Microbial Ecology Group

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A Leading Scientist in TerrArctic Research Project!

by Orhan İnce | Jun 29, 2024

Exciting news from the world of scientific research! A distinguished Turkish scientist, Prof. Dr. Orhan Ince has been selected to participate in the TerrArctic Research Project, supported by a significant grant from the government of the Tyumen Region!

The TerrArctic research project is focused on achieving sustainable land use in the Arctic amidst global natural changes, emphasizing the stability of both natural and anthropogenic factors. The project is set to be carried out at Tyumen State University (UTMN) from 2020 to 2024, funded by a mega-grant from the Tyumen Regional Government. It will take place under the auspices of the West Siberian Interregional REC of the Tyumen Region, encompassing the Khanty-Mansiysk Autonomous Okrug-Yugra and the Yamal-Nenets Autonomous Okrug.

The project will proceed under the supervision of eminent scientist Yakov Kuzyakov from the University of Göttingen, Germany, at the Research Institute of Ecology and Rational Use of Natural Resources. The Laboratory of Soil Science and Isotope Biogeochemistry has acquired scientific equipment for environmental biogeochemistry research and has conducted specialist training.

The TerrArctic project will see a significant advancement in 2024 with Professor Orhan Ince joining as the lead scientist. As the Head of the Microbial Ecology Research Group and Director of the EnviroBioTech+ Program at Istanbul University of Technology, Professor Ince brings a wealth of experience in applying engineering solutions with new technologies to enhance environmental quality, commercialize scientific findings in environmental regulation, and rehabilitate disrupted ecosystems and water bodies. Recently, he has been recognized as one of the top 1% of leading scientists globally in the Stanford ranking.

During the visit, a meeting took place with UTMN colleagues. Andrey Tolstikov, the First Vice-Rector; Andrey Soromotin, Director of the Research Institute of Ecology and Rational Use of Natural Resources at UTMN; and Roman Latyntsev, Coordinator of International Scientific Programs at the Institute of Ecological and Agricultural Biology (X-BIO) of UTMN, were present. Professor Ince spent two weeks familiarizing himself with UTMN's potential research laboratories, aiming not only to advance the TerrArctic project but also to initiate several new joint ventures with ITU, the world's third oldest engineering university established in 1773.

The collaboration with ITU was initiated following a delegation visit to Turkey, led by UTMN Rector Ivan Romanchuk in October 2021. At the meeting with Ismail Koyuncu, rector of the partner university, they discussed plans for executing scientific and technological projects. They also considered joint research initiatives for various regions, including the Arctic. Consequently, Professor Ince was appointed as the coordinator of the agreement, facilitating cooperation between the two universities and exploring opportunities for collaborative projects.

Ivan Romanchuk, the Rector of UTMN, states: "The latest phase of collaboration with the premier technical university of the Republic of Turkey will enable UTMN to engage deeply with research groups. This collaboration is expected to generate a synergistic effect in the quest for the most efficient solutions in the field of engineering ecology. The West Siberian Scientific and Educational Center has been recognized for operating at a high international standard, and the growth of global partnerships through REC mega-grants further confirms this."

The TerrArctic project is anticipated to yield analyses of the main soil types in the subarctic and Arctic zones of Western Siberia for their carbon sequestration potential, as well as assessments of pyrogenic carbon intake by these soils following landscape fires. Additionally, it will propose technologies for the biological reclamation of degraded Arctic lands.

For more information, please refer to the following source,
Leading Scientist from Turkey to Participate in TerrArctic Regional Mega-Grant

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By ABD, 29 Jun, 2024

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ITU-BOUN MEG | Microbial Ecology Group

At the ITU-BOUN Microbial Ecology Group (MEG), we investigate the intricate roles of microorganisms in both engineered systems and natural environments through a multidisciplinary lens. With our experienced team and robust infrastructure, we conduct high-impact research that integrates microbial ecology, environmental biotechnology, molecular biology, and systems-based approaches to address complex ecological and environmental challenges.

What We Do

We conduct both fundamental and applied research to elucidate microbial interactions and functions across a broad spectrum of ecosystems—from engineered environments such as water and wastewater treatment and agro waste/solid waste/manure and sludge management, to natural and extreme habitats including air, water, sediments, hydrothermal systems, and polar permafrost zones.

Our Core Areas of Expertise Include:

Biotreatment and Bioremediation: Development of innovative microbial-based technologies for the treatment of solid, liquid, and gaseous wastes, and the remediation of hydrocarbon- and heavy metal-contaminated ecosystems.
Biomonitoring and Environmental Diagnostics: Application of high-resolution molecular tools (e.g., qPCR, metagenomics, amplicon sequencing, transcriptomics) for real-time monitoring and functional characterization of microbial communities in both environmental and engineered systems.
Bioenergy: Exploration and optimization of anaerobic digestion, biohydrogen, and biogas production processes through microbial process engineering and omics-based process enhancement.
Microbial Resource Exploration: Isolation, identification, and functional profiling of novel microbial taxa—including thermophiles, psychrophiles, halophiles, and extremophiles—from unique and polyextreme environments for biotechnological applications.

