphate synthase [EC:6.3.5.5] was significantly high in the lotus plant microhabitats. On the other hand, a significant increase was observed in the relative abundance of genes encoding isoleucyl-tRNA synthetase [EC:6.1.1.5], penicillin-binding protein 1A [EC:2.4.1.− 3.4.−.−], phosphoribosylformylglycinamidine synthase [EC:6.3.5.3], heterodisulfide reductase subunit A [EC:1.8.98.1] and DNA polymerase III subunit alpha [EC:2.7.7.7] in the Dal Lake water.

4.1. Diversity analysis of prokaryotic communities

Dal Lake is an urban valley lake in Srinagar, India, known for its beauty and cultivation of the Indian lotus (Shah et al. 2014). The present study deciphered the prokaryotic community structure associated with the lake samples and the root, rhizome, leaf, flower, and fruits of lotus cultivated in the Dal Lake. The diversity and species richness were significantly high in the lake water and sediments, and a significant decrease was observed in the plant surfaces. This observation was in corroboration to previous reports highlighting a significant decrease in bacterial diversity and richness from the soil to the roots and other parts of the plant (Yamamoto et al. 2018).

Selection of specific microbial communities in different micro-habitats of lotus plants was evident from the beta diversity plots. Several factors including, ecological drivers like dispersal, diversification, ecological drift, and selection could be responsible for this specific community assemblage on plant surfaces (Sivakumar et al. 2020). Complex interactions between microbe-environment, microbe-microbe, and microbe-plants play an important role in shaping specific prokaryotic communities and making them niche-specific (Rodriguez et al. 2019). Such specific compartmentation of microbial communities was also observed for A. wallichii (Chen et al. 2021).

4.2. Relative abundance of prokaryotic communities in the microhabitats of lotus, and water and sediments of the Dal Lake

The majority of members of microbial communities in the host plant are horizontally acquired from the surrounding environments, and lake prokaryotic communities are the primary reservoir for the communities associated with plants growing in the aquatic ecosystems (Mitter et al. 2017). The members of phylum Proteobacteria perform diverse metabolic functions (Moon et al. 2018), thus the relative abundance of Proteobacteria was consistently higher across all samples including lotus parts and the Dal Lake water and sediments. However, the proportion of Proteobacteria was relatively higher in the lotus plant, which could be attributed to the fact that a large majority of Proteobacteria possess multiple plant growth-promoting activities (Compant et al. 2019; Ren et al. 2019; Chaudhari et al. 2020a; Rahi et al. 2020). On the contrary, a higher abundance of Lokiarchaeota, Deferribacteres, Hadesarchaea, Cyanobacteria and Bathyarchaeota in the lake sediments, indicates their possible role in nutrient cycling in the Dal Lake as reported for the anoxic sediments of other urban water bodies including Aohai Lake and Kunming Lake in Beijing (Wang and Wang 2020).

The differences in the relative abundance were more pronounced at the genera level. Flavobacterium is one of the most abundant bacterial genera in freshwater lakes (Eiler and Bertilsson 2007; Michaud et al. 2012), and a similarly high proportion of Flavobacterium in prokaryotic communities was observed in sediment and water samples of the Dal Lake. On the other hand, the microhabitats of the lotus plant were inhabited by the members of genera, which are known for their beneficial plant growth-promoting activities like Pseudomonas (Vyas et al. 2009; Chen et al. 2021).

A large majority of the studies on plant-associated microbial communities remained restricted to the plant rhizosphere, as it is considered the most active site for plant-microbe interactions (Yurgel et al. 2018; Chen et al. 2019). In the present study, we found that a deeper investigation of the microbial community structure of different plant parts exhibited a differential abundance of prokaryotic taxa across the plant tissue. Lotus flower harboured a higher abundance of bacterial genera, such as Erwinia, Sphingomonas, Dickeya, Escherichia-Shigella, Pantoea, Serratia, Raoultella and Tolumonasi, which was unique to its other microhabitats. Several factors including the frequent visit by the insects and the presence of sugar-rich nectar in the flower could provide an explanation to the development of the flower microbiome, which is unique to that of fruit and leaves (Massoni et al. 2020). Likewise, a higher abundance of Pseudoclavibacter was recorded in lotus fruit, this observation was in corroboration to the previous reports on the high abundance of members of Pseudoclavibacter in the unwashed citrus fruits (Gomba et al. 2017). Further, the lotus leaves and rhizomes exhibited a high abundance of lactic acid bacteria (LAB) like, Weissella and Leuconostoc. These results are in agreement with earlier reports on the higher proportions of LAB in the leaves of various plants like Matricaria chamomilla and Calendula officinalis (Köberl et al. 2019). Additionally, a higher abundance of Clostridium, Deinococcus and Exiguobacterium was recorded in the leaves, members of these genera are tolerant to a wide range of biotic stress like desiccation and radiations and are reported as phyllosphere colonizers (Wang et al. 2019). The higher abundance of genera like Polaromonas, Lactococcus, Paenibacillus, Chryseobacterium, Pelosinus and Sphingobacterium in roots indicated their possible role in plant growth-promoting activities and their preference to utilize organic exudates released by the lotus through its roots. Rhizosphere exudates like organic acids are involved in the bio-stimulation and induction of specific bacterial groups (Macias-Benitez et al., 2020).

