Biology subjects

Pushpakumara, B. L. D. U.

Publications and source records attributed to Pushpakumara, B. L. D. U..

3 recordsLinked to original sources

bioRxiv2023

Molecular Characterization of Fischerella uthpalarensis, the first subsection V cyanobiont from a tropical Azolla species containing dual nitrogenases

There have been theories presented on Azolla cyanobionts, known for voracious nitrogen fixation, vertical transmission of cyanobiont and helping transform a greenhouse planet to an icehouse one ~49 Mya. One such theory encapsulates the existence of two cyanobionts, named Major and Minor. We show here the identity of a possible minor cyanobiont of Azolla named Fischerella uthpalarensis. A likely cyanobiont with straight or curved filaments that were truly branched was isolated. Seven gene fragments, namely 16s rDNA (Forward and Reverse), RNA Polymerase, ITS1 region (Forward and Reverse), nifD and GroEL genes were utilized to identify the isolated cyanobiont. The best match based on BLASTn search tool was found in the RNA Polymerase beta subunit (rpoC) gene fragment, that showed 99.54% identity with 55% coverage to Fischerella muscicola. Phylogenetic inferences with the rpoC genetic locus and the GroEL protein sequence suggest a likely Fischerella genus identity. Furthermore, VnfDG and VnfN fragments too were amplified using PCR and sequenced to demonstrate that this cyanobiont has alternate nitrogenase genes, on top of the molybdenum counterpart, providing an advantage in lifestyle. We encountered a higher level of genomic-level synonymous substitutions, which was not reflected in protein sequences, namely VnfDG and VnfN gene products, which may be due to codon heterogeneity. We also propose for F. uthpalarensis atypicality in codon usage due to the likely acquisition of the V-nitrogenase operon from a presumed recent horizontal gene transfer (HGT) event. The cyanobiont from this study showcases a higher preference for AT over GC at the VnfDG composite locus again hinting at a symbiotic lifestyle.

microbiology↗

bioRxiv2022

The bacterial microbiome of the coral skeleton algal symbiont Ostreobium shows preferential associations and signatures of phylosymbiosis

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria (2) enriched tightly attached and potential intracellular bacteria and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include taxa known as nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.

microbiology↗

bioRxiv2022

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S co-occurrence networks

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

ecology↗