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).