Significant differences recorded in the prokaryotic community structure of water and sediments of the Dal Lake suggested that the lake water is not a mere suspension of sediments as reported previously for the high-altitude Pangong Lake (Chaudhari et al. 2020b). The higher abundance of prokaryotic genera including Geobacter, Thiobacillus, Desulfitobacterium¸ Desulfatiglans, Thermoanaerobaculum, Thermincola, Ferruginibacter, Lutispora and Candidatus Nitrosotalea, which have been known for various biogeochemical processes, was noted in sediments of the Dal Lake. Microbial communities are involved in the decomposition of organic and inorganic matter, and play a key role in determining the structure and functions of aquatic ecosystems (Wang et al. 2022).

4.3. Differentially abundant potential function of prokaryotic communities

A trend similar to the community structure was observed for the predicted functional profiles of communities, indicating a clear distinction among the lotus microhabitats and lake sediment and water. The genes encoding function such as nutrient and mineral acquisition were more abundant for the communities on the lotus microhabitats. The role of microorganisms in maintaining the flow of nutrients to the host plant is crucial for overall plant growth and productivity, as the direct uptake of nutrients by plants via roots can lead to a nutrient depletion zone (Sun et al. 2021).

In contrast, a higher abundance of acetyl-CoA C-acetyltransferase was recorded in lake sediments, which plays an important role in various biosynthesis and degradation pathways (Goudarzi, 2019). Dal Lake water samples showed a higher abundance of several genes encoding key functions that are necessary for cellular processes. Though the function assignments of prokaryotic communities are based on prediction, it still offers a fast and reliable alternative to understanding the potential functions of communities. The relevance of such predictions has been found promising in providing information on ecosystem functioning (Djemiel et al. 2022).

In conclusion, the study reveals that parts of the lotus plant have specific prokaryotic communities and site-specific functions. Furthermore, differences were observed in the community structure of sediment and water samples, with enrichment of genera with the potential to degrade organic and inorganic compounds in sediments of the Dal Lake. Despite the variations, a few prokaryotic genera were found constantly on all microhabitats of the lotus plant, lake water, and sediment samples, forming the core microbiome. Pseudomonas was explicitly enriched in all plant parts, except the flowers, which have a higher abundance of Sphigomonas. These two genera appear to be promising candidates for developing microbial bio-inoculants to promote the growth and health of lotus.

PCoA, Principal Co-ordinate Analysis; NMDS, Non-metric Multidimensional Scaling; OTUs, Operational taxonomic unit; ANOVA, Analysis of variance.

Acknowledgements

This work was supported by funding from the Department of Biotechnology (BT/Coord. II/01/03/2016), Government of India. The authors acknowledge the Director, NCCS, Pune. B.A.M. also acknowledge the funding under Energy Bioscience Overseas Fellowship.

Data availability

The sequence data is available at NCBI SRA submission with SRA no. SRP335402.

Declaration

All authors have read the manuscript and declare no conflict of interest.

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FigS1alpha.pdf
Fig. S1: Box plot representing alpha diversity indices a) observed OTUs b) Shannon c) Simpson, and d) Chao1 across the microhabitats of lotus. The numbers indicate (p-values) calculated using ANOVA and FDR corrections.
FigS2.pdf
Fig. S2: Heat-map representing the differentially abundant predicted genes across the lake water, sediment and microhabitats of lotus.
TableS1.docx
Table S1: Phylum-level mean proportion of prokaryotic communities in the microhabitats of lotus plant and sediments and water of the Dal Lake
TableS2.xlsx
Table S2: Genus-level differentially abundant prokaryotic communities from the microhabitats of lotus and sediment and water of the Dal Lake.
TableS3.xlsx
Table S3: Unique and shared genera, list 1 lotus plant and sediment and water of the Dal Lake; list 2 different microhabitats of lotus plant.
TableS4.xlsx
Table S4: Differentially abundance of predicted genes encoding function of prokaryotic communities from the microhabitats of lotus and sediment and water of the Dal Lake.

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Prokaryotic communities adapted to microhabitats on the Indian lotus (Nelumbo nucifera) growing in the high-altitude urban Dal Lake.

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Version 1

Abstract

Figures

1. Introduction

2. Materials And Methods

2.1. Sample collection

2.2. DNA extraction for lake water and sediments, and plant parts

2.3. Preparation of 16S rRNA gene amplicon libraries and sequencing

2.4. Bioinformatics and statistical analysis

3. Results

3.1. Sequencing results and diversity analyses

3.2. Prokaryotic community structure and differential abundance analysis

3.3. Shared and unique microbial taxa

3.4. Imputation of metabolic potentials of the prokaryotic communities

4. Discussion

4.1. Diversity analysis of prokaryotic communities

4.2. Relative abundance of prokaryotic communities in the microhabitats of lotus, and water and sediments of the Dal Lake

4.3. Differentially abundant potential function of prokaryotic communities

5. Conclusions

Abbreviations

Declarations

References

Supplementary Files

Status:

Version 1