Field-Based Investigations

Our laboratory capabilities are complemented by comprehensive field research programs. Some of our recent and ongoing projects include:

Arctic Ecosystems: Investigations in Russia’s Arctic territories—particularly around the Tazovsky region—focused on the impacts of permafrost thaw, climate change, and land use shifts on microbial community dynamics, biogeochemical cycles, and greenhouse gas emissions.
Salda Lake (Türkiye): As one of the closest terrestrial analogs to Mars' Jezero Crater, Lake Salda offers a unique setting to study microbial life in high-alkaline, magnesium-rich, and ultra-oligotrophic conditions. We explore microbial adaptations, biomineralization processes, and potential biotechnological applications under these extreme conditions.
Marine Microbial Ecology: Biodiversity and function-based assessments in the Black Sea, Mediterranean, Aegean, and Marmara Seas, including anoxic sediments and petroleum-contaminated marine environments.
Urban Aquatic Systems (e.g., Golden Horn): Longitudinal studies on microbial community shifts in response to anthropogenic impacts, environmental restoration, and urban hydrological changes.
Extreme and Polyextreme Environments: Microbial surveys and metagenomic investigations in geothermal fields, deep-sea basins, cold-adapted high-altitude lakes, and other sites with combinations of physicochemical stressors.

Innovation through Molecular and Biotechnological Tools

Our group has developed several patented biotechnological methods and custom-engineered diagnostic platforms that enable:

Tailor-made environmental solutions for complex pollution problems,
Microbial community engineering for waste valorization and resource recovery,
Design of synthetic microbial consortia for climate-resilient bioprocesses.

We are also pioneers in applying integrated omics, synthetic biology, and AI-based modeling for the dynamic control and optimization of microbial systems. Our unique methodologies are applied across diverse sectors—from sanitation to environmental restoration and carbon sequestration.

Global Collaborations and Impact

Our group actively contributes to global-scale research consortia and mega projects, including the TerrArctic Project, where we provide microbial and environmental data to support climate adaptation strategies in Arctic and sub-Arctic regions.

Through our multidisciplinary research, engineering innovations, and field-based insights, we aim to bridge science and practice—delivering sustainable solutions for today’s most pressing environmental challenges.

Cutting-Edge Molecular Techniques and Technologies at MEG Laboratories

At MEG, we utilize a wide array of state-of-the-art molecular biology tools and technologies to investigate microbial communities, host-microbe interactions, and environmental microbiomes. Our infrastructure supports both fundamental research and applied biotechnology development. Below is an overview of the core techniques currently in use at our laboratories:

Next-Generation Sequencing (NGS) Platforms

We employ a broad range of high-throughput sequencing methods to explore genetic, transcriptomic, and epigenetic landscapes.

Whole Genome Sequencing (WGS):
Comprehensive analysis enabling the detection of single nucleotide polymorphisms (SNPs), structural variations (insertions, deletions, inversions), copy number variations (CNVs), and rare mutations in microbial and host genomes.
Metagenomic Sequencing (Shotgun & Amplicon-Based):
Culture-independent analysis of microbial diversity and function from environmental samples (e.g., soil, water, sludge). Both shotgun metagenomics and targeted amplicon sequencing (e.g., 16S/18S rRNA, ITS) are used.
Total RNA Sequencing (RNA-Seq):
Analysis of transcriptomes to quantify gene expression, alternative splicing events, and non-coding RNA activity in microbial communities and host systems.
ChIP-Seq (Chromatin Immunoprecipitation Sequencing):
Used in epigenomic studies to detect protein-DNA interactions, transcription factor binding sites, and histone modifications.
Targeted DNA Sequencing:
Enables deep sequencing of specific genomic regions of interest (e.g., microbial virulence genes, ARGs, or cancer-associated genes) for high-sensitivity variant detection.
Methyl-Seq & ATAC-Seq:
Applied for DNA methylation profiling and chromatin accessibility studies in host-microbe interaction models.

Third-Generation & Portable Sequencing Technologies

Nanopore Sequencing (Oxford Nanopore – MinION & MinIT):
Real-time, long-read sequencing technology for field and lab-based applications including:

De novo genome assembly
Rapid diagnostics
Plasmid tracking
Mobile sequencing in remote sites

Miseq (Illumina):
Short-read sequencing for amplicon, small genome, and targeted sequencing applications, often integrated with our metagenomic and microbiome workflows.

Conventional and Targeted Sequencing

Sanger Sequencing (Standard & Targeted):
Applied for mutation screening, plasmid verification, and validation of NGS data. Still widely used for precision sequencing in specific gene targets.

Quantitative and Digital PCR-Based Technologies

Quantitative PCR (qPCR):
Used for accurate quantification of microbial load, gene expression, and pathogen detection. Applied in environmental, clinical, and industrial microbiology.
Digital Droplet PCR (ddPCR):
Advanced absolute quantification method providing superior precision and sensitivity, especially for low abundance targets and rare variant detection.

Complementary Molecular Tools

Microarray Technologies:
Applied for high-throughput screening of gene expression or microbial community profiling in large sample cohorts.
CRISPR-Cas Systems:
Used in functional gene studies, microbial strain editing, and diagnostic tool development.
Library Preparation Automation (e.g., NEBNext, Illumina DNA Prep):
Enhances reproducibility and throughput in NGS workflows.

Message From The Coordinators

Prof. Dr. Orhan İnce

"At MEG, we continuously push the boundaries of microbial ecology by integrating cutting-edge molecular technologies with a multidisciplinary approach. Our strong infrastructure and collaborative spirit allow us to lead ambitious and transformative projects."

Prof. Dr. Bahar İnce

"Imagine a vibrant, research-driven group where every idea matters and where young scientists are empowered. At MEG, we cultivate innovation, excellence, and a sense of family — our roots are strong, and our future is bold."

İTÜ Microbial Ecology Group - Telefon (212) 285 ----

İTÜ Microbial Ecology Group - Fax (212) 285 ----

İTÜ Microbial Ecology Group - Adres İstanbul Teknik Üniversitesi, Ayazağa Kampüsü, Maslak Sarıyer, İstanbul