Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere

Abstract

The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice.

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome

“…Their population was much influenced by the cultivation methods particularly under the SRI method, and our earlier reports demonstrated their beneficial effects on soil and plant attributes . In another study, Venkatachalam et al observed that the diversity of cyanobacteria on the surface of rice leaves was modified by the fertilizer application and two different modes of experimentation (pot vs. field experiments). Bodenhausen et al observed that leaf and endophytic root compartments do not differ significantly in their diversity, richness, and evenness; however, the community composition is different.…”

“…This is supported by the insignificant differences observed in the nitrogen content of leaves across treatments. Our previous study illustrated the nitrogen-fixing potential of rice phyllosphere isolates, particularly among the cyanobacterial members, after their enrichment under aerobic and anaerobic conditions [5]. Knief et al [7] detected the presence of genes encoding dinitrogenase and dinitrogenase reductase in the phyllosphere and also reported the presence of nitrogen fixing bacteria in the rice phyllosphere, although they were fewer, as compared to the rhizosphere.…”

“…protozoa, and nematodes [3,4]. In our earlier study on the phyllosphere microbiome, even the members of the phylum Cyanobacteria were observed, with greater diversity and species richness in the pot grown than in the field grown rice plants [5]. Most studies on the taxonomic annotation of microorganisms in the rice phyllosphere reported an enormous diversity of bacteria compared to fungi [6].…”

Understanding and exploiting plant beneficial microbes

“…The definition of large scale, in fact, has changed rapidly from hundreds [16] to tens of thousands [20] of strains. Recent plant-associated bacterial and fungal isolate collections (summarized in Table 1) are derived from sugarcane [20]; grapevine [21–23]; potato [24]; tomato [25]; eucalyptus [25]; rice [26,27]; ancient wheat ancestors [19]; lettuce [28]; Arabidopsis [16, 29]; poplar [29]; and from plants growing in an arsenic-contaminated soils [30]. The increasing volume of isolate collections will tax existing repositories; yet the genomic diversity contained in the bacterial isolates that are being obtained is not nearing saturation [16].…”

Estimating genetic structure and diversity of cyanobacterial communities in Atlantic forest phyllosphere

“…Even though several studies have characterized the bacterial community in phyllosphere of plants of tropical forests, reports on cyanobacteria community composition in the phyllosphere are scarce (Fürnkranz et al 2008, Rigonato et al 2012, Alvarenga et al, 2016, Venkatachalam et al, 2016. Herein, the community structure of cyanobacteria inhabiting phyllosphere of four plant species from the Brazilian Atlantic Forest biome was accessed using cultivationindependent molecular approaches.…”