Abu Bakar Siddique, PhD

Summary

Abu Bakar Siddique is a bioinformatician and researcher with expertise in meta-genomics, metabarcoding, RNAseq, bioinformatics, environmental microbial ecology, plant-microbe/insect interaction, endophytic fungal community diversity, function, and evolution, plant pathology, mycovirus and fungal genomics, and plant ecology and evolution. He was born in Bangladesh in 1985 and obtained a PhD in molecular mycology and ecology from the University of Greifswald in Germany. He has worked as a postdoctoral researcher in fungal virology at the Czech Academy of Science and at Umeå University in Sweden. Currently, he works at the Swedish Agricultural University as a bioinformatician. He has conducted multiple research projects, including TanAsp (mycobiome and metabolites in European Aspen), Sweden Biodiversity in Time and Space (SweBITS) through meta-genomics, mycoviruses, leaf-inhabiting endophytes of European beech trees, and plant-fungi-insect interaction in Swedish Aspen.

Research interests

Meta-genomics, Bioinformatics, Environmental microbial ecology; Plant-myco-/microbiome-insect interaction; Endophytic fungal community, diversity, function, and evolution; Bioinformatics; Plant pathology; Mycovirus and fungal genomics; Plant ecology and evolution.

Bioinformatic Projects

Viruses: BMYV, BYV of Sugarbeet
Metagenomics: leaf litter,
metatranscriptomics: bioreactor
transcriptomics: Potato rnaseq, commercial potato, red-clover rnaseq, beet, mustard
ampliseq: European beech, aspen, 18s, soil, 16s, 28s, AMF

Research Project

TanAsp (mycobiome and metabolites in European Aspen)
Sweden Biodiversity in time and space (SweBITS) through meta genomics
Mycoviruses (finished)
Leaf inhabiting endophytes of European beech trees (completed)
Plant fungi insect interaction of Swedish Aspen (completed)
Bio-control of leaf-blight of masterd (completed)

Short Bio

My name is Abu Bakar Siddique, but you can call me Biplob. I wear many hats: I'm a father, a husband, a mentor, a dedicated researcher, a bioinformatician, a molecular ecologist, a plant pathologist, and a fungal virologist.

My journey began in Begumganj, Noakhali, Bangladesh, where I was born on October 19th, 1985. My parents, Abdur Rab Chowdhury and Nurjahan Begum, nurtured me alongside my younger brother, Tanvir Ahmed Siddique, and my older sister, Shiuly Begum.

My educational path started in 1991 at Boromehedipur Primary School, and soon after, I transferred to Chhayani Primary School in 1993. I completed my SSC at Chhayani High School in 2001 and my HSC at Noakhali Government College in 2003. My academic journey took me to Sher-e-Bangla Agricultural University in Dhaka, where I earned my Bachelor's degree in Agriculture in 2008 and my first Master's degree in Plant Pathology.

In 2010, I embarked on an international adventure for higher education. I graduated with a second Master's degree in Ecology from the University of Umeå in Sweden in 2013. My thirst for knowledge led me to Germany, where I earned a PhD in Molecular Mycology and Ecology from the University of Greifswald in 2017. My postdoctoral research took me to the Czech Academy of Sciences, where I delved into fungal virology, and later to Umeå University in Sweden for further postdoctoral studies.

My research passion lies in the fascinating world of fungi. Since 2009, I've been exploring plant-inhabiting fungi, studying their identity, biodiversity, genetics, pathology, ecology, and their intricate relationships with plants and the environment. My Master's thesis focused on disease control using endophytic fungi as biocontrol agents. This journey led me to Sweden, where I studied the leaf-inhabiting endophytic fungi of Swedish aspen trees. These microscopic communities within the leaves reveal much about the health of trees and their surrounding ecosystems.

In Germany, I delved deeper into the mycobiome and bioinformatics, uncovering the relationship between endophytes and the genetic identities of trees. These fungi are shaped by their local environments and have significant connections with micro-climate, leaf age, biochemistry, and seasons.

My postdoctoral research in the Czech Republic focused on fungal viruses, or mycoviruses. These viruses infect fungi, and their impact can range from harmful to beneficial. My work aimed to understand how mycoviruses affect fungal growth and their potential benefits to plants by reducing fungal disease infections.

In 2020, I returned to Sweden to focus on bioinformatics and metagenomic data analysis from 40 years of air filters, tracking fungal species diversity, trends, phenology, and biosurveillance. In 2022, I began my career as a bioinformatician at the Swedish Agricultural University (SLU), providing bioinformatic services, support, and training to SLU staff.

Research life

In 2009, I embarked on my research journey by joining Dr. Abu Bakr's lab at the Bangladesh Agricultural Research Institute (BARI) in the Plant Pathology Division. As a master's thesis student, I delved into the efficacy of potential biocontrol agents against crop diseases. My thesis focused on testing Trichoderma and botanical leaf extracts against the severe leaf-blight disease of mustard in field conditions. The goal was to control the disease using selected strains of Trichoderma Herzlianum and plant extracts.

During my second master's, I expanded my interests in plant pathology and ecology, focusing on plant-fungi-insect interactions. In 2012, I joined Dr. Benedicte R. Arbrectsen’s lab at Umeå University in Sweden. My research explored the ecological connection between foliar endophytes and European aspen (Populus tremula) in the presence and absence of specialist beetles (Chrysomela tremula). We confirmed the genetic match between endophyte composition and the host chemotype, discovering a negative relationship between the stress compound (salicinoid) and endophyte richness. Beetle activity introduced generalist morphs to the mycobiome, overriding the initial host association.

In 2013, I joined M. Unterseher’s lab as a PhD student at Greifswald University in Germany. Utilizing direct sequencing (Illumina MiSeq), I tackled biological questions that had been elusive a decade ago. My Ph.D. research revealed a strong seasonal turnover in phyllosphere fungi across attitudinally distinct habitats over two years, suggesting that the plant-fungal system responds not only to cyclic climatic conditions but also to various parameters such as geographic position, substrate age, and surrounding vegetation.

In 2018, I joined the Biology Centre in the Czech Republic as a postdoc, studying the occurrence of viruses in mixed infections of fungi using real-time PCR, cloning techniques, transformation, and microscopy.

In 2020, I returned to my previous department, Ecology & Environmental Science at Umeå University in Sweden. My work focused on bioinformatics, analyzing the biodiversity of organisms' DNA trapped in air filters over a 40-year time series. I sought to answer the question of which pathogens were rising in Sweden.